erga_ear: make_EAR.py annotate

annotate make_EAR.py @ 2:0efed25f6d38 draft default tip

planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c

author	bgruening
date	Tue, 15 Oct 2024 12:52:44 +0000
parents	82450f7907ef
children

rev	line source
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	2 import argparse
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	3 import logging
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	4 import math
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	5 import os
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	6 import re
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	7 import sys
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	8 from datetime import datetime
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	9
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	10 import pytz
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	11 import requests
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	12 import yaml
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	13 from reportlab.lib import colors
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	14 from reportlab.lib.pagesizes import A4
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	15 from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	16 from reportlab.lib.units import cm
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	17 from reportlab.platypus import Image, PageBreak, Paragraph, SimpleDocTemplate, Spacer, Table, TableStyle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	18
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	19
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	20 # make_EAR_glxy.py
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	21 # CAUTION: This is for the Galaxy version!
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	22 # by Diego De Panis
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	23 # ERGA Sequencing and Assembly Committee
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	24 EAR_version = "v24.10.15"
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	25
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	26
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	27 def make_report(yaml_file):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	28 logging.basicConfig(filename='EAR.log', level=logging.INFO)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	29 # Read the content from EAR.yaml file
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	30 with open(yaml_file, "r") as file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	31 yaml_data = yaml.safe_load(file)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	32
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	33 # FUNCTIONS ###################################################################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	34
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	35 def format_number(value):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	36 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	37 value_float = float(value)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	38 if value_float.is_integer():
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	39 # format as integer if no decimal
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	40 return f'{int(value_float):,}'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	41 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	42 # format as a float
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	43 return f'{value_float:,}'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	44 except ValueError:
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	45 # return original value if can't be converted to float
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	46 return value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	47
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	48 # extract gfastats values
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	49 def extract_gfastats_values(content, keys):
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	50 values = []
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	51 for key in keys:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	52 # colon-separated as default format first
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	53 match = re.search(rf"{re.escape(key)}:\s*(.+)", content)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	54 if not match:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	55 # If not try galaxy's tab-separated
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	56 match = re.search(rf"{re.escape(key)}\t(.+)", content)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	57 if match:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	58 values.append(match.group(1).strip())
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	59 else:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	60 values.append("N/A")
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	61 return values
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	62
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	63 keys = [
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	64 "Total scaffold length",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	65 "GC content %",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	66 "# gaps in scaffolds",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	67 "Total gap length in scaffolds",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	68 "# scaffolds",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	69 "Scaffold N50",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	70 "Scaffold L50",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	71 "Scaffold L90",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	72 "# contigs",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	73 "Contig N50",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	74 "Contig L50",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	75 "Contig L90",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	76 ]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	77
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	78 display_names = keys.copy()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	79 display_names[display_names.index("Total scaffold length")] = "Total bp"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	80 total_length_index = keys.index("Total scaffold length")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	81 display_names[display_names.index("GC content %")] = "GC %"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	82 display_names[display_names.index("Total gap length in scaffolds")] = "Total gap bp"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	83 display_names[display_names.index("# scaffolds")] = "Scaffolds"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	84 display_names[display_names.index("# contigs")] = "Contigs"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	85
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	86 gaps_index = keys.index("# gaps in scaffolds")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	87 exclusion_list = ["# gaps in scaffolds"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	88
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	89 # extract Total bp from gfastats report
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	90 def extract_total_bp_from_gfastats(gfastats_path):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	91 with open(gfastats_path, "r") as f:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	92 content = f.read()
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	93 # Try colon-separated format first
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	94 match = re.search(r"Total scaffold length:\s*(.+)", content)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	95 if not match:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	96 # If not found, try tab-separated format
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	97 match = re.search(r"Total scaffold length\t(.+)", content)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	98 if match:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	99 total_bp = match.group(1).replace(',', '')
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	100 return "{:,}".format(int(total_bp))
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	101 else:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	102 logging.error(f"Could not find Total scaffold length in {gfastats_path}")
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	103 return "N/A"
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	104
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	105 # compute EBP quality metric
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	106 def compute_ebp_metric(haplotype, gfastats_path, qv_value):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	107 keys_needed = ["Contig N50", "Scaffold N50"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	108 content = ''
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	109 with open(gfastats_path, "r") as f:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	110 content = f.read()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	111
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	112 values = extract_gfastats_values(content, keys_needed)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	113 contig_n50_log = math.floor(math.log10(int(values[0].replace(',', ''))))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	114 scaffold_n50_log = math.floor(math.log10(int(values[1].replace(',', ''))))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	115 return f"Obtained EBP quality metric for {haplotype}: {contig_n50_log}.{scaffold_n50_log}.Q{math.floor(float(qv_value))}"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	116
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	117 # extract qv values
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	118 def get_qv_value(file_path, order, tool, haplotype):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	119 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	120 with open(file_path, 'r') as file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	121 lines = file.readlines()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	122 if len(lines) > order and (len(lines) == 1 or lines[2].split('\t')[0].strip() == "Both"):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	123 target_line = lines[order]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	124 fourth_column_value = target_line.split('\t')[3]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	125 return fourth_column_value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	126 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	127 logging.error(f"Error reading {file_path} for tool {tool} and haplotype {haplotype}: {str(e)}")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	128 return ''
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	129
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	130 # extract Kmer completeness values
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	131 def get_completeness_value(file_path, order, tool, haplotype):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	132 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	133 with open(file_path, 'r') as file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	134 lines = file.readlines()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	135 if len(lines) > order:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	136 target_line = lines[order]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	137 fifth_column_value = target_line.split('\t')[4].strip()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	138 return fifth_column_value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	139 except Exception as e:
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	140 logging.error(f"Error reading {file_path} for tool {tool} and haplotype {haplotype}: {str(e)}")
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	141 return ''
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	142
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	143 # get unique part in file names
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	144 def find_unique_parts(file1, file2):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	145 # Split filenames into parts
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	146 parts1 = file1.split('.')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	147 parts2 = file2.split('.')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	148 # Find unique parts
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	149 unique_parts1 = [part for part in parts1 if part not in parts2]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	150 unique_parts2 = [part for part in parts2 if part not in parts1]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	151 return ' '.join(unique_parts1), ' '.join(unique_parts2)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	152
