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Add json version of qualimap genome results parser
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| #!/usr/bin/env python | ||
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| import argparse | ||
| import json | ||
| import os | ||
| import sys | ||
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| def get_section_lines(report_path, section_name): | ||
| """ | ||
| """ | ||
| section_lines = [] | ||
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| with open(report_path, 'r') as f: | ||
| # skip lines until we reach the input section | ||
| # indicated by the line starting with '>>>>>>> Input' | ||
| for line in f: | ||
| if line.startswith(f'>>>>>>> {section_name}'): | ||
| break | ||
| for line in f: | ||
| if line.startswith('>>>>>>>'): | ||
| break | ||
| if line.strip() != '': | ||
| section_lines.append(line.strip()) | ||
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| return section_lines | ||
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| def parse_input_section(report_path): | ||
| """ | ||
| """ | ||
| section_lines = get_section_lines(report_path, 'Input') | ||
| input_section = {} | ||
| for line in section_lines: | ||
| key, value = line.split('=') | ||
| key = key.strip().replace(' ', '_').lower() | ||
| value = value.strip() | ||
| input_section[key] = value | ||
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| return input_section | ||
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| def parse_reference_section(report_path): | ||
| """ | ||
| """ | ||
| section_lines = get_section_lines(report_path, 'Reference') | ||
| reference_section = {} | ||
| keys_with_units = [ | ||
| 'number_of_bases', | ||
| ] | ||
| int_keys = [ | ||
| 'number_of_bases', | ||
| 'number_of_contigs', | ||
| ] | ||
| for line in section_lines: | ||
| key, value = line.split('=') | ||
| key = key.strip().replace(' ', '_').lower() | ||
| value = value.strip() | ||
| if key in keys_with_units: | ||
| value, unit = value.split() | ||
| if key in int_keys: | ||
| value = value.replace(',', '') | ||
| value = int(value) | ||
| reference_section[key] = value | ||
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| return reference_section | ||
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| def parse_int_with_percentage(value): | ||
| """ | ||
| Convert a string like "20,096,173 (99.89%)" to a tuple (20096173, 99.89) | ||
| """ | ||
| value, percentage = value.split() | ||
| value = value.replace(',', '') | ||
| value = int(value) | ||
| percentage = percentage.strip('()').replace('%', '') | ||
| percentage = float(percentage) | ||
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| return value, percentage | ||
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| def parse_globals_section(report_path): | ||
| """ | ||
| """ | ||
| section_lines = get_section_lines(report_path, 'Globals') | ||
| globals_section = {} | ||
| int_keys = [ | ||
| 'number_of_windows', | ||
| 'number_of_reads', | ||
| 'number_of_secondary_alignments', | ||
| 'number_of_mapped_paired_reads_first_in_pair', | ||
| 'number_of_mapped_paired_reads_second_in_pair', | ||
| 'number_of_mapped_paired_reads_both_in_pair', | ||
| 'number_of_mapped_paired_reads_singletons', | ||
| 'number_of_overlapping_read_pairs', | ||
| 'number_of_duplicated_reads_flagged', | ||
| ] | ||
| int_with_unit_keys = [ | ||
| 'number_of_mapped_bases', | ||
| 'number_of_sequenced_bases', | ||
| 'number_of_aligned_bases', | ||
| ] | ||
| int_with_percentage_keys = [ | ||
| 'number_of_mapped_reads', | ||
| 'number_of_supplementary_alignments', | ||
| ] | ||
| for line in section_lines: | ||
| key, value = line.split('=') | ||
| key = key.strip().replace(' ', '_').replace('(', '').replace(')', '').lower() | ||
| value = value.strip() | ||
| if key in int_keys: | ||
| value = value.replace(',', '') | ||
| value = int(value) | ||
| elif key in int_with_percentage_keys: | ||
| value, percentage = parse_int_with_percentage(value) | ||
| percentage_key = key.replace('number_of_', 'percent_') | ||
| globals_section[percentage_key] = percentage | ||
