Mercurial > repos > davidvanzessen > shm_csr

annotate split_imgt_file.py @ 92:cf8ad181628f draft

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planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c
author rhpvorderman
date Mon, 12 Dec 2022 12:32:44 +0000
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92
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1 #!/usr/bin/env python3
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2
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3 """
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4 Script to split IMGT file into several archives for each of the genes
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5
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6 Rather than creating each new archive individually this script will read
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7 the input files only once and as such enormously shorten processing time.
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8 """
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9
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10 import argparse
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11 import io
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12 import os
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13 import tarfile
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14 import tempfile
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15 from typing import Iterator, List, Tuple
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16
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17
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18 def merged_txt_to_match_dict(merged: str):
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19 with open(merged, "rt") as f:
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20 header = next(f).strip("\n")
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21 column_names = header.split("\t")
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22 # For the baseline result there is no best_match column
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23 if "best_match" in column_names:
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24 best_match_index = column_names.index("best_match")
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25 else:
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26 best_match_index = None
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27 sequence_id_index = column_names.index("Sequence.ID")
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28 match_dict = {}
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29 for line in f:
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30 values = line.strip().split("\t")
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31 sequence_id = values[sequence_id_index]
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32 if best_match_index is not None:
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33 best_match = values[best_match_index]
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34 if "unmatched" in best_match:
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35 # For some reason the table has values such as: unmatched, IGA2
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36 continue
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37 else:
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38 best_match = ""
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39 match_dict[sequence_id] = best_match
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40 return match_dict
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41
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42
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43 def imgt_to_tables(imgt_file: str) -> Iterator[Tuple[str, io.TextIOWrapper]]:
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44 print(f"opening IMGT file: {imgt_file}")
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45 with tarfile.open(imgt_file, "r") as archive:
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46 while True:
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47 member = archive.next()
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48 if member is None:
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49 return
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50 if member.name in {"README.txt"}:
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51 continue
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52 if member.name.startswith("11_"):
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53 continue
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54 f = archive.extractfile(member)
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55 f_text = io.TextIOWrapper(f)
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56 yield member.name, f_text
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57 f_text.close()
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58
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59
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60 def split_imgt(imgt_file: str, merged_file: str, outdir: str, genes: List[str],
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61 prefix: str):
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62 """
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63 This function creates a separate tar file for each of the gene matches
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64 based on the merged file. Unmatched genes are left out.
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65 :param imgt_file: The original IMGT file
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66 :param merged_file: The merged data file generated by SHM&CSR pipeline
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67 :param outdir: The output directory.
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68 :param genes: The genes to split out. Use '-' for all identified genes.
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69 :return:
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70 """
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71 match_dict = merged_txt_to_match_dict(merged_file)
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72 gene_tarfiles = []
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73 os.makedirs(outdir, exist_ok=True)
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74 for gene in genes:
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75 new_filename = f"{prefix}_{gene}.txz" if gene else f"{prefix}.txz"
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76 gene_tarfiles.append(
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77 tarfile.open(os.path.join(outdir, new_filename), mode="w:xz")
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78 )
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79 for name, table in imgt_to_tables(imgt_file):
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80 # Read each table one by one and per line select in which output
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81 # files it should go.
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82 gene_files = []
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83 for gene in genes:
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84 fp, fname = tempfile.mkstemp()
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85 # The file pointer fp will be wrapped in a python file object
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86 # so we can ensure there remain no open files.
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87 f = open(fp, mode="wt")
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88 gene_files.append((gene, f, fname))
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89 header = next(table)
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90 header_number_of_tabs = header.count('\t')
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91 column_names = header.strip("\n").split("\t")
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92 fr1_columns = [index for index, column in enumerate(column_names)
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93 if column.startswith("FR1")]
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94 sequence_id_index = column_names.index("Sequence ID")
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95 for _, gene_file, _ in gene_files:
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96 gene_file.write(header)
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97 for line in table:
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98 # IMGT sometimes delivers half-empty rows.
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99 row_number_of_tabs = line.count("\t")
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100 missing_tabs = header_number_of_tabs - row_number_of_tabs
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101 if missing_tabs:
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102 line = line.strip("\n") + missing_tabs * "\t" + "\n"
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103 values = line.strip("\n").split("\t")
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104 sequence_id = values[sequence_id_index]
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105 match = match_dict.get(sequence_id)
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106 if match is None:
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107 continue
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108 if name.startswith("8_"):
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109 # change the FR1 columns to 0 in the "8_..." file
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110 for index in fr1_columns:
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111 values[index] = "0"
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112 line = "\t".join(values) + "\n"
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113 for gene, gene_file, _ in gene_files:
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114 if gene in match:
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115 gene_file.write(line)
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116 for gene_tarfile, (_, gene_file, fname) in zip(gene_tarfiles, gene_files):
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117 gene_file.flush()
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118 gene_tarfile.add(fname, name)
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119 gene_file.close()
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120 os.remove(fname)
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121 for gene_tarfile in gene_tarfiles:
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122 gene_tarfile.close()
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123
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124
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125 def argument_parser() -> argparse.ArgumentParser:
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126 parser = argparse.ArgumentParser()
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127 parser.add_argument("imgt_file", help="The original IMGT FILE")
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128 parser.add_argument("merged", help="merged.txt file")
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129 parser.add_argument("--outdir", help="output directory")
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130 parser.add_argument(
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131 "genes",
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132 nargs="+",
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133 help="The genes to split out. Use '-' for all identified genes.")
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134 parser.add_argument("--prefix", help="Prefix for the archives and "
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135 "directories")
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136 return parser
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137
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138
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139 def main():
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140 args = argument_parser().parse_args()
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141 genes = ["" if gene == "-" else gene for gene in args.genes]
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142 split_imgt(args.imgt_file, args.merged, args.outdir, genes,
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143 args.prefix)
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144
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145
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146 if __name__ == "__main__":
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147 main()