erga_ear: make_EAR.py annotate

annotate make_EAR.py @ 1:82450f7907ef draft

planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176

author	bgruening
date	Fri, 30 Aug 2024 09:27:17 +0000
parents	6af76d4371f8
children	0efed25f6d38

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
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	24 EAR_version = "v24.08.26"
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():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	39 # format as an integer if no decimal part
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:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	45 # return the original value if it can't be converted to a float
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):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	50 return [re.findall(f"{key}: (.+)", content)[0] for key in keys]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	51
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	52 keys = [
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	53 "Total scaffold length",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	54 "GC content %",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	55 "# gaps in scaffolds",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	56 "Total gap length in scaffolds",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	57 "# scaffolds",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	58 "Scaffold N50",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	59 "Scaffold L50",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	60 "Scaffold L90",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	61 "# contigs",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	62 "Contig N50",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	63 "Contig L50",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	64 "Contig L90",
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	65 ]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	66
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	67 display_names = keys.copy()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	68 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	69 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	70 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	71 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	72 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	73 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	74
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	75 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	76 exclusion_list = ["# gaps in scaffolds"]
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 # 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	79 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	80 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	81 content = f.read()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	82 total_bp = re.search(r"Total scaffold length: (.+)", content).group(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	83 total_bp = int(total_bp.replace(',', ''))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	84 return "{:,}".format(total_bp)
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 # compute EBP quality metric
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	87 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	88 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	89 content = ''
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	90 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	91 content = f.read()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	92
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	93 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	94 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	95 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	96
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	97 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	98
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	99 # extract qv values
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	100 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	101 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	102 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	103 lines = file.readlines()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	104 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	105 target_line = lines[order]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	106 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	107 return fourth_column_value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	108 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	109 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	110 return ''
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 # extract Kmer completeness values
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	113 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	114 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	115 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	116 lines = file.readlines()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	117 if len(lines) > order:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	118 target_line = lines[order]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	119 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	120 return fifth_column_value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	121 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	122 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	123 return ''
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	124
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	125 # 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	126 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	127 # Split filenames into parts
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	128 parts1 = file1.split('.')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	129 parts2 = file2.split('.')
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	130 # Find unique parts
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	131 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	132 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	133 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	134
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	135 # extract BUSCO values
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	136 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	137 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	138 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	139 content = file.read()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	140 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	141 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	142 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	143 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	144 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	145 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	146 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	147 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	148 return '', '', '', ''
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	149
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	150 # extract BUSCO info
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	151 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	152 busco_version = None
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	153 lineage_info = None
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	154
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 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	159 if version_match:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	160 busco_version = version_match.group(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	161 lineage_match = re.search(r"The lineage dataset is: (.?) \(Creation date:.?, number of genomes: (\d+), number of BUSCOs: (\d+)\)", content)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	162 if lineage_match:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	163 lineage_info = lineage_match.groups()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	164 if not lineage_info:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	165 lineage_match = re.search(r"The lineage dataset is: (.?) \(Creation date:.?, number of species: (\d+), number of BUSCOs: (\d+)\)", content)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	166 if lineage_match:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	167 lineage_info = lineage_match.groups()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	168
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	169 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	170 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	171
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	172 return busco_version, lineage_info
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	173
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	174 # 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	175 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	176 paragraphs = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	177 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	178 if trait == "Haploid size (bp)":
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	179 expected_val = int(expected.replace(',', ''))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	180 observed_val = int(observed.replace(',', ''))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	181 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	182 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	183 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	184 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	185 # 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	186 expected_val = int(expected)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	187 observed_val = int(observed)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	188 if expected_val != observed_val:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	189 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	190 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	191 elif trait == "Sample Sex":
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	192 # 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	193 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	194 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	195 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	196 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	197 logging.warning(f"Error in generating warning for {trait}: {str(e)}")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	198 return paragraphs
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	199
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	200 # 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	201 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	202 paragraphs = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	203 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	204 # 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	205 qv_val = float(qv_value)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	206 completeness_val = float(completeness_value)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	207 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	208 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	209
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	210 # Check QV value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	211 if qv_val < 40:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	212 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	213 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	214
