Mercurial > repos > iss > eurl_vtec_wgs_pt

annotate scripts/modules/run_rematch.py @ 3:0506503db01d draft

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planemo upload commit 0708bd0601ac65e8a1c7cdd2504cebdf45755828
author iss
date Thu, 19 Oct 2023 12:31:29 +0000
parents c6bab5103a14
children
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1 import functools
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2 import os
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3 import sys
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4 import multiprocessing
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5
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6 try:
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7 import modules.utils as utils
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8 except ImportError:
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9 from pathotyping.modules import utils as utils
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12 # {'noMatter': '/home/ubuntu/NGStools/patho_typing/mpmachado_stuff.out_test/rematch/sample.noMatter.fasta', 'correct': '/home/ubuntu/NGStools/patho_typing/mpmachado_stuff.out_test/rematch/sample.correct.fasta', 'alignment': '/home/ubuntu/NGStools/patho_typing/mpmachado_stuff.out_test/rematch/sample.alignment.fasta'}
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15 def remove_alignment(alignment_file):
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16 directory = os.path.dirname(alignment_file)
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17 files = [f for f in os.listdir(directory) if not f.startswith('.') and os.path.isfile(os.path.join(directory, f))]
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18 for file_found in files:
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19 if file_found.startswith(os.path.splitext(os.path.basename(alignment_file))[0]):
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20 file_found = os.path.join(directory, file_found)
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21 os.remove(file_found)
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24 def remove_reference_stuff(outdir, reference_file):
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25 files = [f for f in os.listdir(outdir) if not f.startswith('.') and os.path.isfile(os.path.join(outdir, f))]
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26 for file_found in files:
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27 if file_found.startswith(os.path.splitext(os.path.basename(reference_file))[0]):
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28 file_found = os.path.join(outdir, file_found)
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29 os.remove(file_found)
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32 def clean_rematch_folder(consensus_files, bam_file, reference_file, outdir, doNotRemoveConsensus, debug_mode_true):
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33 if not debug_mode_true:
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34 if not doNotRemoveConsensus:
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35 for consensus_type, file_path in list(consensus_files.items()):
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36 if os.path.isfile(file_path):
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37 os.remove(file_path)
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38 if bam_file is not None:
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39 remove_alignment(bam_file)
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40 remove_reference_stuff(outdir, reference_file)
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42
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43 def sequence_data(sample, reference_file, bam_file, outdir, threads, length_extra_seq, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele, debug_mode_true, rematch):
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44 sequence_data_outdir = os.path.join(outdir, 'sequence_data', '')
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45 utils.removeDirectory(sequence_data_outdir)
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46 os.mkdir(sequence_data_outdir)
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47
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48 sequences, headers = utils.get_sequence_information(reference_file, length_extra_seq)
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49
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50 pool = multiprocessing.Pool(processes=threads)
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51 for sequence_counter in sequences:
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52 sequence_dir = os.path.join(sequence_data_outdir, str(sequence_counter), '')
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53 utils.removeDirectory(sequence_dir)
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54 os.makedirs(sequence_dir)
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55 pool.apply_async(rematch.analyse_sequence_data, args=(bam_file, sequences[sequence_counter], sequence_dir, sequence_counter, reference_file, length_extra_seq, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele,))
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56 pool.close()
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57 pool.join()
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58
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59 run_successfully, sample_data, consensus_files, consensus_sequences = rematch.gather_data_together(sample, sequence_data_outdir, sequences, outdir.rsplit('/', 2)[0], debug_mode_true, length_extra_seq, False)
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60
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61 return run_successfully, sample_data, consensus_files, consensus_sequences
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62
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63
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64 def determine_general_statistics(sample_data, minimum_gene_coverage, minimum_gene_identity):
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65 print('Writing report file')
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66 number_absent_genes = 0