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	153 # extract BUSCO values
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	154 def extract_busco_values(file_path):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	155 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	156 with open(file_path, 'r') as file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	157 content = file.read()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	158 results_line = re.findall(r"C:.*n:\d+", content)[0]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	159 s_value = re.findall(r"S:(\d+\.\d+%)", results_line)[0]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	160 d_value = re.findall(r"D:(\d+\.\d+%)", results_line)[0]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	161 f_value = re.findall(r"F:(\d+\.\d+%)", results_line)[0]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	162 m_value = re.findall(r"M:(\d+\.\d+%)", results_line)[0]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	163 return s_value, d_value, f_value, m_value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	164 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	165 logging.warning(f"Error reading {file_path}: {str(e)}")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	166 return '', '', '', ''
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	167
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	168 # extract BUSCO info
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	169 def extract_busco_info(file_path):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	170 busco_version = None
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	171 lineage_info = None
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	172 busco_mode = None
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	173 busco_pred = None
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	174
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	175 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	176 with open(file_path, 'r') as file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	177 content = file.read()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	178 version_match = re.search(r"# BUSCO version is: ([\d.]+)", content)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	179 if version_match:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	180 busco_version = version_match.group(1)
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	181 lineage_match = re.search(r"The lineage dataset is: (.?) \(Creation date:.?, number of (genomes\|species): (\d+), number of BUSCOs: (\d+)\)", content)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	182 if lineage_match:
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	183 lineage_info = (lineage_match.group(1), lineage_match.group(3), lineage_match.group(4))
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	184 mode_match = re.search(r"# BUSCO was run in mode: (\w+)", content)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	185 if mode_match:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	186 busco_mode = mode_match.group(1)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	187 pred_match = re.search(r"# Gene predictor used: (\w+)", content)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	188 if pred_match:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	189 busco_pred = pred_match.group(1)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	190
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	191 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	192 logging.warning(f"Error reading {file_path}: {str(e)}")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	193
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	194 return busco_version, lineage_info, busco_mode, busco_pred
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	195
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	196 # Function to check and generate warning messages
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	197 def generate_warning_paragraphs(expected, observed, trait):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	198 paragraphs = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	199 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	200 if trait == "Haploid size (bp)":
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	201 expected_val = int(expected.replace(',', ''))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	202 observed_val = int(observed.replace(',', ''))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	203 if abs(expected_val - observed_val) / expected_val > 0.20:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	204 message = f". Observed {trait} has >20% difference with Expected"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	205 paragraphs.append(Paragraph(message, styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	206 elif trait in ["Haploid Number", "Ploidy"]:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	207 # Ensure both values are integers for comparison
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	208 expected_val = int(expected)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	209 observed_val = int(observed)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	210 if expected_val != observed_val:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	211 message = f". Observed {trait} is different from Expected"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	212 paragraphs.append(Paragraph(message, styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	213 elif trait == "Sample Sex":
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	214 # Compare case-insensitive and trimmed strings
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	215 if expected.strip().lower() != observed.strip().lower():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	216 message = ". Observed sex is different from Sample sex"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	217 paragraphs.append(Paragraph(message, styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	218 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	219 logging.warning(f"Error in generating warning for {trait}: {str(e)}")
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	220
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	221 return paragraphs
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	222
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	223 # Generate warnings for curated haplotypes (qv, kcomp, busco)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	224 def generate_curated_warnings(haplotype, qv_value, completeness_value, busco_scores):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	225 paragraphs = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	226 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	227 # Ensure values are correctly interpreted as floats
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	228 qv_val = float(qv_value)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	229 completeness_val = float(completeness_value)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	230 s_value = float(busco_scores[0].rstrip('%'))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	231 d_value = float(busco_scores[1].rstrip('%'))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	232
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	233 # Check QV value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	234 if qv_val < 40:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	235 message = f". QV value is less than 40 for {haplotype}"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	236 paragraphs.append(Paragraph(message, styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	237
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	238 # Check Kmer completeness value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	239 if completeness_val < 90:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	240 message = f". Kmer completeness value is less than 90 for {haplotype}"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	241 paragraphs.append(Paragraph(message, styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	242
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	243 # Check BUSCO s_value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	244 if s_value < 90:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	245 message = f". BUSCO single copy value is less than 90% for {haplotype}"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	246 paragraphs.append(Paragraph(message, styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	247
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	248 # Check BUSCO d_value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	249 if d_value > 5:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	250 message = f". BUSCO duplicated value is more than 5% for {haplotype}"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	251 paragraphs.append(Paragraph(message, styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	252
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	253 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	254 logging.warning(f"Error in generating warnings for {haplotype}: {str(e)}")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	255
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	256 return paragraphs
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	257
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	258 # Generate warnings for curated haplotypes (loss, gaps, 90inChrom)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	259 def generate_assembly_warnings(asm_data, gaps_per_gbp_data, obs_haploid_num):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	260 warnings = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	261
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	262 # Iterate over haplotypes and generate warnings based on the criteria
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	263 for haplotype in asm_stages:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	264 pre_curation_bp = extract_total_bp_from_gfastats(asm_data['Pre-curation'][haplotype]['gfastats--nstar-report_txt'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	265 curated_bp = extract_total_bp_from_gfastats(asm_data['Curated'][haplotype]['gfastats--nstar-report_txt'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	266 scaffold_l90 = float(gfastats_data[('Curated', haplotype)][display_names.index('Scaffold L90')].replace(',', ''))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	267
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	268 # Check for assembly length loss > 3%
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	269 if pre_curation_bp and curated_bp:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	270 loss_percentage = (float(pre_curation_bp.replace(',', '')) - float(curated_bp.replace(',', ''))) / float(pre_curation_bp.replace(',', '')) * 100
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	271 if loss_percentage > 3:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	272 warnings.append(Paragraph(f". Assembly length loss > 3% for {haplotype}", styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	273
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	274 # Check for more than 1000 gaps/Gbp
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	275 gaps_gbp = gaps_per_gbp_data.get(('Curated', haplotype), 0)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	276 if gaps_gbp > 1000:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	277 warnings.append(Paragraph(f". More than 1000 gaps/Gbp for {haplotype}", styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	278
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	279 # Check if Scaffold L90 value is more than Observed Haploid number
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	280 if scaffold_l90 > float(obs_haploid_num):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	281 warnings.append(Paragraph(f". Not 90% of assembly in chromosomes for {haplotype}", styles["midiStyle"]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	282
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	283 return warnings
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	284
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	285 # Parse pipeline and generate "tree"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	286 def generate_pipeline_tree(pipeline_data):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	287 tree_lines = []
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	288 indent = " " * 2 # Adjust indent spacing
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	289
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	290 if isinstance(pipeline_data, dict):
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	291 for tool, version_param in pipeline_data.items():
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	292 # Tool line
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	293 tool_line = f"- <b>{tool}</b>"
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	294 tree_lines.append(tool_line)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	295