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	215 # Check Kmer completeness value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	216 if completeness_val < 90:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	217 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	218 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	219
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	220 # Check BUSCO s_value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	221 if s_value < 90:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	222 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	223 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	224
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	225 # Check BUSCO d_value
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	226 if d_value > 5:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	227 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	228 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	229
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	230 except Exception as e:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	231 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	232
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	233 return paragraphs
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	234
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	235 # 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	236 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	237 warnings = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	238
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	239 # 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	240 for haplotype in asm_stages:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	241 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	242 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	243 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	244
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	245 # 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	246 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	247 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	248 if loss_percentage > 3:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	249 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	250
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	251 # 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	252 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	253 if gaps_gbp > 1000:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	254 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	255
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	256 # 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	257 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	258 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	259
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	260 return 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 # Parse pipeline and generate "tree"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	263 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	264 tree_lines = []
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	265 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	266
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	267 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	268 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	269 # Tool line
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	270 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	271 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	272
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	273 # 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	274 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	275 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	276 version = parts[0]
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	277 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	278
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	279 # Version line
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	280 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	281 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	282
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	283 # Param line(s)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	284 if params:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	285 for param in params:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	286 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	287 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	288 else:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	289 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	290 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	291 else:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	292 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	293
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	294 # 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	295 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	296 return tree_diagram
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	297
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	298 # 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	299
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	300 # Check for required fields
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	301 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	302 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	303
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	304 if missing_fields:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	305 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	306 sys.exit(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	307
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	308 # 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	309 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	310 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	311 sys.exit(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	312
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	313 # 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	314 tol_id = yaml_data["ToLID"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	315 species = yaml_data["Species"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	316 sex = yaml_data["Sex"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	317 submitter = yaml_data["Submitter"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	318 affiliation = yaml_data["Affiliation"]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	319 tags = yaml_data["Tags"]
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 # 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	322 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	323 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	324 tags += "[INVALID TAG]"
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	325 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	326
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	327 # 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	328 # 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	329 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	330
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	331 # Get stuff from GoaT
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	332 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	333 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	334
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	335 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	336
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	337 goat_results = goat_data['results']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	338
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	339 class_name = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	340 order_name = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	341 haploid_number = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	342 haploid_source = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	343 ploidy = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	344 ploidy_source = 'NA'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	345
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	346 for result in goat_results:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	347 lineage = result['result']['lineage']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	348 for node in lineage:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	349 if node['taxon_rank'] == 'class':
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	350 class_name = node['scientific_name']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	351 if node['taxon_rank'] == 'order':
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	352 order_name = node['scientific_name']
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 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	355 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	356
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	357 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	358
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	359 ploidy = ploidy_info['value']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	360 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	361
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	362 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	363
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	364 haploid_number = haploid_info['value']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	365 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	366
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	367 sp_data = [
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	368 ["TxID", "ToLID", "Species", "Class", "Order"],
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	369 [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	370 ]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	371
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	372 # Transpose the data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	373 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	374
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	375 # 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	376
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	377 # get DATA section from yaml
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	378 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	379
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	380 # Prepare headers
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	381 headers = ['Data']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	382 data_values = ['Coverage']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	383
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	384 # 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	385 for item in data_list:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	386 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	387 headers.append(technology)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	388 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	389
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	390 # 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	391 table_data = [headers, data_values]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	392
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	393 # Extract pipeline data
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	394 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	395 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	396
