Mercurial > repos > tduigou > create_assembly_picklists

annotate CreateAssemblyPicklists_script.py @ 9:c3951e41e488 draft default tip

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit ed922f834f891e6048385803c3004465551c911d-dirty
author tduigou
date Thu, 07 Aug 2025 12:37:19 +0000
parents 196e13c09881
children
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1 #!/usr/bin/env python
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2 # coding: utf-8
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3 # Code copied from CUBA backend tools.py and create_assembly_picklists/CreateAssemblyPicklistsView.py
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4 # Code modified for running in a script in Galaxy.
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5 ##############################################################################
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6 ##############################################################################
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7 # App code
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8 ## EGF Galaxy Create assembly picklists -- script
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9
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10 ##############################################################################
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11 # IMPORTS
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12 import argparse
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13 import os
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14 from io import StringIO, BytesIO
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15 import re
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16 from base64 import b64encode, b64decode
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17 from copy import deepcopy
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18 import sys
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19
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20 from collections import OrderedDict
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21 from fuzzywuzzy import process
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22 import matplotlib.pyplot as plt
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23 from matplotlib.backends.backend_pdf import PdfPages
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24 import pandas
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26 from Bio import SeqIO
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27 from Bio.SeqRecord import SeqRecord
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28 from Bio.Seq import Seq
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29
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30 import bandwagon as bw
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31 import crazydoc
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32 from dnachisel.biotools import sequence_to_biopython_record
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33 import dnacauldron
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34 import flametree
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35 from plateo import AssemblyPlan
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36 from plateo.parsers import plate_from_content_spreadsheet
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37 from plateo.containers import Plate4ti0960
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38 from plateo.exporters import AssemblyPicklistGenerator, picklist_to_assembly_mix_report
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39 from plateo.exporters import (
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40 picklist_to_labcyte_echo_picklist_file,
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41 picklist_to_tecan_evo_picklist_file,
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42 plate_to_platemap_spreadsheet,
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43 PlateTextPlotter,
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44 )
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45 from plateo.tools import human_volume
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46 from snapgene_reader import snapgene_file_to_seqrecord
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47
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48
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49 ##############################################################################
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50 # FUNCTIONS
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51
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52 def fix_and_rename_paths(paths):
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53 fixed_paths = []
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54 for path in paths:
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55 new_path = path.replace("__sq__", "'")
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56 if new_path != path:
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57 os.rename(path, new_path)
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58 fixed_paths.append(new_path)
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59 return fixed_paths
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60
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61
1
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62 def parse_optional_float(x):
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63 if x == '':
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64 return None
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65 return float(x)
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66
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67
0
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68 def did_you_mean(name, other_names, limit=5, min_score=50): # test
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69 results = process.extract(name, list(other_names), limit=limit)
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70 return [e for (e, score) in results if score >= min_score]
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71
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72
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73 def fix_ice_genbank(genbank_txt):
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74 lines = genbank_txt.splitlines()
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75 lines[0] += max(0, 80 - len(lines[0])) * " "
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76 return "\n".join(lines)
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77
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78
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79 def write_record(record, target, fmt="genbank"):
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80 """Write a record as genbank, fasta, etc. via Biopython, with fixes"""
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81 record = deepcopy(record)
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82 if fmt == "genbank":
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83 if isinstance(record, (list, tuple)):
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84 for r in record:
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85 r.name = r.name[:20]
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86 else:
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87 record.name = record.name[:20]
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88 if hasattr(target, "open"):
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89 target = target.open("w")
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90 SeqIO.write(record, target, fmt)
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91
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92
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93 def autoname_genbank_file(record):
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94 return record.id.replace(".", "_") + ".gb"
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95
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96
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97 def string_to_records(string):
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98 """Convert a string of a fasta, genbank... into a simple ATGC string.
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99
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100 Can also be used to detect a format.