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67 number_genes_multiple_alleles = 0
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68 mean_sample_coverage = 0
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69
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70 with open('output_dir/rematch/rematchModule_report.txt', 'wt') as writer:
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71 writer.write('\t'.join(['#gene', 'percentage_gene_coverage', 'gene_mean_read_coverage', 'percentage_gene_low_coverage', 'number_positions_multiple_alleles', 'percentage_gene_identity']) + '\n')
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72 for i in range(1, len(sample_data) + 1):
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73 writer.write('\t'.join([sample_data[i]['header'], str(round(sample_data[i]['gene_coverage'], 2)), str(round(sample_data[i]['gene_mean_read_coverage'], 2)), str(round(sample_data[i]['gene_low_coverage'], 2)), str(sample_data[i]['gene_number_positions_multiple_alleles']), str(round(sample_data[i]['gene_identity'], 2))]) + '\n')
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74
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75 if sample_data[i]['gene_coverage'] < minimum_gene_coverage or sample_data[i]['gene_identity'] < minimum_gene_identity:
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76 number_absent_genes += 1
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77 else:
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78 mean_sample_coverage += sample_data[i]['gene_mean_read_coverage']
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79 if sample_data[i]['gene_number_positions_multiple_alleles'] > 0:
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80 number_genes_multiple_alleles += 1
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81
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82 if len(sample_data) - number_absent_genes > 0:
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83 mean_sample_coverage = float(mean_sample_coverage) / float(len(sample_data) - number_absent_genes)
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84 else:
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85 mean_sample_coverage = 0
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86
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87 writer.write('\n'.join(['#general', '>number_absent_genes', str(number_absent_genes), '>number_genes_multiple_alleles', str(number_genes_multiple_alleles), '>mean_sample_coverage', str(round(mean_sample_coverage, 2))]) + '\n')
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88
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89 print('\n'.join([str('number_absent_genes: ' + str(number_absent_genes)),
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90 str('number_genes_multiple_alleles: ' + str(number_genes_multiple_alleles)),
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91 str('mean_sample_coverage: ' + str(round(mean_sample_coverage, 2)))]) + '\n')
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92
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93 return number_absent_genes, number_genes_multiple_alleles, mean_sample_coverage
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94
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95 module_timer = functools.partial(utils.timer, name='Module ReMatCh')
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96
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97
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98 @module_timer
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99 def run_rematch(rematch, outdir, reference_file, bam_file, threads, length_extra_seq, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele, minimum_gene_coverage, minimum_gene_identity, debug_mode_true, doNotRemoveConsensus):
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100 module_dir = os.path.join(outdir, 'rematch', '')
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101 utils.removeDirectory(module_dir)
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102 os.makedirs(module_dir)
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103
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104 sys.path.append(os.path.join(os.path.dirname(rematch), 'modules'))
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105 import rematch_module as rematch
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106
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107 print('Analysing alignment data')
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108 run_successfully, sample_data, consensus_files, consensus_sequences = sequence_data('sample', reference_file, bam_file, module_dir, threads, length_extra_seq, minimum_depth_presence, minimum_depth_call, minimum_depth_frequency_dominant_allele, debug_mode_true, rematch)
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109
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110 if run_successfully:
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111 number_absent_genes, number_genes_multiple_alleles, mean_sample_coverage = \
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112 determine_general_statistics(sample_data=sample_data, minimum_gene_coverage=minimum_gene_coverage,
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113 minimum_gene_identity=minimum_gene_identity)
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114
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115 if not debug_mode_true:
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116 utils.removeDirectory(module_dir)
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117
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118 clean_rematch_folder(consensus_files, bam_file, reference_file, outdir, doNotRemoveConsensus, debug_mode_true)
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119
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120 return run_successfully, {'number_absent_genes': number_absent_genes if 'number_absent_genes' in locals() else None, 'number_genes_multiple_alleles': number_genes_multiple_alleles if 'number_genes_multiple_alleles' in locals() else None, 'mean_sample_coverage': round(mean_sample_coverage, 2) if 'mean_sample_coverage' in locals() else None}, sample_data if 'sample_data' in locals() else None