annotate draw_amr_matrix.py @ 2:9fcc1ffd7526 draft

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author greg
date Fri, 10 Feb 2023 17:27:33 +0000
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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import csv
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5 import os
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6
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7 import numpy
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8 import pandas
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9 import matplotlib.pyplot as pyplot
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10
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11
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12 def get_amr_in_feature_hits(amr_feature_hits):
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13 for k in amr_feature_hits.keys():
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14 if k.lower().find('amr') >= 0:
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15 return amr_feature_hits[k]
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16 return None
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19 def draw_amr_matrix(amr_feature_hits_files, amr_deletions_file, amr_mutations_file, amr_gene_drug_file, output_dir):
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20 ofh = open('process_log', 'w')
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21
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22 # Read amr_feature_hits_files.
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23 amr_feature_hits = pandas.Series(dtype=object)
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24 for amr_feature_hits_file in amr_feature_hits_files:
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25 feature_name = os.path.basename(amr_feature_hits_file)
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26 # Make sure the file is not empty.
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27 if os.path.isfile(amr_feature_hits_file) and os.path.getsize(amr_feature_hits_file) > 0:
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28 best_hits = pandas.read_csv(filepath_or_buffer=amr_feature_hits_file, sep='\t', header=None)
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29 ofh.write("\nFeature file %s will be processed\n" % os.path.basename(amr_feature_hits_file))
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30 else:
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31 ofh.write("\nEmpty feature file %s will NOT be processed\n" % os.path.basename(amr_feature_hits_file))
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32 best_hits = None
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33 amr_feature_hits[feature_name] = best_hits
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35 amr_hits = get_amr_in_feature_hits(amr_feature_hits)
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36 ofh.write("\namr_hits:\n%s\n" % str(amr_hits))
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37 if amr_hits is not None:
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38 amr_to_draw = pandas.DataFrame(columns=['gene', 'drug'])
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39 ofh.write("\namr_to_draw:\n%s\n" % str(amr_to_draw))
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40 # Read amr_drug_gene_file.
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41 amr_gene_drug = pandas.read_csv(amr_gene_drug_file, index_col=None, sep='\t', quoting=csv.QUOTE_NONE, header=None)
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42 ofh.write("\namr_gene_drug:\n%s\n" % str(amr_gene_drug))
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43
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44 # Roll up AMR gene hits.
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45 ofh.write("\namr_hits.shape[0]:%s\n" % str(amr_hits.shape[0]))
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46 if amr_hits.shape[0] > 0:
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47 for gene_idx, gene in amr_hits.iterrows():
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48 ofh.write("gene_idx:%s\n" % str(gene_idx))
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49 ofh.write("gene:%s\n" % str(gene))
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50 gene_name = gene[3]
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51 ofh.write("gene_name: %s\n" % str(gene_name))
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52 ofh.write("amr_gene_drug[0]: %s\n" % str(amr_gene_drug[0]))
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53 drugs = amr_gene_drug.loc[amr_gene_drug[0] == gene_name, :][1]
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54 ofh.write("drugs:%s\n" % str(drugs))
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55 for drug in drugs:
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56 amr_to_draw = amr_to_draw.append(pandas.Series([gene_name, drug], name=amr_to_draw.shape[0], index=amr_to_draw.columns))
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57 ofh.write("\amr_to_draw:%s\n" % str(amr_to_draw))
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58
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59 if amr_mutations_file is not None:
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60 # TODO: So far, no samples have produced mutations, so we haven't been able
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61 # to produce a populated VarScan VCF file of mutations - https://github.com/appliedbinf/pima_md/blob/main/pima.py#L2923.
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62 # The call_amr_mutations Galaxy tool will currently produce this VarScan VCF file, but we need a sample that
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63 # will produce a populated file. After we find one, we'll need to figure out how to implement this loop
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64 # https://github.com/appliedbinf/pima_md/blob/main/pima.py#L2925 in a Galaxy tool so that the VarScan VCF
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65 # file will be converted to the TSV amr_mutations_file that thsi tool expects.
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66 # Roll up potentially resistance conferring mutations.