| elif key in int_with_unit_keys: | ||
| value, unit = value.split() | ||
| value = value.replace(',', '') | ||
| value = int(value) | ||
| globals_section[key] = value | ||
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| return globals_section | ||
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| def parse_insert_size_section(report_path): | ||
| """ | ||
| """ | ||
| insert_size_section = {} | ||
| section_lines = get_section_lines(report_path, 'Insert size') | ||
| float_keys = [ | ||
| 'mean_insert_size', | ||
| 'std_insert_size', | ||
| ] | ||
| int_keys = [ | ||
| 'median_insert_size', | ||
| ] | ||
| for line in section_lines: | ||
| key, value = line.split('=') | ||
| key = key.strip().replace(' ', '_').lower() | ||
| value = value.strip() | ||
| if key in float_keys: | ||
| value = value.replace(',', '') | ||
| value = float(value) | ||
| elif key in int_keys: | ||
| value = value.replace(',', '') | ||
| value = int(value) | ||
| insert_size_section[key] = value | ||
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| return insert_size_section | ||
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| def parse_actg_content_section(report_path): | ||
| """ | ||
| """ | ||
| actg_content_section = {} | ||
| section_lines = get_section_lines(report_path, 'ACTG content') | ||
| int_with_units_and_percentage_keys = [ | ||
| 'number_of_a_bases', | ||
| 'number_of_c_bases', | ||
| 'number_of_g_bases', | ||
| 'number_of_t_bases', | ||
| 'number_of_n_bases', | ||
| ] | ||
| percentage_keys = [ | ||
| 'gc_percentage', | ||
| ] | ||
| for line in section_lines: | ||
| key, value = line.split('=') | ||
| key = key.strip().replace(' ', '_').replace("'", "_base").lower() | ||
| value = value.strip() | ||
| if key in int_with_units_and_percentage_keys: | ||
| value_split = value.split() | ||
| value_without_units = ' '.join([value_split[0], value_split[2]]) | ||
| value, percentage = parse_int_with_percentage(value_without_units) | ||
| percentage_key = key.replace('number_of_', 'percent_') | ||
| actg_content_section[percentage_key] = percentage | ||
| elif key in percentage_keys: | ||
| value = value.replace('%', '') | ||
| value = float(value) | ||
| actg_content_section[key] = value | ||
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| return actg_content_section | ||
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| def parse_mismatches_and_indels_section(report_path): | ||
| """ | ||
| """ | ||
| mismatches_and_indels_section = {} | ||
| section_lines = get_section_lines(report_path, 'Mismatches and indels') | ||
| int_keys = [ | ||
| 'number_of_mismatches', | ||
| 'number_of_insertions', | ||
| 'number_of_deletions', | ||
| ] | ||
| float_keys = [ | ||
| 'general_error_rate', | ||
| ] | ||
| percentage_keys = [ | ||
| 'mapped_reads_with_insertion_percentage', | ||
| 'mapped_reads_with_deletion_percentage', | ||
| 'homopolymer_indels', | ||
| ] | ||
| for line in section_lines: | ||
| key, value = line.split('=') | ||
| key = key.strip().replace(' ', '_').lower() | ||
| value = value.strip() | ||
| if key in int_keys: | ||
| value = value.replace(',', '') | ||
| value = int(value) | ||
| elif key in float_keys: | ||
| value = float(value) | ||
| elif key in percentage_keys: | ||
| value = value.replace('%', '') | ||
| value = float(value) | ||
| if key == 'homopolymer_indels': | ||
| key = 'homopolymer_indels_percentage' | ||
| mismatches_and_indels_section[key] = value | ||
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| return mismatches_and_indels_section | ||
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| def parse_percent_coverage_line(line): | ||
| """ | ||
| Convert lines that look like: | ||
| There is a 100% of reference with a coverageData >= 1X | ||
| ...into a tuple (1, 100) | ||
| """ | ||
| line_split = line.split() | ||
| coverage = line_split[-1] | ||
| percentage = line_split[3] | ||
| coverage = int(coverage.strip('X')) | ||
| percentage = float(percentage.strip('%')) | ||
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| return coverage, percentage | ||
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| def parse_coverage_section(report_path): | ||