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	397 # 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	398 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	399 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	400
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	401 # 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	402 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	403
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	404 # 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	405 if not profiling_data:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	406 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	407 sys.exit(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	408
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	409 # 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	410 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	411 if not genomescope_data:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	412 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	413 sys.exit(1)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	414
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	415 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	416 if not genomescope_summary:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	417 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	418 sys.exit(1)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	419
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	420 # 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	421 try:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	422 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	423 summary_txt = f.read()
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	424 # 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	425 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	426 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	427 except Exception as e:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	428 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	429 sys.exit(1)
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	430
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	431 # 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	432 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	433 if smudgeplot_data:
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	434 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	435 if smudgeplot_summary:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	436 try:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	437 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	438 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	439 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	440 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	441 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	442 break
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	443 except Exception as e:
82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	444 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	445 else:
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	446 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	447 else:
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	448 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	449
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	450 # 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	451
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	452 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	453
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	454 # 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	455 asm_stages = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	456 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	457 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	458 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	459 asm_stages.append(haplotypes)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	460
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	461 # get gfastats-based data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	462 gfastats_data = {}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	463 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	464 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	465 if isinstance(haplotype_properties, dict):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	466 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	467 file_path = haplotype_properties['gfastats--nstar-report_txt']
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	468 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	469 content = file.read()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	470 gfastats_data[(asm_stage, haplotypes)] = extract_gfastats_values(content, keys)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	471
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	472 gaps_per_gbp_data = {}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	473 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	474 try:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	475 gaps = float(values[gaps_index])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	476 total_length = float(values[total_length_index])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	477 gaps_per_gbp = round((gaps / total_length * 1_000_000_000), 2)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	478 gaps_per_gbp_data[(asm_stage, haplotypes)] = gaps_per_gbp
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	479 except (ValueError, ZeroDivisionError):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	480 gaps_per_gbp_data[(asm_stage, haplotypes)] = ''
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	481
1 82450f7907ef planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 bgruening parents: 0 diff changeset	482 # 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	483 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	484
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	485 # 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	486 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	487 metric = display_names[i]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	488 if metric not in exclusion_list:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	489 asm_table_data.append([metric] + [format_number(gfastats_data.get((asm_stage, haplotypes), [''])[i]) if (asm_stage, haplotypes) in gfastats_data else '' 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	490
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	491 # Add the gaps/gbp in between
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	492 asm_table_data.insert(gaps_index + 1, ['Gaps/Gbp'] + [format_number(gaps_per_gbp_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	493
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	494 # 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	495 qv_data = {}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	496 completeness_data = {}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	497 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	498 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	499 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	500 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	501 haplotype_properties = stage_properties[haplotypes]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	502 if isinstance(haplotype_properties, dict):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	503 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	504 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	505 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	506 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	507 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	508 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	509 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	510 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	511 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	512 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	513
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	514 # 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	515 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	516
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	517 # 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	518 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	519
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	520 # 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	521 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	522 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	523
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	524 # 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	525
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	526 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	527 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	528 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	529 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	530 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	531
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	532 # 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	533 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	534 total_bp_values = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	535 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	536 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	537 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	538 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	539
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	540 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	541
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	542 # Create table data
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	543 genome_traits_table_data = [
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	544 ["Genome Traits", "Expected", "Observed"],
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	545 ["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	546 ["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	547 ["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	548 ["Sample Sex", sex, obs_sex]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	549 ]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	550
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	551 # Get curator notes
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	552 curator_notes_text = (
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	553 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	554 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	555 f". Other observations: "{other_notes}""
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	556 )
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 # PDF CONSTRUCTION ############################################################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	559
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	560 # Set up the PDF file
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	561 pdf_filename = "EAR.pdf"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	562 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	563 pdf = SimpleDocTemplate(pdf_filename,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	564 pagesize=A4,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	565 leftMargin=margin,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	566 rightMargin=margin,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	567 topMargin=margin,
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	568 bottomMargin=margin)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	569 elements = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	570
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	571 # Set all the styles