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101 """
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102 matches = re.match("([ATGC][ATGC]*)", string)
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103 # print("============", len(matches.groups()[0]), len(string))
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104 # print (matches.groups()[0] == string)
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105 if (matches is not None) and (matches.groups()[0] == string):
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106 return [SeqRecord(Seq(string))], "ATGC"
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107
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108 for fmt in ("fasta", "genbank"):
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109 if fmt == "genbank":
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110 string = fix_ice_genbank(string)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
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111 try:
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112 stringio = StringIO(string)
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113 records = list(SeqIO.parse(stringio, fmt))
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114 if len(records) > 0:
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115 return (records, fmt)
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116 except:
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117 pass
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118 try:
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119 record = snapgene_file_to_seqrecord(filecontent=StringIO(string))
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120 return [record]
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121 except:
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122 pass
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123 raise ValueError("Invalid sequence format")
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124
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125
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126 def file_to_filelike_object(file_, type="byte"):
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127 content = file_.content.split("base64,")[1]
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128 filelike = BytesIO if (type == "byte") else StringIO
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129 return filelike(b64decode(content))
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130
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131
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132 def spreadsheet_file_to_dataframe(filedict, header="infer"):
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133 filelike = file_to_filelike_object(filedict)
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134 if filedict.name.endswith(".csv"):
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135 return pandas.read_csv(filelike, header=header)
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136 else:
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137 return pandas.read_excel(filelike, header=header)
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138
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139
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140 def records_from_zip_file(zip_file, use_file_names_as_ids=False):
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141 zip_name = zip_file.name
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142 zip_file = flametree.file_tree(file_to_filelike_object(zip_file))
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143 records = []
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144 for f in zip_file._all_files:
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145 ext = f._extension.lower()
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146 if ext in ["gb", "gbk", "fa", "dna"]:
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147 try:
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148 new_records, fmt = string_to_records(f.read())
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149 if not isinstance(new_records, list):
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150 new_records = [new_records]
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151 except:
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152 content_stream = BytesIO(f.read("rb"))
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153 try:
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154 record = snapgene_file_to_seqrecord(fileobject=content_stream)
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155 new_records, fmt = [record], "snapgene"
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156 except:
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157 try:
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158 parser = crazydoc.CrazydocParser(
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159 ["highlight_color", "bold", "underline"]
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160 )
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161 new_records = parser.parse_doc_file(content_stream)
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162 fmt = "doc"
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163 except:
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164 raise ValueError("Format not recognized for file " + f._path)
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165
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166 single_record = len(new_records) == 1
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167 for i, record in enumerate(new_records):
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168 name = record.id
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169 if name in [
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170 None,
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171 "",
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172 "<unknown id>",
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173 ".",
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174 " ",
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175 "<unknown name>",
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176 ]:
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177 number = "" if single_record else ("%04d" % i)
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178 name = f._name_no_extension.replace(" ", "_") + number
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179 record.id = name
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180 record.name = name
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181 record.file_name = f._name_no_extension
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182 record.zip_file_name = zip_name
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183 if use_file_names_as_ids and single_record:
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184 basename = os.path.basename(record.file_name)
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185 basename_no_extension = os.path.splitext(basename)[0]
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186 record.id = basename_no_extension
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187 records += new_records
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188 return records
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189
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190
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191 def records_from_data_file(data_file):
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192 content = b64decode(data_file.content.split("base64,")[1])
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193 try:
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194 records, fmt = string_to_records(content.decode("utf-8"))
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195 except:
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196 try:
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197 record = snapgene_file_to_seqrecord(fileobject=BytesIO(content))
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198 records, fmt = [record], "snapgene"
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199 except:
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200 try:
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201 parser = crazydoc.CrazydocParser(
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202 ["highlight_color", "bold", "underline"]
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203 )
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204 records = parser.parse_doc_file(BytesIO(content))
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205 fmt = "doc"
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206 except:
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207 try:
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208 df = spreadsheet_file_to_dataframe(data_file, header=None)
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209 records = [
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210 sequence_to_biopython_record(sequence=seq, id=name, name=name)