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	296 # Convert version_param to string and split
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	297 version_param_str = str(version_param)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	298 parts = version_param_str.split('/')
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	299 version = parts[0]
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	300 params = [p for p in parts[1:] if p] # This will remove empty strings
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	301
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	302 # Version line
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	303 version_line = f"{indent * 2}\|_ <i>ver:</i> {version}"
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	304 tree_lines.append(version_line)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	305
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	306 # Param line(s)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	307 if params:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	308 for param in params:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	309 param_line = f"{indent * 2}\|_ <i>key param:</i> {param}"
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	310 tree_lines.append(param_line)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	311 else:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	312 param_line = f"{indent * 2}\|_ <i>key param:</i> NA"
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	313 tree_lines.append(param_line)
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	314 else:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	315 tree_lines.append("Invalid pipeline data format")
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	316
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	317 # Join lines with HTML break for paragraph
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	318 tree_diagram = "<br/>".join(tree_lines)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	319 return tree_diagram
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	320
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	321 # Reading SAMPLE INFORMATION section from yaml ################################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	322
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	323 # Check for required fields
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	324 required_fields = ["ToLID", "Species", "Sex", "Submitter", "Affiliation", "Tags"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	325 missing_fields = [field for field in required_fields if field not in yaml_data or not yaml_data[field]]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	326
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	327 if missing_fields:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	328 logging.error(f"# GENERAL INFORMATION section in the yaml file is missing or empty for the following information: {', '.join(missing_fields)}")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	329 sys.exit(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	330
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	331 # Check that "Species" field is a string
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	332 if not isinstance(yaml_data["Species"], str):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	333 logging.error(f"# GENERAL INFORMATION section in the yaml file contains incorrect data type for 'Species'. Expected 'str' but got '{type(yaml_data['Species']).__name__}'.")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	334 sys.exit(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	335
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	336 # Get data for Header, ToLID table and submitter
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	337 tol_id = yaml_data["ToLID"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	338 species = yaml_data["Species"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	339 sex = yaml_data["Sex"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	340 submitter = yaml_data["Submitter"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	341 affiliation = yaml_data["Affiliation"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	342 tags = yaml_data["Tags"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	343
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	344 # Check if tag is valid
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	345 valid_tags = ["ERGA-BGE", "ERGA-Pilot", "ERGA-Community", "ERGA-testing"]
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	346 if tags not in valid_tags:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	347 tags += "[INVALID TAG]"
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	348 logging.warning("# SAMPLE INFORMATION section in the yaml file contains an invalid tag. Valid tags are ERGA-BGE, ERGA-Pilot and ERGA-Community.")
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	349
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	350 # Get data from GoaT based on species name
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	351 # urllib.parse.quote to handle special characters and spaces in the species name
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	352 species_name = requests.utils.quote(species)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	353
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	354 # Get stuff from GoaT
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	355 goat_response = requests.get(f'https://goat.genomehubs.org/api/v2/search?query=tax_name%28{species_name}%29&result=taxon')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	356 goat_data = goat_response.json() # convert json to dict
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	357
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	358 taxon_number = goat_data['results'][0]['result']['taxon_id']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	359
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	360 goat_results = goat_data['results']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	361
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	362 class_name = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	363 order_name = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	364 haploid_number = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	365 haploid_source = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	366 ploidy = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	367 ploidy_source = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	368
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	369 for result in goat_results:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	370 lineage = result['result']['lineage']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	371 for node in lineage:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	372 if node['taxon_rank'] == 'class':
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	373 class_name = node['scientific_name']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	374 if node['taxon_rank'] == 'order':
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	375 order_name = node['scientific_name']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	376
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	377 goat_second_response = requests.get(f'https://goat.genomehubs.org/api/v2/record?recordId={taxon_number}&result=taxon&taxonomy=ncbi')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	378 goat_second_data = goat_second_response.json()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	379
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	380 ploidy_info = goat_second_data['records'][0]['record']['attributes']['ploidy']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	381
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	382 ploidy = ploidy_info['value']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	383 ploidy_source = ploidy_info['aggregation_source']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	384
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	385 haploid_info = goat_second_data['records'][0]['record']['attributes']['haploid_number']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	386
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	387 haploid_number = haploid_info['value']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	388 haploid_source = haploid_info['aggregation_source']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	389
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	390 sp_data = [
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	391 ["TxID", "ToLID", "Species", "Class", "Order"],
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	392 [taxon_number, tol_id, species, class_name, order_name]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	393 ]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	394
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	395 # Transpose the data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	396 transposed_sp_data = list(map(list, zip(*sp_data)))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	397
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	398 # Reading SEQUENCING DATA section from yaml ###################################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	399
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	400 # get DATA section from yaml
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	401 data_list = yaml_data.get('DATA', [])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	402
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	403 # Prepare headers
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	404 headers = ['Data']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	405 data_values = ['Coverage']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	406
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	407 # Extract data from YAML and format it for the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	408 for item in data_list:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	409 for technology, coverage in item.items():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	410 headers.append(technology)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	411 data_values.append('NA' if not coverage else coverage)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	412
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	413 # Create a list of lists for the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	414 table_data = [headers, data_values]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	415
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	416 # Extract pipeline data
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	417 asm_pipeline_data = yaml_data.get('PIPELINES', {}).get('Assembly', {})
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	418 curation_pipeline_data = yaml_data.get('PIPELINES', {}).get('Curation', {})
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	419
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	420 # Extract pipeline data from 'Curated' category
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	421 asm_pipeline_tree = generate_pipeline_tree(asm_pipeline_data)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	422 curation_pipeline_tree = generate_pipeline_tree(curation_pipeline_data)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	423
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	424 # Reading GENOME PROFILING DATA section from yaml #############################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	425 profiling_data = yaml_data.get('PROFILING')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	426
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	427 # Check if profiling_data is available
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	428 if not profiling_data:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	429 logging.error('Error: No profiling data found in the YAML file.')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	430 sys.exit(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	431
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	432 # Check for GenomeScope data (mandatory)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	433 genomescope_data = profiling_data.get('GenomeScope')
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	434 if not genomescope_data:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	435 logging.error("Error: GenomeScope data is missing in the YAML file. This is mandatory.")
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	436 sys.exit(1)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	437
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	438 genomescope_summary = genomescope_data.get('genomescope_summary_txt')
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	439 if not genomescope_summary:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	440 logging.error("Error: GenomeScope summary file path is missing in the YAML file.")