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	572 styles = getSampleStyleSheet()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	573 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	574 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	575 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	576 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	577 # 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	578 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	579 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	580 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	581
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	582 # PDF SECTION 1 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	583
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	584 # Add the title
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	585 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	586 elements.append(title)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	587
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	588 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	589 elements.append(Spacer(1, 12))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	590
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	591 # Add version
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	592 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	593 elements.append(ver_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	594
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	595 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	596 elements.append(Spacer(1, 12))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	597
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	598 # Add tags
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	599 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	600 elements.append(tags_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	601
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	602 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	603 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	604
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	605 # 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	606 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	607
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	608 # Style the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	609 sp_data_table.setStyle(TableStyle([
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	610 ("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	611 ("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	612 ("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	613 ('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	614 ('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	615 ('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	616 ('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	617 ("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	618 ('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	619 ("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	620 ]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	621
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	622 # Add SPECIES DATA table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	623 elements.append(sp_data_table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	624
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	625 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	626 elements.append(Spacer(1, 32))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	627
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	628 # Create the GENOME TRAITS table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	629 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	630
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	631 # Style the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	632 genome_traits_table.setStyle(TableStyle([
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	633 ('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	634 ('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	635 ('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	636 ('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	637 ('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	638 ("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	639 ]))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	640
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	641 # Add GENOME TRAITS table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	642 elements.append(genome_traits_table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	643
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	644 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	645 elements.append(Spacer(1, 28))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	646
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	647 # Add EBP METRICS SECTION subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	648 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	649 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	650
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	651 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	652 elements.append(Spacer(1, 24))
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 # 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	655 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	656 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	657
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	658 for haplotype in haplotype_names:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	659 properties = curated_assemblies[haplotype]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	660 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	661 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	662 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	663 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	664
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	665 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	666 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	667
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	668 # 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	669 elements.append(EBP_metric_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	670
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	671 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	672 elements.append(Spacer(1, 8))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	673
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	674 # Add sentence
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	675 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	676 elements.append(Textline)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	677
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	678 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	679 elements.append(Spacer(1, 4))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	680
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	681 # 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	682 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	683 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	684 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	685 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	686
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	687 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	688 elements.append(Spacer(1, 4))
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 # 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	691 for haplotype in haplotype_names:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	692 properties = curated_assemblies[haplotype]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	693 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	694 order = haplotype_names.index(haplotype)
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 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	697 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	698
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	699 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	700 elements += warnings
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	701
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	702 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	703 elements.extend(assembly_warnings)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	704
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	705 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	706 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	707
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	708 # 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	709 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	710 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	711
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	712 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	713 elements.append(Spacer(1, 8))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	714
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	715 # Curator notes
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	716 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	717 elements.append(curator_notes_paragraph)
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 # Page break
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	720 elements.append(PageBreak())
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 # PDF SECTION 2 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	723
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	724 # Add quality metrics section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	725 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	726 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	727
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	728 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	729 elements.append(Spacer(1, 48))
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 # create QUALITY METRICS table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	732 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	733
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	734 # Style the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	735 asm_table.setStyle(TableStyle([
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	736 ('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	737 ('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	738 ('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	739 ('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	740 ('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	741 ("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	742 ]))
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 # Add QUALITY METRICS table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	745 elements.append(asm_table)
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 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	748 elements.append(Spacer(1, 5))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	749
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	750 # Store BUSCO version and lineage information from each file in list
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	751 busco_info_list = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	752 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	753 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	754 if isinstance(haplotype_properties, dict):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	755 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	756 busco_version, lineage_info = extract_busco_info(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	757 if busco_version and lineage_info:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	758 busco_info_list.append((busco_version, lineage_info))