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211 for name, seq in df.values
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212 ]
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213 fmt = "spreadsheet"
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214 except:
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215 raise ValueError("Format not recognized for file " + data_file.name)
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216 if not isinstance(records, list):
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217 records = [records]
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218 return records, fmt
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219
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220
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221 def record_to_formated_string(record, fmt="genbank", remove_descr=False):
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222 if remove_descr:
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223 record = deepcopy(record)
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224 if isinstance(record, (list, tuple)):
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225 for r in record:
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226 r.description = ""
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227 else:
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228 record.description = ""
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229 fileobject = StringIO()
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230 write_record(record, fileobject, fmt)
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231 return fileobject.getvalue().encode("utf-8")
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232
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233
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234 def records_from_data_files(data_files, use_file_names_as_ids=False):
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235 records = []
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236 for file_ in data_files:
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237 circular = ("circular" not in file_) or file_.circular
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238 if file_.name.lower().endswith("zip"):
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239 records += records_from_zip_file(
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240 file_, use_file_names_as_ids=use_file_names_as_ids
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241 )
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diff changeset
242 continue
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243 recs, fmt = records_from_data_file(file_)
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244 single_record = len(recs) == 1
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245 for i, record in enumerate(recs):
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246 record.circular = circular
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247 record.linear = not circular
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248 name_no_extension = "".join(file_.name.split(".")[:-1])
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249 name = name_no_extension + ("" if single_record else ("%04d" % i))
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250 name = name.replace(" ", "_")
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251 UNKNOWN_IDS = [
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252 "None",
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253 "",
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254 "<unknown id>",
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255 ".",
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256 "EXPORTED",
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257 "<unknown name>",
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258 "Exported",
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259 ]
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260 # Sorry for this parts, it took a lot of "whatever works".
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261 # keep your part names under 20c and pointless, and everything
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diff changeset
262 # will be good
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263 if str(record.id).strip() in UNKNOWN_IDS:
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264 record.id = name
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265 if str(record.name).strip() in UNKNOWN_IDS:
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266 record.name = name
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267 record.file_name = name_no_extension
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268 if use_file_names_as_ids and single_record:
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269 basename = os.path.basename(record.source_file)
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270 basename_no_extension = os.path.splitext(basename)[0]
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271 record.id = basename_no_extension
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272 records += recs
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273 return records
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274
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275
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276 def data_to_html_data(data, datatype, filename=None):
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277 """Data types: zip, genbank, fasta, pdf"""
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278 datatype = {
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279 "zip": "application/zip",
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280 "genbank": "application/genbank",
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281 "fasta": "application/fasta",
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282 "pdf": "application/pdf",
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283 "xlsx": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
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284 }.get(datatype, datatype)
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285 datatype = "data:%s;" % datatype
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286 data64 = "base64,%s" % b64encode(data).decode("utf-8")
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287 headers = ""
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288 if filename is not None:
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289 headers += "headers=filename%3D" + filename + ";"
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290 return datatype + headers + data64
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291
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292
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293 def zip_data_to_html_data(data):
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294 return data_to_html_data(data, "application/zip")
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295
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296
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297 LADDERS = {"100_to_4k": bw.ladders.LADDER_100_to_4k}
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298
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299
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300 def matplotlib_figure_to_svg_base64_data(fig, **kwargs):
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301 """Return a string of the form 'data:image/svg+xml;base64,XXX' where XXX
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302 is the base64-encoded svg version of the figure."""
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303 output = BytesIO()
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304 fig.savefig(output, format="svg", **kwargs)
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305 svg_txt = output.getvalue().decode("utf-8")
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306 svg_txt = "\n".join(svg_txt.split("\n")[4:])
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307 svg_txt = "".join(svg_txt.split("\n"))
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308
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309 content = b64encode(svg_txt.encode("utf-8"))
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310 result = (b"data:image/svg+xml;base64," + content).decode("utf-8")
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311
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312 return result
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313
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314
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315 def matplotlib_figure_to_bitmap_base64_data(fig, fmt="png", **kwargs):
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316 """Return a string of the form 'data:image/png;base64,XXX' where XXX
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317 is the base64-encoded svg version of the figure."""