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	441 sys.exit(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	442
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	443 # Read the content of the GenomeScope summary file
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	444 try:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	445 with open(genomescope_summary, "r") as f:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	446 summary_txt = f.read()
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	447 # Extract values from summary.txt
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	448 genome_haploid_length = re.search(r"Genome Haploid Length\s+([\d,]+) bp", summary_txt).group(1)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	449 proposed_ploidy = re.search(r"p = (\d+)", summary_txt).group(1)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	450 except Exception as e:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	451 logging.error(f"Error reading GenomeScope summary file: {str(e)}")
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	452 sys.exit(1)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	453
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	454 # Check for Smudgeplot data (optional)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	455 smudgeplot_data = profiling_data.get('Smudgeplot')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	456 if smudgeplot_data:
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	457 smudgeplot_summary = smudgeplot_data.get('smudgeplot_verbose_summary_txt')
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	458 if smudgeplot_summary:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	459 try:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	460 with open(smudgeplot_summary, "r") as f:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	461 smud_summary_txt = f.readlines()
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	462 for line in smud_summary_txt:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	463 if line.startswith("* Proposed ploidy"):
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	464 proposed_ploidy = line.split(":")[1].strip()
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	465 break
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	466 except Exception as e:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	467 logging.warning(f"Error reading Smudgeplot summary file: {str(e)}. Using GenomeScope ploidy.")
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	468 else:
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	469 logging.warning("Smudgeplot summary file path is missing. Using GenomeScope ploidy.")
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	470 else:
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	471 logging.info("Smudgeplot data not provided. Using GenomeScope ploidy.")
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	472
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	473 # Reading ASSEMBLY DATA section from yaml #####################################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	474
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	475 asm_data = yaml_data.get('ASSEMBLIES', {})
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	476
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	477 # make a list from the assemblies available in asm_data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	478 asm_stages = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	479 for asm_stage, stage_properties in asm_data.items():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	480 for haplotypes in stage_properties.keys():
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	481 if haplotypes not in asm_stages:
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	482 asm_stages.append(haplotypes)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	483
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	484 # get gfastats-based data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	485 gfastats_data = {}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	486 for asm_stage, stage_properties in asm_data.items():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	487 for haplotypes, haplotype_properties in stage_properties.items():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	488 if isinstance(haplotype_properties, dict):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	489 if 'gfastats--nstar-report_txt' in haplotype_properties:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	490 file_path = haplotype_properties['gfastats--nstar-report_txt']
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	491 try:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	492 with open(file_path, 'r') as file:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	493 content = file.read()
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	494 gfastats_data[(asm_stage, haplotypes)] = extract_gfastats_values(content, keys)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	495 except FileNotFoundError:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	496 logging.error(f"Gfastats file not found: {file_path}")
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	497 except Exception as e:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	498 logging.error(f"Error processing gfastats file {file_path}: {str(e)}")
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	499
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	500 gaps_per_gbp_data = {}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	501 for (asm_stage, haplotypes), values in gfastats_data.items():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	502 try:
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	503 gaps = float(values[gaps_index].replace(',', ''))
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	504 total_length = float(values[total_length_index].replace(',', ''))
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	505 if total_length > 0:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	506 gaps_per_gbp = round((gaps / total_length * 1_000_000_000), 2)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	507 gaps_per_gbp_data[(asm_stage, haplotypes)] = gaps_per_gbp
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	508 else:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	509 logging.warning(f"Total length is zero for {asm_stage} {haplotypes}")
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	510 gaps_per_gbp_data[(asm_stage, haplotypes)] = 'N/A'
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	511 except (ValueError, IndexError):
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	512 logging.warning(f"Could not calculate gaps per Gbp for {asm_stage} {haplotypes}")
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	513 gaps_per_gbp_data[(asm_stage, haplotypes)] = 'N/A'
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	514
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	515 # Define the contigging table (column names)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	516 asm_table_data = [["Metrics"] + [f'{asm_stage} \n {haplotypes}' for asm_stage in asm_data for haplotypes in asm_stages if haplotypes in asm_data[asm_stage]]]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	517
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	518 # Fill the table with the gfastats data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	519 for i in range(len(display_names)):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	520 metric = display_names[i]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	521 if metric not in exclusion_list:
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	522 asm_table_data.append([metric] + [format_number(gfastats_data.get((asm_stage, haplotypes), ['N/A'] * len(keys))[i]) if (asm_stage, haplotypes) in gfastats_data else 'N/A' for asm_stage in asm_data for haplotypes in asm_stages if haplotypes in asm_data[asm_stage]])
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	523
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	524 # Add the gaps/gbp in between
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	525 asm_table_data.insert(gaps_index + 1, ['Gaps/Gbp'] + [format_number(gaps_per_gbp_data.get((asm_stage, haplotypes), 'N/A')) for asm_stage in asm_data for haplotypes in asm_stages if haplotypes in asm_data[asm_stage]])
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	526 # get QV, Kmer completeness and BUSCO data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	527 qv_data = {}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	528 completeness_data = {}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	529 busco_data = {metric: {} for metric in ['BUSCO sing.', 'BUSCO dupl.', 'BUSCO frag.', 'BUSCO miss.']}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	530 for asm_stage, stage_properties in asm_data.items():
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	531 asm_stage_elements = list(stage_properties.keys())
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	532 for i, haplotypes in enumerate(asm_stage_elements):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	533 haplotype_properties = stage_properties[haplotypes]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	534 if isinstance(haplotype_properties, dict):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	535 if 'merqury_qv' in haplotype_properties:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	536 qv_data[(asm_stage, haplotypes)] = get_qv_value(haplotype_properties['merqury_qv'], i, asm_stage, haplotypes)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	537 if 'merqury_completeness_stats' in haplotype_properties:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	538 completeness_data[(asm_stage, haplotypes)] = get_completeness_value(haplotype_properties['merqury_completeness_stats'], i, asm_stage, haplotypes)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	539 if 'busco_short_summary_txt' in haplotype_properties:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	540 s_value, d_value, f_value, m_value = extract_busco_values(haplotype_properties['busco_short_summary_txt'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	541 busco_data['BUSCO sing.'].update({(asm_stage, haplotypes): s_value})
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	542 busco_data['BUSCO dupl.'].update({(asm_stage, haplotypes): d_value})
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	543 busco_data['BUSCO frag.'].update({(asm_stage, haplotypes): f_value})
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	544 busco_data['BUSCO miss.'].update({(asm_stage, haplotypes): m_value})
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	545
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	546 # Fill the table with the QV data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	547 asm_table_data.append(['QV'] + [qv_data.get((asm_stage, haplotypes), '') for asm_stage in asm_data for haplotypes in asm_stages if haplotypes in asm_data[asm_stage]])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	548
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	549 # Fill the table with the Kmer completeness data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	550 asm_table_data.append(['Kmer compl.'] + [completeness_data.get((asm_stage, haplotypes), '') for asm_stage in asm_data for haplotypes in asm_stages if haplotypes in asm_data[asm_stage]])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	551
