Mercurial > repos > public-health-bioinformatics > fastp_json_to_tabular

comparison fastp_json_to_tabular.py @ 4:b86961fa4ac4 draft default tip

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit 0cedf8014d943912974969f1ed294f6d0ec8f258"
author public-health-bioinformatics
date Thu, 10 Mar 2022 19:14:05 +0000
parents e342bf27e717
children
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3:e342bf27e717 4:b86961fa4ac4
8 fastp_report = json.load(f) 8 fastp_report = json.load(f)
9 9
10 reads_single_paired = fastp_report['summary']['sequencing'].split(' ')[0] 10 reads_single_paired = fastp_report['summary']['sequencing'].split(' ')[0]
11 11
12 if reads_single_paired == 'paired': 12 if reads_single_paired == 'paired':
13 total_read_pairs_before_filtering = str(int(fastp_report['summary']['before_filtering']['total_reads']) / 2) 13 total_read_pairs_before_filtering = str(int(int(fastp_report['summary']['before_filtering']['total_reads']) / 2))
14 total_read_pairs_after_filtering = str(int(fastp_report['summary']['after_filtering']['total_reads']) / 2) 14 total_read_pairs_after_filtering = str(int(int(fastp_report['summary']['after_filtering']['total_reads']) / 2))
15 read2_mean_length_before_filtering = fastp_report['summary']['before_filtering']['read2_mean_length'] 15 read2_mean_length_before_filtering = fastp_report['summary']['before_filtering']['read2_mean_length']
16 read2_mean_length_after_filtering = fastp_report['summary']['after_filtering']['read2_mean_length'] 16 read2_mean_length_after_filtering = fastp_report['summary']['after_filtering']['read2_mean_length']
17 else: 17 else:
18 total_read_pairs_before_filtering = 'NA' 18 total_read_pairs_before_filtering = 'NA'
19 total_read_pairs_after_filtering = 'NA' 19 total_read_pairs_after_filtering = 'NA'