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318 output = BytesIO()
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319 fig.savefig(output, format=fmt, **kwargs)
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320 bitmap = output.getvalue()
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321 content = b64encode(bitmap)
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322 result = (b"data:image/%s;base64,%s" % (fmt.encode("utf-8"), content)).decode(
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323 "utf-8"
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324 )
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325 return result
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326
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327
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328 def figures_to_pdf_report_data(figures, filename="report.pdf"):
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329 pdf_io = BytesIO()
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330 with PdfPages(pdf_io) as pdf:
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331 for fig in figures:
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332 pdf.savefig(fig, bbox_inches="tight")
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333 return {
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334 "data": (
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335 "data:application/pdf;base64,"
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336 + b64encode(pdf_io.getvalue()).decode("utf-8")
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337 ),
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338 "name": filename,
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339 "mimetype": "application/pdf",
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340 }
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341
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342
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343 def csv_to_list(csv_string, sep=","):
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344 return [
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345 element.strip()
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346 for line in csv_string.split("\n")
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347 for element in line.split(sep)
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348 if len(element.strip())
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349 ]
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350
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351
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352 def set_record_topology(record, topology):
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353 """Set the Biopython record's topology, possibly passing if already set.
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354
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355 This actually sets the ``record.annotations['topology']``.The ``topology``
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356 parameter can be "circular", "linear", "default_to_circular" (will default
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357 to circular if ``annotations['topology']`` is not already set) or
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358 "default_to_linear".
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359 """
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360 valid_topologies = [
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361 "circular",
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362 "linear",
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363 "default_to_circular",
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364 "default_to_linear",
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365 ]
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366 if topology not in valid_topologies:
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367 raise ValueError(
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368 "topology (%s) should be one of %s."
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369 % (topology, ", ".join(valid_topologies))
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370 )
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371 annotations = record.annotations
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372 default_prefix = "default_to_"
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373 if topology.startswith(default_prefix):
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374 if "topology" not in annotations:
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375 annotations["topology"] = topology[len(default_prefix) :]
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376 else:
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377 annotations["topology"] = topology
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378
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379
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380 ##############################################################################
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381 def main():
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382
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383 parser = argparse.ArgumentParser(description="Generate picklist for DNA assembly.")
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384 parser.add_argument("--parts_files", help="Directory with parts data or file with part sizes")
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385 parser.add_argument("--picklist", type=str, help="Path to the assembly plan CSV or Excel file")
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386 parser.add_argument("--source_plate", help="Source plate file (CSV or Excel)")
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387 parser.add_argument("--backbone_name", required=False, help="Name of the backbone")
0
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388 parser.add_argument("--result_zip", help="Name of the output zip file")
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389 parser.add_argument("--part_backbone_ratio", type=parse_optional_float, required=False, help="Part to backbone molar ratio")
0
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390 parser.add_argument("--quantity_unit", choices=["fmol", "nM", "ng"], help="Quantity unit")
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391 parser.add_argument("--part_quantity", type=float, help="Quantity of each part")
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392 parser.add_argument("--buffer_volume", type=float, help="Buffer volume in µL")
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393 parser.add_argument("--total_volume", type=float, help="Total reaction volume in µL")
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394 parser.add_argument("--dispenser", choices=["labcyte_echo", "tecan_evo"], help="Dispenser machine")
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395
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396 args = parser.parse_args()
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397
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398 # Parameters:
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399 picklist = args.picklist # assembly plan
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400 # directory or can be a csv/Excel with part sizes
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401 if isinstance(args.parts_files, str):
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402 args.parts_files = args.parts_files.split(",")
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403 parts_dir = fix_and_rename_paths(args.parts_files)
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404 source_plate_path = args.source_plate
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405 backbone_name = args.backbone_name
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406 part_backbone_ratio = args.part_backbone_ratio
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407 result_zip_file = args.result_zip # output file name "picklist.zip"
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408 ##############################################################################
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409 # Defaults:
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410 destination_plate = None
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411 destination_type = "new" # this parameter is not actually used
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412 destination_size = 96 # this parameter is not actually used
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413 fill_by = "column" # this parameter is not actually used