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	552 # Fill the table with the BUSCO data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	553 for metric in ['BUSCO sing.', 'BUSCO dupl.', 'BUSCO frag.', 'BUSCO miss.']:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	554 asm_table_data.append([metric] + [busco_data[metric].get((asm_stage, haplotypes), '') for asm_stage in asm_data for haplotypes in asm_stages if haplotypes in asm_data[asm_stage]])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	555
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	556 # Reading CURATION NOTES section from yaml ####################################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	557
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	558 obs_haploid_num = yaml_data.get("NOTES", {}).get("Obs_Haploid_num", "NA")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	559 obs_sex = yaml_data.get("NOTES", {}).get("Obs_Sex", "NA")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	560 interventions_per_gb = yaml_data.get("NOTES", {}).get("Interventions_per_Gb", "NA")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	561 contamination_notes = yaml_data.get("NOTES", {}).get("Contamination_notes", "NA")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	562 other_notes = yaml_data.get("NOTES", {}).get("Other_notes", "NA")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	563
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	564 # Extract Total bp for each haplotype and find the maximum
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	565 curated_assemblies = yaml_data.get('ASSEMBLIES', {}).get('Curated', {})
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	566 total_bp_values = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	567 for haplotype, properties in curated_assemblies.items():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	568 if 'gfastats--nstar-report_txt' in properties:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	569 total_bp = extract_total_bp_from_gfastats(properties['gfastats--nstar-report_txt'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	570 total_bp_values.append(total_bp)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	571
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	572 max_total_bp = max(total_bp_values, default='NA')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	573
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	574 # Create table data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	575 genome_traits_table_data = [
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	576 ["Genome Traits", "Expected", "Observed"],
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	577 ["Haploid size (bp)", genome_haploid_length, f"{max_total_bp}"],
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	578 ["Haploid Number", f"{haploid_number} (source: {haploid_source})", obs_haploid_num],
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	579 ["Ploidy", f"{ploidy} (source: {ploidy_source})", proposed_ploidy],
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	580 ["Sample Sex", sex, obs_sex]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	581 ]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	582
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	583 # Get curator notes
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	584 curator_notes_text = (
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	585 f". Interventions/Gb: {interventions_per_gb}<br/>"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	586 f". Contamination notes: "{contamination_notes}"<br/>"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	587 f". Other observations: "{other_notes}""
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	588 )
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	589
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	590 # PDF CONSTRUCTION ############################################################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	591
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	592 # Set up the PDF file
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	593 pdf_filename = "EAR.pdf"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	594 margin = 0.5 * 72 # 0.5 inch in points (normal margin is 1 inch)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	595 pdf = SimpleDocTemplate(pdf_filename,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	596 pagesize=A4,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	597 leftMargin=margin,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	598 rightMargin=margin,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	599 topMargin=margin,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	600 bottomMargin=margin)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	601 elements = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	602
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	603 # Set all the styles
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	604 styles = getSampleStyleSheet()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	605 styles.add(ParagraphStyle(name='TitleStyle', fontName='Courier', fontSize=20))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	606 styles.add(ParagraphStyle(name='subTitleStyle', fontName='Courier', fontSize=16))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	607 styles.add(ParagraphStyle(name='normalStyle', fontName='Courier', fontSize=12))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	608 styles.add(ParagraphStyle(name='midiStyle', fontName='Courier', fontSize=10))
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	609 # styles.add(ParagraphStyle(name='LinkStyle', fontName='Courier', fontSize=10, textColor='blue', underline=True))
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	610 styles.add(ParagraphStyle(name='treeStyle', fontName='Courier', fontSize=10, leftIndent=12))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	611 styles.add(ParagraphStyle(name='miniStyle', fontName='Courier', fontSize=8))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	612 styles.add(ParagraphStyle(name='FileNameStyle', fontName='Courier', fontSize=6))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	613
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	614 # PDF SECTION 1 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	615
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	616 # Add the title
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	617 title = Paragraph("ERGA Assembly Report", styles['TitleStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	618 elements.append(title)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	619
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	620 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	621 elements.append(Spacer(1, 12))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	622
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	623 # Add version
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	624 ver_paragraph = Paragraph(EAR_version, styles['normalStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	625 elements.append(ver_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	626
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	627 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	628 elements.append(Spacer(1, 12))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	629
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	630 # Add tags
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	631 tags_paragraph = Paragraph(f"Tags: {tags}", styles['normalStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	632 elements.append(tags_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	633
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	634 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	635 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	636
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	637 # Create the SPECIES DATA table with the transposed data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	638 sp_data_table = Table(transposed_sp_data)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	639
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	640 # Style the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	641 sp_data_table.setStyle(TableStyle([
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	642 ("BACKGROUND", (0, 0), (0, -1), '#e7e7e7'), # Grey background for column 1
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	643 ("BACKGROUND", (1, 0), (1, -1), colors.white), # White background for column 2
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	644 ("ALIGN", (0, 0), (-1, -1), "CENTER"),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	645 ('FONTNAME', (0, 0), (0, 0), 'Courier'), # Regular font for row1, col1
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	646 ('FONTNAME', (1, 0), (1, 0), 'Courier'),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	647 ('FONTNAME', (0, 1), (-1, -1), 'Courier'), # Regular font for the rest of the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	648 ('FONTNAME', (1, 1), (1, 1), 'Courier-Bold'), # Bold font for row1, col2
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	649 ("FONTSIZE", (0, 0), (-1, -1), 14),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	650 ('BOTTOMPADDING', (0, 0), (-1, -1), 8),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	651 ("GRID", (0, 0), (-1, -1), 0.5, colors.black)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	652 ]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	653
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	654 # Add SPECIES DATA table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	655 elements.append(sp_data_table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	656
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	657 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	658 elements.append(Spacer(1, 32))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	659
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	660 # Create the GENOME TRAITS table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	661 genome_traits_table = Table(genome_traits_table_data)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	662
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	663 # Style the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	664 genome_traits_table.setStyle(TableStyle([
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	665 ('BACKGROUND', (0, 0), (0, -1), '#e7e7e7'),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	666 ('ALIGN', (0, 0), (-1, -1), 'CENTER'),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	667 ('FONTNAME', (0, 0), (-1, -1), 'Courier'),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	668 ('FONTSIZE', (0, 0), (-1, -1), 12),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	669 ('BOTTOMPADDING', (0, 0), (-1, -1), 8),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	670 ("GRID", (0, 0), (-1, -1), 0.5, colors.black)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	671 ]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	672
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	673 # Add GENOME TRAITS table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	674 elements.append(genome_traits_table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	675
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	676 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	677 elements.append(Spacer(1, 28))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	678
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	679 # Add EBP METRICS SECTION subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	680 subtitle = Paragraph("EBP metrics summary and curation notes", styles['subTitleStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	681 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	682