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 # Checking if all elements in the list are identical
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	761 if all(info == busco_info_list[0] for info in busco_info_list):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	762 busco_version, (lineage_name, num_genomes, num_buscos) = busco_info_list[0]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	763 elements.append(Paragraph(f"BUSCO {busco_version} Lineage: {lineage_name} (genomes:{num_genomes}, BUSCOs:{num_buscos})", styles['miniStyle']))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	764 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	765 elements.append(Paragraph("Warning: BUSCO versions or lineage datasets are not the same across results", styles['miniStyle']))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	766 logging.warning("WARNING!!! BUSCO versions or lineage datasets are not the same across results")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	767
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	768 # Page break
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	769 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	770
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	771 # PDF SECTION 3 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	772
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	773 # Add hic maps section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	774 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	775 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	776
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	777 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	778 elements.append(Spacer(1, 36))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	779
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	780 # Initialize counter
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	781 tool_count = 0
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	782
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	783 # 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	784 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	785 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	786 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	787
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	788 images_with_names = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	789
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	790 for haplotype in tool_elements:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	791 haplotype_properties = stage_properties[haplotype]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	792
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	793 # 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	794 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	795 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	796
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	797 # 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	798 if png_file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	799 # Create image object
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	800 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	801 images_with_names.append([img])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	802 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	803 # Add paragraph for missing image
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	804 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	805 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	806
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	807 # Add paragraph for the link
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	808 if link:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	809 link_html = f'<b>{haplotype}</b> <link href="{link}" color="blue">[LINK]</link>'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	810 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	811 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	812
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	813 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	814 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	815
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	816 # 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	817 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	818 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	819
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	820 # 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	821 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	822 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	823
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	824 # 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	825 table = Table(elements_to_add)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	826 table.hAlign = 'CENTER'
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	827 elements.append(table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	828
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	829 # Add a page break conditionally
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	830 next_elements_start = i + 4
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	831 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	832 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	833 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	834
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	835 tool_count += 1
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 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	838
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	839 # PDF SECTION 4 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	840
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	841 # Add kmer spectra section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	842 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	843 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	844
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	845 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	846 elements.append(Spacer(1, 48))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	847
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	848 # Initialize counter
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	849 counter = 0
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	850
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	851 # 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	852 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	853
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	854 # Get paths for spectra files
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	855 spectra_files = {
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	856 'hap1': {
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	857 'spectra_cn_png': curated_assemblies.get('hap1', {}).get('merqury_hap_spectra_cn_png', None),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	858 },
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	859 'hap2': {
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	860 'spectra_cn_png': curated_assemblies.get('hap2', {}).get('merqury_hap_spectra_cn_png', None),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	861 },
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	862 'common': {
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	863 'spectra_cn_png': curated_assemblies.get('hap1', {}).get('merqury_spectra_cn_png', None),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	864 'spectra_asm_png': curated_assemblies.get('hap1', {}).get('merqury_spectra_asm_png', None),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	865 }
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	866 }
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	867
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	868 # Filter out None values and empty strings
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	869 spectra_files = {k: {sk: v for sk, v in sv.items() if v} for k, sv in spectra_files.items()}
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	870
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	871 # 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	872 spectra_cn_files = [
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	873 spectra_files['common'].get('spectra_cn_png', None),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	874 spectra_files['hap1'].get('spectra_cn_png', None),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	875 spectra_files['hap2'].get('spectra_cn_png', None)
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 spectra_cn_files = [f for f in spectra_cn_files if f] # Filter out None values
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 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	880 # For 3 spectra-cn files
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	881 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	882 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	883 if similar_files:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	884 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	885 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	886 shortest_spectra_cn_file = spectra_cn_files[0] if spectra_cn_files else None
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	887 unique_name1 = unique_name2 = None
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	888
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	889 # 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	890 images = []
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	891
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	892 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	893 for key, png_file in file_dict.items():
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	894 if png_file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	895 image = Image(png_file, width=8.4 * cm, height=7 * cm)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	896 filename = os.path.basename(png_file)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	897
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	898 if filename.endswith("spectra-asm.ln.png"):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	899 text = "Distribution of k-mer counts coloured by their presence in reads/assemblies"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	900 elif filename.endswith("spectra-cn.ln.png"):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	901 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	902 # For 3 spectra-cn files use particular text
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	903 if png_file == shortest_spectra_cn_file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	904 text = "Distribution of k-mer counts per copy numbers found in asm (dipl.)"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	905 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	906 if png_file == spectra_files['hap1'].get('spectra_cn_png', None):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	907 text = f"Distribution of k-mer counts per copy numbers found in <b>{unique_name1}</b> (hapl.)"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	908 elif png_file == spectra_files['hap2'].get('spectra_cn_png', None):
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	909 text = f"Distribution of k-mer counts per copy numbers found in <b>{unique_name2}</b> (hapl.)"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	910 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	911 text = "Distribution of k-mer counts per copy numbers found in asm"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	912 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	913 # For 2 spectra-cn files use same text