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414 quantity_unit = args.quantity_unit
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415 part_quantity = args.part_quantity # 1.3
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416 buffer_volume = args.buffer_volume # 0.3 # (µL)
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417 total_volume = args.total_volume # 1 # (µL)
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418 dispenser_machine = args.dispenser
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419 dispenser_min_volume = 0.5 # (nL), this parameter is not actually used
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420 dispenser_max_volume = 5 # (µL), this parameter is not actually used
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421 dispenser_resolution = 2.5 # (nL), this parameter is not actually used
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422 dispenser_dead_volume = 8 # (µL), this parameter is not actually used
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423 use_file_names_as_ids = True
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424
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425 # CODE
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426 if picklist.endswith(".csv"):
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427 csv = picklist.read().decode()
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428 rows = [line.split(",") for line in csv.split("\n") if len(line)]
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429 else:
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430 dataframe = pandas.read_excel(picklist)
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431 rows = [row for i, row in dataframe.iterrows()]
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432
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433 assembly_plan = AssemblyPlan(
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434 OrderedDict(
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435 [
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436 (
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437 row[0],
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438 [
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439 str(e).strip()
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440 for e in row[1:]
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441 if str(e).strip() not in ["-", "nan", ""]
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442 ],
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443 )
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444 for row in rows
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445 if row[0] not in ["nan", "Construct name", "constructs", "construct"]
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446 ]
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447 )
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448 )
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449 for assembly, parts in assembly_plan.assemblies.items():
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450 assembly_plan.assemblies[assembly] = [part.replace(" ", "_") for part in parts]
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451
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452 # Reading part infos
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453 if not isinstance(parts_dir, list):
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454 if parts_dir.endswith((".csv", ".xls", ".xlsx")): # part sizes specified in table
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455 if parts_dir.endswith(".csv"):
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456 dataframe = pandas.read_csv(parts_dir)
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457 else:
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458 dataframe = pandas.read_excel(parts_dir)
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459 parts_data = {row.part: {"size": row["size"]} for i, row in dataframe.iterrows()}
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460 else: # input records
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461 records = dnacauldron.biotools.load_records_from_files(
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462 files=parts_dir, use_file_names_as_ids=use_file_names_as_ids
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463 )
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464 parts_data = {rec.id.replace(" ", "_").lower(): {"record": rec} for rec in records}
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465 #parts_data = process_parts_with_mapping(records, args.file_name_mapping)
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466 assembly_plan.parts_data = parts_data
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467 parts_without_data = assembly_plan.parts_without_data()
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468 if len(parts_without_data):
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469 print("success: False")
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470 print("message: Some parts have no provided record or data.")
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471 print("missing_parts: ", parts_without_data)
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472 sys.exit()
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473 # Reading protocol
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474 if quantity_unit == "fmol":
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475 part_mol = part_quantity * 1e-15
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diff changeset
476 part_g = None
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
477 if quantity_unit == "nM":
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
478 part_mol = part_quantity * total_volume * 1e-15
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
479 part_g = None
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
480 if quantity_unit == "ng":
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
481 part_mol = None
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
482 part_g = part_quantity * 1e-9
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
483 # Backbone:part molar ratio calculation is not performed in this case.
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
484 # This ensures no change regardless of form input:
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
485 part_backbone_ratio = 1
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
486 print("Generating picklist")
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
487 picklist_generator = AssemblyPicklistGenerator(
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
488 part_mol=part_mol,
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
489 part_g=part_g,
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
490 complement_to=total_volume * 1e-6, # convert uL to L
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
491 buffer_volume=buffer_volume * 1e-6,
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
492 volume_rounding=2.5e-9, # not using parameter from form
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
493 minimal_dispense_volume=5e-9, # Echo machine's minimum dispense -
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
494 )
1
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
495 if backbone_name != '' and backbone_name != 'Non':
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
496 backbone_name_list = backbone_name.split(",")
0
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
497 source_plate = plate_from_content_spreadsheet(source_plate_path)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
498
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
499 for well in source_plate.iter_wells():
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
500 if well.is_empty:
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
501 continue
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
502 quantities = well.content.quantities
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
503 part, quantity = list(quantities.items())[0]
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
504 quantities.pop(part)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
505 quantities[part.replace(" ", "_")] = quantity
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
506
1
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
507 if backbone_name != '' and backbone_name != 'Non':
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
508 if part in backbone_name_list:
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
509 # This section multiplies the backbone concentration with the
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
510 # part:backbone molar ratio. This tricks the calculator into making
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
511 # a picklist with the desired ratio.