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	683 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	684 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	685
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	686 # Iterate over haplotypes in the Curated category to get data for EBP metrics
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	687 curated_assemblies = yaml_data.get('ASSEMBLIES', {}).get('Curated', {})
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	688 haplotype_names = list(curated_assemblies.keys())
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	689
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	690 for haplotype in haplotype_names:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	691 properties = curated_assemblies[haplotype]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	692 if 'gfastats--nstar-report_txt' in properties and 'merqury_qv' in properties:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	693 gfastats_path = properties['gfastats--nstar-report_txt']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	694 order = haplotype_names.index(haplotype) # Determine the order based on the position of the haplotype in the list
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	695 qv_value = get_qv_value(properties['merqury_qv'], order, 'Curated', haplotype)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	696
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	697 ebp_quality_metric = compute_ebp_metric(haplotype, gfastats_path, qv_value)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	698 EBP_metric_paragraph = Paragraph(ebp_quality_metric, styles["midiStyle"])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	699
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	700 # Add the EBP quality metric paragraph to elements
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	701 elements.append(EBP_metric_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	702
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	703 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	704 elements.append(Spacer(1, 8))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	705
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	706 # Add sentence
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	707 Textline = Paragraph("The following metrics were automatically flagged as below EBP recommended standards or different from expected:", styles['midiStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	708 elements.append(Textline)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	709
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	710 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	711 elements.append(Spacer(1, 4))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	712
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	713 # Apply checks and add warning paragraphs to elements
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	714 elements += generate_warning_paragraphs(genome_haploid_length, max_total_bp, "Haploid size (bp)")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	715 elements += generate_warning_paragraphs(haploid_number, obs_haploid_num, "Haploid Number")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	716 elements += generate_warning_paragraphs(proposed_ploidy, ploidy, "Ploidy")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	717 elements += generate_warning_paragraphs(sex, obs_sex, "Sample Sex")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	718
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	719 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	720 elements.append(Spacer(1, 4))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	721
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	722 # Iterate over haplotypes in the Curated category and apply checks
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	723 for haplotype in haplotype_names:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	724 properties = curated_assemblies[haplotype]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	725 if isinstance(properties, dict) and 'merqury_qv' in properties and 'merqury_completeness_stats' in properties and 'busco_short_summary_txt' in properties:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	726 order = haplotype_names.index(haplotype)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	727 qv_value = get_qv_value(properties['merqury_qv'], order, "Curated", haplotype)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	728 completeness_value = get_completeness_value(properties['merqury_completeness_stats'], order, "Curated", haplotype)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	729 busco_scores = extract_busco_values(properties['busco_short_summary_txt'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	730
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	731 warnings = generate_curated_warnings(haplotype, qv_value, completeness_value, busco_scores)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	732 elements += warnings
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	733
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	734 assembly_warnings = generate_assembly_warnings(asm_data, gaps_per_gbp_data, obs_haploid_num)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	735 elements.extend(assembly_warnings)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	736
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	737 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	738 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	739
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	740 # Add small subtitle for Curator notes
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	741 subtitle = Paragraph("Curator notes", styles['normalStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	742 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	743
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	744 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	745 elements.append(Spacer(1, 8))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	746
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	747 # Curator notes
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	748 curator_notes_paragraph = Paragraph(curator_notes_text, styles["midiStyle"])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	749 elements.append(curator_notes_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	750
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	751 # Page break
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	752 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	753
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	754 # PDF SECTION 2 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	755
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	756 # Add quality metrics section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	757 subtitle = Paragraph("Quality metrics table", styles['TitleStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	758 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	759
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	760 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	761 elements.append(Spacer(1, 48))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	762
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	763 # create QUALITY METRICS table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	764 asm_table = Table(asm_table_data)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	765
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	766 # Style the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	767 asm_table.setStyle(TableStyle([
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	768 ('BACKGROUND', (0, 0), (-1, 0), '#e7e7e7'), # grey background for the header
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	769 ('ALIGN', (0, 0), (-1, -1), 'CENTER'), # center alignment
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	770 ('FONTNAME', (0, 0), (-1, -1), 'Courier'), # bold font for the header
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	771 ('FONTSIZE', (0, 0), (-1, -1), 11), # font size
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	772 ('BOTTOMPADDING', (0, 0), (-1, -1), 8),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	773 ("GRID", (0, 0), (-1, -1), 0.5, colors.black)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	774 ]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	775
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	776 # Add QUALITY METRICS table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	777 elements.append(asm_table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	778
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	779 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	780 elements.append(Spacer(1, 5))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	781
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	782 # Store BUSCO information from each file in a list
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	783 busco_info_list = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	784 for asm_stages, stage_properties in asm_data.items():
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	785 for i, haplotype_properties in stage_properties.items():
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	786 if isinstance(haplotype_properties, dict):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	787 if 'busco_short_summary_txt' in haplotype_properties:
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	788 busco_info = extract_busco_info(haplotype_properties['busco_short_summary_txt'])
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	789 if all(busco_info):
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	790 busco_info_list.append(busco_info)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	791
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	792 # Function to format BUSCO information
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	793 def format_busco_info(info):
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	794 version, (lineage, genomes, buscos), mode, predictor = info
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	795 return f"BUSCO: {version} ({mode}, {predictor}) / Lineage: {lineage} (genomes:{genomes}, BUSCOs:{buscos})"
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	796
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	797 # Checking if all elements in the list are identical
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	798 if busco_info_list and all(info == busco_info_list[0] for info in busco_info_list):
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	799 busco_text = format_busco_info(busco_info_list[0])
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	800 elements.append(Paragraph(busco_text, styles['miniStyle']))
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	801 else:
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	802 elements.append(Paragraph("Warning! BUSCO versions or lineage datasets are not the same across results:", styles['miniStyle']))
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	803 logging.warning("WARNING: BUSCO versions or lineage datasets are not the same across results")
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	804 for info in busco_info_list:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	805 busco_text = format_busco_info(info)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	806 elements.append(Paragraph(busco_text, styles['miniStyle']))
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	807