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	914 text = "Distribution of k-mer counts per copy numbers found in asm"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	915 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	916 text = filename
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	917
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	918 images.append([image, Paragraph(text, styles["midiStyle"])])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	919
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	920 # Filter None values
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	921 images = [img for img in images if img[0] is not None]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	922
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	923 # Get number of rows and columns for the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	924 num_rows = (len(images) + 1) // 2 # +1 to handle odd numbers of images
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	925 num_columns = 2
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	926
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	927 # Create the table with dynamic size
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	928 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)]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	929 image_table = Table(image_table_data)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	930
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	931 # Style the "table"
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	932 table_style = TableStyle([
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	933 ('VALIGN', (0, 0), (-1, -1), 'MIDDLE'),
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	934 ('BOTTOMPADDING', (0, 0), (-1, -1), 20), # 20 here is a spacer between rows
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	935 ])
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	936
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	937 # Set the style
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	938 image_table.setStyle(table_style)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	939
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	940 # Add image table to elements
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	941 elements.append(image_table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	942
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	943 # 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	944 counter += len(images)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	945
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	946 # 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	947 if counter % 4 == 0:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	948 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	949
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	950 # Add spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	951 elements.append(Spacer(1, 12))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	952
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	953 # 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	954 if counter % 4 != 0:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	955 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	956
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	957 # PDF SECTION 5 -------------------------------------------------------------------------------
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	958
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	959 # Add contamination section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	960 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	961 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	962
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	963 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	964 elements.append(Spacer(1, 36))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	965
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	966 # Initialize counter
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	967 tool_count = 0
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	968
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	969 # 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	970 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	971 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	972 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	973
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	974 for haplotype in tool_elements:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	975 haplotype_properties = stage_properties[haplotype]
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	976 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	977 # Get image path
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	978 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	979
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	980 # 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	981 if png_file:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	982 # Create image object
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	983 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	984 elements.append(img)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	985
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	986 # 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	987 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	988 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	989 elements.append(blob_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	990 else:
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	991 # Add paragraph for missing image
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	992 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	993 elements.append(missing_png_paragraph)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	994
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	995 # 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	996 elements.append(PageBreak())
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	997
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	998 tool_count += 1
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	999
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1000 # SECTION 6 -----------------------------------------------------------------------------------
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 # Add data profile section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1003 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	1004 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1005
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1006 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1007 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1008
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1009 # Create the DATA PROFILE table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1010 data_table = Table(table_data)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1011
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1012 # Style the table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1013 data_table.setStyle(TableStyle([
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1014 ('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	1015 ('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	1016 ('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	1017 ('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	1018 ('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	1019 ("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	1020 ]))
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 # Add DATA PROFILE table
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1023 elements.append(data_table)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1024
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1025 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1026 elements.append(Spacer(1, 32))
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 # Add assembly pipeline section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1029 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	1030 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1031
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1032 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1033 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1034
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1035 # Add ASM PIPELINE tree
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1036 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	1037
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1038 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1039 elements.append(Spacer(1, 32))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1040
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1041 # Add curation pipeline section subtitle
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1042 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	1043 elements.append(subtitle)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1044
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1045 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1046 elements.append(Spacer(1, 24))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1047
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1048 # Add CURATION PIPELINE tree
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1049 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	1050
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1051 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1052 elements.append(Spacer(1, 48))
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 # Add submitter, affiliation
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1055 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	1056 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	1057 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	1058
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1059 # Spacer
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1060 elements.append(Spacer(1, 8))
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1061
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1062 # 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	1063 cet = pytz.timezone("CET")
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1064 current_datetime = datetime.now(cet)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1065 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	1066 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	1067
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1068 # Build the PDF ###############################################################################
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1069 pdf.build(elements)
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1070
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1071
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1072 if __name__ == "__main__":
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1073 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	1074 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	1075 args = parser.parse_args()
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1076
6af76d4371f8 planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit a08f73e00550020ac83f4d45045075962a8a2251 bgruening parents: diff changeset	1077 make_report(args.yaml_file)

Mercurial > repos > bgruening > erga_ear

annotate make_EAR.py @ 1:82450f7907ef draft