| """ | ||
| """ | ||
| coverage_section = { | ||
| 'coverage_profile': [], | ||
| } | ||
| section_lines = get_section_lines(report_path, 'Coverage') | ||
| float_x_keys = [ | ||
| 'mean_coverage', | ||
| 'std_coverage', | ||
| 'paired-end_adapted_mean_coverage', | ||
| ] | ||
| for line in section_lines: | ||
| if line.startswith('There is a'): | ||
| coverage, value = parse_percent_coverage_line(line) | ||
| coverage_profile_record = { | ||
| 'depth_threshold': coverage, | ||
| 'percent_reference_covered': value, | ||
| } | ||
| coverage_section['coverage_profile'].append(coverage_profile_record) | ||
| else: | ||
| key, value = line.split('=') | ||
| key = key.strip().replace(' ', '_').replace('coverageData', 'coverage').lower() | ||
| value = value.strip() | ||
| if key in float_x_keys: | ||
| value = value.replace('X', '') | ||
| value = float(value) | ||
| coverage_section[key] = value | ||
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| return coverage_section | ||
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| def parse_coverage_per_contig_section(report_path): | ||
| """ | ||
| """ | ||
| coverage_per_contig_section = [] | ||
| section_lines = get_section_lines(report_path, 'Coverage per contig') | ||
| section_headers = [ | ||
| 'name', | ||
| 'length', | ||
| 'mapped_bases', | ||
| 'mean_coverage', | ||
| 'standard_deviation', | ||
| ] | ||
| int_keys = [ | ||
| 'length', | ||
| 'mapped_bases', | ||
| ] | ||
| float_keys = [ | ||
| 'mean_coverage', | ||
| 'standard_deviation', | ||
| ] | ||
| for line in section_lines: | ||
| line_split = line.split('\t') | ||
| contig_data = {} | ||
| for i, header in enumerate(section_headers): | ||
| value = line_split[i] | ||
| if header in int_keys: | ||
| value = int(value) | ||
| elif header in float_keys: | ||
| value = float(value) | ||
| contig_data[header] = value | ||
| coverage_per_contig_section.append(contig_data) | ||
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| return coverage_per_contig_section | ||
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| def main(args): | ||
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| parsed_genome_results = {} | ||
| input_section = parse_input_section(args.input) | ||
| parsed_genome_results['input'] = input_section | ||
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| reference_section = parse_reference_section(args.input) | ||
| parsed_genome_results['reference'] = reference_section | ||
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| globals_section = parse_globals_section(args.input) | ||
| parsed_genome_results['globals'] = globals_section | ||
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| insert_size_section = parse_insert_size_section(args.input) | ||
| parsed_genome_results['insert_size'] = insert_size_section | ||
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| actg_content_section = parse_actg_content_section(args.input) | ||
| parsed_genome_results['actg_content'] = actg_content_section | ||
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| mismatches_and_indels_section = parse_mismatches_and_indels_section(args.input) | ||
| parsed_genome_results['mismatches_and_indels'] = mismatches_and_indels_section | ||
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| coverage_section = parse_coverage_section(args.input) | ||
| parsed_genome_results['coverage'] = coverage_section | ||
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| coverage_per_contig_section = parse_coverage_per_contig_section(args.input) | ||
| parsed_genome_results['coverage_per_contig'] = coverage_per_contig_section | ||
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| print(json.dumps(parsed_genome_results, indent=4)) | ||
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| if __name__ == '__main__': | ||
| parser = argparse.ArgumentParser(description='Description of your script') | ||
| parser.add_argument('--input', type=str, required=True, help='Path to the input file') | ||
| args = parser.parse_args() | ||
| main(args) | ||
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