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	808 # Page break
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	809 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	810
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	811 # PDF SECTION 3 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	812
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	813 # Add hic maps section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	814 subtitle = Paragraph("HiC contact map of curated assembly", styles['TitleStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	815 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	816
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	817 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	818 elements.append(Spacer(1, 36))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	819
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	820 # Initialize counter
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	821 tool_count = 0
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	822
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	823 # Add title and images for each step
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	824 for asm_stages, stage_properties in asm_data.items():
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	825 if asm_stages == 'Curated':
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	826 tool_elements = list(stage_properties.keys())
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	827
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	828 images_with_names = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	829
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	830 for haplotype in tool_elements:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	831 haplotype_properties = stage_properties[haplotype]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	832
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	833 # Check if there is an image and/or a link
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	834 png_file = haplotype_properties.get('hic_FullMap_png', '')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	835 link = haplotype_properties.get('hic_FullMap_link', '')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	836
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	837 # Prepare paragraphs for the image and link
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	838 if png_file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	839 # Create image object
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	840 img = Image(png_file, width=11 * cm, height=11 * cm)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	841 images_with_names.append([img])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	842 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	843 # Add paragraph for missing image
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	844 missing_png_paragraph = Paragraph(f"<b>{haplotype}</b> HiC PNG is missing!", styles["midiStyle"])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	845 images_with_names.append([missing_png_paragraph])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	846
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	847 # Add paragraph for the link
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	848 if link:
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	849 link_html = f'<b>{haplotype}</b> <link href="{link}" color="blue">[non-permanent LINK]</link>'
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	850 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	851 link_html = f'<b>{haplotype}</b> File link is missing!'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	852
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	853 link_paragraph = Paragraph(link_html, styles["midiStyle"])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	854 images_with_names.append([link_paragraph])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	855
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	856 # Append a spacer only if the next element is an image
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	857 if len(tool_elements) > 1 and tool_elements.index(haplotype) < len(tool_elements) - 1:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	858 images_with_names.append([Spacer(1, 12)])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	859
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	860 # Add images and names to the elements in pairs
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	861 for i in range(0, len(images_with_names), 4): # Process two images (and their names) at a time
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	862 elements_to_add = images_with_names[i: i + 4]
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	863
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	864 # Create table for the images and names
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	865 table = Table(elements_to_add)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	866 table.hAlign = 'CENTER'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	867 elements.append(table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	868
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	869 # Add a page break conditionally
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	870 next_elements_start = i + 4
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	871 if next_elements_start < len(images_with_names):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	872 if len(images_with_names[next_elements_start]) > 0 and isinstance(images_with_names[next_elements_start][0], Image):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	873 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	874
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	875 tool_count += 1
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	876
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	877 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	878
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	879 # PDF SECTION 4 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	880
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	881 # Add kmer spectra section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	882 subtitle = Paragraph("K-mer spectra of curated assembly", styles['TitleStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	883 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	884
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	885 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	886 elements.append(Spacer(1, 48))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	887
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	888 # Initialize counter
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	889 counter = 0
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	890
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	891 # Iterate over haplotypes in the Curated category to get K-mer spectra images
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	892 curated_assemblies = yaml_data.get('ASSEMBLIES', {}).get('Curated', {})
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	893
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	894 # Get paths for spectra files
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	895 spectra_files = {'common': {}}
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	896 for assembly_type, assembly_data in curated_assemblies.items():
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	897 if 'merqury_hap_spectra_cn_png' in assembly_data:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	898 spectra_files[assembly_type] = {'spectra_cn_png': assembly_data['merqury_hap_spectra_cn_png']}
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	899 if 'merqury_spectra_cn_png' in assembly_data:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	900 spectra_files['common']['spectra_cn_png'] = assembly_data['merqury_spectra_cn_png']
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	901 if 'merqury_spectra_asm_png' in assembly_data:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	902 spectra_files['common']['spectra_asm_png'] = assembly_data['merqury_spectra_asm_png']
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	903
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	904 # Determine the number of spectra-cn files and assign unique names if needed
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	905 spectra_cn_files = [
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	906 file_dict.get('spectra_cn_png', None)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	907 for file_dict in spectra_files.values()
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	908 if file_dict.get('spectra_cn_png')
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	909 ]
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	910 spectra_cn_files = list(set(spectra_cn_files)) # Remove duplicates
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	911
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	912 if len(spectra_cn_files) == 3:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	913 shortest_spectra_cn_file = min(spectra_cn_files, key=lambda f: len(os.path.basename(f)), default=None)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	914 similar_files = [f for f in spectra_cn_files if f != shortest_spectra_cn_file]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	915 if similar_files:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	916 unique_name1, unique_name2 = find_unique_parts(os.path.basename(similar_files[0]), os.path.basename(similar_files[1]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	917 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	918 shortest_spectra_cn_file = spectra_cn_files[0] if spectra_cn_files else None
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	919 # unique_name1 = unique_name2 = None
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	920
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	921 # Create image objects and add filename below each image
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	922 images = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	923 for label, file_dict in spectra_files.items():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	924 for key, png_file in file_dict.items():
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	925 if png_file and os.path.exists(png_file):
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	926 try:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	927 image = Image(png_file, width=8.4 * cm, height=7 * cm)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	928 filename = os.path.basename(png_file)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	929
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	930 if filename.endswith("spectra-asm.ln.png"):
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	931 text = "Distribution of k-mer counts coloured by their presence in reads/assemblies"
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	932 elif filename.endswith("spectra-cn.ln.png"):
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	933 if len(spectra_cn_files) == 3:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	934 if png_file == shortest_spectra_cn_file:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	935 text = "Distribution of k-mer counts per copy numbers found in asm (dipl.)"
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	936 else:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	937 text = f"Distribution of k-mer counts per copy numbers found in {label} (hapl.)"
