Mercurial > repos > public-health-bioinformatics > fastp_json_to_tabular

diff fastp_json_to_tabular.py @ 0:091a2fb2e7ad 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 888d26702a84c2f8fd1428aff8cd869e94cc0bae"
author public-health-bioinformatics
date Thu, 10 Mar 2022 21:59:56 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastp_json_to_tabular.py	Thu Mar 10 21:59:56 2022 +0000
@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+def main(args):
+    with open(args.fastp_json, 'r') as f:
+        fastp_report = json.load(f)
+
+    reads_single_paired = fastp_report['summary']['sequencing'].split(' ')[0]
+
+    if reads_single_paired == 'paired':
+        total_read_pairs_before_filtering = str(int(int(fastp_report['summary']['before_filtering']['total_reads']) / 2))
+        total_read_pairs_after_filtering = str(int(int(fastp_report['summary']['after_filtering']['total_reads']) / 2))
+        read2_mean_length_before_filtering = fastp_report['summary']['before_filtering']['read2_mean_length']
+        read2_mean_length_after_filtering = fastp_report['summary']['after_filtering']['read2_mean_length']
+    else:
+        total_read_pairs_before_filtering = 'NA'
+        total_read_pairs_after_filtering = 'NA'
+        read2_mean_length_before_filtering = 'NA'
+        read2_mean_length_after_filtering = 'NA'
+
+    total_reads_before_filtering = fastp_report['summary']['before_filtering']['total_reads']
+    total_reads_after_filtering = fastp_report['summary']['after_filtering']['total_reads']
+
+    total_bases_before_filtering = fastp_report['summary']['before_filtering']['total_bases']
+    total_bases_after_filtering = fastp_report['summary']['after_filtering']['total_bases']
+
+    read1_mean_length_before_filtering = fastp_report['summary']['before_filtering']['read1_mean_length']
+    read1_mean_length_after_filtering = fastp_report['summary']['after_filtering']['read1_mean_length']
+
+    q20_bases_before_filtering = fastp_report['summary']['before_filtering']['q20_bases']
+    q20_bases_after_filtering = fastp_report['summary']['after_filtering']['q20_bases']
+
+    q20_rate_before_filtering = fastp_report['summary']['before_filtering']['q20_rate']
+    q20_rate_after_filtering = fastp_report['summary']['after_filtering']['q20_rate']
+
+    q30_bases_before_filtering = fastp_report['summary']['before_filtering']['q30_bases']
+    q30_bases_after_filtering = fastp_report['summary']['after_filtering']['q30_bases']
+
+    q30_rate_before_filtering = fastp_report['summary']['before_filtering']['q30_rate']
+    q30_rate_after_filtering = fastp_report['summary']['after_filtering']['q30_rate']
+
+    gc_content_before_filtering = fastp_report['summary']['before_filtering']['gc_content']
+    gc_content_after_filtering = fastp_report['summary']['after_filtering']['gc_content']
+    if 'adapter_cutting' in fastp_report:
+        adapter_trimmed_reads = fastp_report['adapter_cutting']['adapter_trimmed_reads']
+        adapter_trimmed_bases = fastp_report['adapter_cutting']['adapter_trimmed_bases']
+    else:
+        adapter_trimmed_reads = 0
+        adapter_trimmed_bases = 0
+
+    output_fields = [
+        'total_reads_before_filtering',
+        'total_read_pairs_before_filtering',
+        'total_reads_after_filtering',
+        'total_read_pairs_after_filtering',
+        'total_bases_before_filtering',
+        'total_bases_after_filtering',
+        'read1_mean_length_before_filtering',
+        'read1_mean_length_after_filtering',
+        'read2_mean_length_before_filtering',
+        'read2_mean_length_after_filtering',
+        'q20_bases_before_filtering',
+        'q20_bases_after_filtering',
+        'q20_rate_before_filtering',
+        'q20_rate_after_filtering',
+        'q30_bases_before_filtering',
+        'q30_bases_after_filtering',
+        'q30_rate_before_filtering',
+        'q30_rate_after_filtering',
+        'gc_content_before_filtering',
+        'gc_content_after_filtering',
+        'adapter_trimmed_reads',
+        'adapter_trimmed_bases',
+    ]
+
+    output_data = []
+    if args.sample_id:
+        output_fields = ['sample_id'] + output_fields
+        output_data = [args.sample_id]
+
+    print(args.delimiter.join(output_fields))
+
+    output_data = output_data + [
+        total_reads_before_filtering,
+        total_read_pairs_before_filtering,
+        total_reads_after_filtering,
+        total_read_pairs_after_filtering,
+        total_bases_before_filtering,
+        total_bases_after_filtering,
+        read1_mean_length_before_filtering,
+        read1_mean_length_after_filtering,
+        read2_mean_length_before_filtering,
+        read2_mean_length_after_filtering,
+        q20_bases_before_filtering,
+        q20_bases_after_filtering,
+        q20_rate_before_filtering,
+        q20_rate_after_filtering,
+        q30_bases_before_filtering,
+        q30_bases_after_filtering,
+        q30_rate_before_filtering,
+        q30_rate_after_filtering,
+        gc_content_before_filtering,
+        gc_content_after_filtering,
+        adapter_trimmed_reads,
+        adapter_trimmed_bases,
+    ]
+    print(args.delimiter.join(map(str, output_data)))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('fastp_json')
+    parser.add_argument('-s', '--sample-id')
+    parser.add_argument('-d', '--delimiter', default='\t')
+    args = parser.parse_args()
+    main(args)