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
512 # For example, a part:backbone = 2:1 will multiply the
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
513 # backbone concentration by 2, therefore half as much of it will be
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
514 # added to the well.
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
515 quantities[part.replace(" ", "_")] = quantity * part_backbone_ratio
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
516 else:
196e13c09881 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
tduigou
parents: 0
diff changeset
517 quantities[part.replace(" ", "_")] = quantity
0
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
518
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
519 source_plate.name = "Source"
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
520 if destination_plate:
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
521 dest_filelike = file_to_filelike_object(destination_plate)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
522 destination_plate = plate_from_content_spreadsheet(destination_plate)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
523 else:
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
524 destination_plate = Plate4ti0960("Mixplate")
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
525 destination_wells = (
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
526 well for well in destination_plate.iter_wells(direction="column") if well.is_empty
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
527 )
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
528 picklist, picklist_data = picklist_generator.make_picklist(
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
529 assembly_plan,
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
530 source_wells=source_plate.iter_wells(),
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
531 destination_wells=destination_wells,
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
532 )
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
533 if picklist is None:
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
534 print("success: False")
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
535 print("message: Some parts in the assembly plan have no corresponding well.")
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
536 print("picklist_data: ", picklist_data)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
537 print("missing_parts:", picklist_data.get("missing_parts", None))
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
538 sys.exit()
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
539
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
540 future_plates = picklist.simulate(inplace=False)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
541
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
542
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
543 def text(w):
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
544 txt = human_volume(w.content.volume)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
545 if "construct" in w.data:
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
546 txt = "\n".join([w.data["construct"], txt])
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
547 return txt
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
548
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
549
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
550 plotter = PlateTextPlotter(text)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
551 ax, _ = plotter.plot_plate(future_plates[destination_plate], figsize=(20, 8))
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
552
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
553 ziproot = flametree.file_tree(result_zip_file, replace=True)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
554
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
555 # MIXPLATE MAP PLOT
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
556 ax.figure.savefig(
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
557 ziproot._file("final_mixplate.pdf").open("wb"),
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
558 format="pdf",
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
559 bbox_inches="tight",
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
560 )
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
561 plt.close(ax.figure)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
562 plate_to_platemap_spreadsheet(
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
563 future_plates[destination_plate],
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
564 lambda w: w.data.get("construct", ""),
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
565 filepath=ziproot._file("final_mixplate.xls").open("wb"),
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
566 )
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
567
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
568 # ASSEMBLY REPORT
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
569 print("Writing report...")
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
570 picklist_to_assembly_mix_report(
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
571 picklist,
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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572 ziproot._file("assembly_mix_picklist_report.pdf").open("wb"),
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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573 data=picklist_data,
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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574 )
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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575 assembly_plan.write_report(ziproot._file("assembly_plan_summary.pdf").open("wb"))
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
576
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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577 # MACHINE PICKLIST
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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578
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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579 if dispenser_machine == "labcyte_echo":
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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580 picklist_to_labcyte_echo_picklist_file(
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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581 picklist, ziproot._file("ECHO_picklist.csv").open("w")
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
582 )
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
583 else:
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
584 picklist_to_tecan_evo_picklist_file(
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
585 picklist, ziproot._file("EVO_picklist.gwl").open("w")
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
586 )
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
587 # We'll not write the input source plate.
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
588 # raw = file_to_filelike_object(source_plate_path).read()
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
589 # f = ziproot.copy(source_plate_path)
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
590 # f.write(raw, mode="wb")
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
591 ziproot._close()
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
592 print("success: True")
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
593
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
594
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
diff changeset
595 if __name__ == "__main__":
4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
tduigou
parents:
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596 main()