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	938 else:
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	939 text = "Distribution of k-mer counts per copy numbers found in asm"
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	940 else:
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	941 text = filename
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	942
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	943 images.append([image, Paragraph(text, styles["midiStyle"])])
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	944 except Exception as e:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	945 logging.error(f"Error processing image {png_file}: {str(e)}")
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	946
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	947 # Create the table with dynamic size
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	948 if images:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	949 num_rows = (len(images) + 1) // 2
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	950 num_columns = 2
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	951 image_table_data = [[images[i * num_columns + j] if i * num_columns + j < len(images) else [] for j in range(num_columns)] for i in range(num_rows)]
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	952 image_table = Table(image_table_data)
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	953
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	954 # Style the table
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	955 table_style = TableStyle([
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	956 ('VALIGN', (0, 0), (-1, -1), 'MIDDLE'),
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	957 ('BOTTOMPADDING', (0, 0), (-1, -1), 20), # 20 here is a spacer between rows
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	958 ])
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	959
2 0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	960 image_table.setStyle(table_style)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	961 elements.append(image_table)
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	962 else:
0efed25f6d38 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit 720787c4fb8885f5127ab6ada2813f8dd580921c bgruening parents: 1 diff changeset	963 elements.append(Paragraph("No K-mer spectra images available.", styles["midiStyle"]))
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	964
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	965 # Increase counter by the number of PNGs added
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	966 counter += len(images)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	967
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	968 # If counter is a multiple of 4, insert a page break and reset counter
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	969 if counter % 4 == 0:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	970 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	971
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	972 # Add spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	973 elements.append(Spacer(1, 12))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	974
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	975 # If we have processed all haps and the last page does not contain exactly 4 images, insert a page break
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	976 if counter % 4 != 0:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	977 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	978
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	979 # PDF SECTION 5 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	980
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	981 # Add contamination section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	982 subtitle = Paragraph("Post-curation contamination screening", styles['TitleStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	983 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	984
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	985 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	986 elements.append(Spacer(1, 36))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	987
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	988 # Initialize counter
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	989 tool_count = 0
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	990
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	991 # Add title and images for each step
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	992 for asm_stages, stage_properties in asm_data.items():
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	993 if asm_stages == 'Curated': # Check if the current stage is 'Curated'
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	994 tool_elements = list(stage_properties.keys())
0 6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	995
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	996 for haplotype in tool_elements:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	997 haplotype_properties = stage_properties[haplotype]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	998 if isinstance(haplotype_properties, dict) and 'blobplot_cont_png' in haplotype_properties:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	999 # Get image path
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1000 png_file = haplotype_properties['blobplot_cont_png']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1001
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1002 # If png_file is not empty, display it
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1003 if png_file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1004 # Create image object
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1005 img = Image(png_file, width=20 * cm, height=20 * cm)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1006 elements.append(img)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1007
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1008 # Create paragraph for filename with haplotype name
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1009 blob_text = f"<b>{haplotype}.</b> Bubble plot circles are scaled by sequence length, positioned by coverage and GC proportion, and coloured by taxonomy. Histograms show total assembly length distribution on each axis."
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1010 blob_paragraph = Paragraph(blob_text, styles["midiStyle"])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1011 elements.append(blob_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1012 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1013 # Add paragraph for missing image
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1014 missing_png_paragraph = Paragraph(f"<b>{haplotype}</b> PNG is missing!", styles["midiStyle"])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1015 elements.append(missing_png_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1016
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1017 # Add a page break after each image and its description
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1018 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1019
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1020 tool_count += 1
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1021
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1022 # SECTION 6 -----------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1023
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1024 # Add data profile section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1025 subtitle = Paragraph("Data profile", styles['TitleStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1026 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1027
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1028 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1029 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1030
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1031 # Create the DATA PROFILE table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1032 data_table = Table(table_data)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1033
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1034 # Style the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1035 data_table.setStyle(TableStyle([
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1036 ('BACKGROUND', (0, 0), (0, -1), '#e7e7e7'), # grey background for the first column
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1037 ('ALIGN', (0, 0), (-1, -1), 'CENTER'), # center alignment
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1038 ('FONTNAME', (0, 0), (-1, -1), 'Courier'), # remove bold font
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1039 ('FONTSIZE', (0, 0), (-1, -1), 12), # font size for the header
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1040 ('BOTTOMPADDING', (0, 0), (-1, -1), 8),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1041 ("GRID", (0, 0), (-1, -1), 0.5, colors.black)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1042 ]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1043
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1044 # Add DATA PROFILE table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1045 elements.append(data_table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1046
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1047 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1048 elements.append(Spacer(1, 32))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1049
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1050 # Add assembly pipeline section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1051 subtitle = Paragraph("Assembly pipeline", styles['TitleStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1052 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1053
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1054 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1055 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1056
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1057 # Add ASM PIPELINE tree
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1058 elements.append(Paragraph(asm_pipeline_tree, styles['treeStyle']))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1059
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1060 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1061 elements.append(Spacer(1, 32))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1062
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1063 # Add curation pipeline section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1064 subtitle = Paragraph("Curation pipeline", styles['TitleStyle'])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1065 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1066
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1067 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1068 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1069
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1070 # Add CURATION PIPELINE tree
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1071 elements.append(Paragraph(curation_pipeline_tree, styles['treeStyle']))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1072
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1073 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1074 elements.append(Spacer(1, 48))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1075
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1076 # Add submitter, affiliation
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1077 submitter_paragraph_style = ParagraphStyle(name='SubmitterStyle', fontName='Courier', fontSize=10)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1078 elements.append(Paragraph(f"Submitter: {submitter}", submitter_paragraph_style))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1079 elements.append(Paragraph(f"Affiliation: {affiliation}", submitter_paragraph_style))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1080
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1081 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1082 elements.append(Spacer(1, 8))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1083
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1084 # Add the date and time (CET) of the document creation
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1085 cet = pytz.timezone("CET")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1086 current_datetime = datetime.now(cet)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1087 formatted_datetime = current_datetime.strftime("%Y-%m-%d %H:%M:%S %Z")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1088 elements.append(Paragraph(f"Date and time: {formatted_datetime}", submitter_paragraph_style))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1089
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1090 # Build the PDF ###############################################################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1091 pdf.build(elements)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1092
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1093
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1094 if __name__ == "__main__":
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1095 parser = argparse.ArgumentParser(description='Create an ERGA Assembly Report (EAR) from a YAML file. Visit https://github.com/ERGA-consortium/EARs for more information')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1096 parser.add_argument('yaml_file', type=str, help='Path to the YAML file')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1097 args = parser.parse_args()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1098
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1099 make_report(args.yaml_file)

Mercurial > repos > bgruening > erga_ear

annotate make_EAR.py @ 2:0efed25f6d38 draft default tip