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67 for mutation_region, mutation_hits in amr_mutations.iteritems():
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68 for mutation_idx, mutation_hit in mutation_hits.iterrows():
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69 mutation_name = mutation_region + ' ' + mutation_hit['REF'] + '->' + mutation_hit['ALT']
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70 amr_to_draw = amr_to_draw.append(pandas.Series([mutation_name, mutation_hit['DRUG']], name=amr_to_draw.shape[0], index=amr_to_draw.columns))
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72 if amr_deletions_file is not None:
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73 # TODO: So far, no samples have produced deletions, but we do have all the pices in place
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74 # within the workflow to receive the amr_deletions_file here, although it is currently
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75 # always empty...
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76 # Roll up deletions that might confer resistance.
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77 amr_deletions = pandas.read_csv(filepath_or_buffer=amr_deletions_file, sep='\t', header=None)
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78 if amr_deletions.shape[0] > 0:
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79 amr_deletions.columns = ['contig', 'start', 'stop', 'name', 'type', 'drug', 'note']
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80 amr_deletions = amr_deletions.loc[amr_deletions['type'].isin(['large-deletion', 'any']), :]
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81 for deletion_idx, deleted_gene in amr_deletions.iterrows():
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82 amr_to_draw = amr_to_draw.append(pandas.Series(['\u0394' + deleted_gene[3], deleted_gene[5]], name=amr_to_draw.shape[0], index=amr_to_draw.columns))
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84 if amr_to_draw.shape[0] > 1:
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85 ofh.write("\nDrawing AMR matrix...\n")
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86 present_genes = amr_to_draw['gene'].unique()
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87 present_drugs = amr_to_draw['drug'].unique()
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88 amr_matrix = pandas.DataFrame(0, index=present_genes, columns=present_drugs)
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89 for hit_idx, hit in amr_to_draw.iterrows():
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90 amr_matrix.loc[hit[0], hit[1]] = 1
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91 amr_matrix_png = os.path.join(output_dir, 'amr_matrix.png')
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92 int_matrix = amr_matrix[amr_matrix.columns].astype(int)
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93 figure, axis = pyplot.subplots()
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94 axis.invert_yaxis()
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95 axis.set_yticks(numpy.arange(0.5, len(amr_matrix.index)), minor=False)
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96 axis.set_yticklabels(int_matrix.index.values)
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97 axis.set_xticks(numpy.arange(0.5, len(amr_matrix.columns)), minor=False)
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98 axis.set_xticklabels(amr_matrix.columns.values, rotation=90)
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99 axis.xaxis.tick_top()
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100 axis.xaxis.set_label_position('top')
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101 pyplot.tight_layout()
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102 pyplot.savefig(amr_matrix_png, dpi=300)
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103 else:
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104 ofh.write("\nEmpty AMR matrix, nothing to draw...\n")
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105 ofh.close()
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106
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108 if __name__ == '__main__':
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109 parser = argparse.ArgumentParser()
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110
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111 parser.add_argument('--amr_feature_hits_dir', action='store', dest='amr_feature_hits_dir', help='Directory of tabular files containing feature hits')
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112 parser.add_argument('--amr_deletions_file', action='store', dest='amr_deletions_file', default=None, help='AMR deletions BED file')
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113 parser.add_argument('--amr_mutations_file', action='store', dest='amr_mutations_file', default=None, help='AMR mutations TSV file')
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114 parser.add_argument('--amr_gene_drug_file', action='store', dest='amr_gene_drug_file', help='AMR_gene_drugs tsv file')
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115 parser.add_argument('--output_dir', action='store', dest='output_dir', help='Output directory')
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116
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117 args = parser.parse_args()
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118
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119 # Get thge collection of feature hits files. The collection
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120 # will be sorted alphabetically and will contain 2 files
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121 # named something like AMR_CDS_311_2022_12_20.fasta and
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122 # Incompatibility_Groups_2023_01_01.fasta.
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123 amr_feature_hits_files = []
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124 for file_name in sorted(os.listdir(args.amr_feature_hits_dir)):
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125 file_path = os.path.abspath(os.path.join(args.amr_feature_hits_dir, file_name))
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126 amr_feature_hits_files.append(file_path)
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128 draw_amr_matrix(amr_feature_hits_files, args.amr_deletions_file, args.amr_mutations_file, args.amr_gene_drug_file, args.output_dir)