Mercurial > repos > public-health-bioinformatics > adjust_bracken_for_unclassified_reads
changeset 4:42e34f1f61a1 draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/adjust_bracken_for_unclassified_reads commit 9c95d7322121c8a4d8f36adf8e0d821992cf9173-dirty"
| author | public-health-bioinformatics |
|---|---|
| date | Wed, 09 Mar 2022 19:41:08 +0000 |
| parents | f5481e8b716d |
| children | 78b5452a5720 |
| files | adjust_bracken_for_unclassified_reads.py |
| diffstat | 1 files changed, 11 insertions(+), 5 deletions(-) [+] |
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--- a/adjust_bracken_for_unclassified_reads.py Mon Feb 28 23:29:01 2022 +0000 +++ b/adjust_bracken_for_unclassified_reads.py Wed Mar 09 19:41:08 2022 +0000 @@ -17,7 +17,7 @@ b['kraken_assigned_reads'] = int(row['kraken_assigned_reads']) b['added_reads'] = int(row['added_reads']) b['new_est_reads'] = int(row['new_est_reads']) - b['fraction_total_reads'] = float(row['fraction_total_reads']) + b['bracken_fraction_total_reads'] = float(row['fraction_total_reads']) bracken_abundances.append(b) return bracken_abundances @@ -57,7 +57,8 @@ 'kraken_assigned_reads': kraken_report_unclassified_reads, 'added_reads': 0, 'new_est_reads': kraken_report_unclassified_reads, - 'fraction_total_reads': percent_unclassified, + 'kraken_fraction_total_reads': percent_unclassified, + 'bracken_fraction_total_reads': 0.0, } bracken_abundances = [bracken_unclassified_entry] + bracken_abundances @@ -69,15 +70,20 @@ 'kraken_assigned_reads', 'added_reads', 'new_est_reads', - 'fraction_total_reads', + 'total_reads', + 'kraken_fraction_total_reads', + 'bracken_fraction_total_reads', ] writer = csv.DictWriter(sys.stdout, fieldnames=output_fieldnames, dialect='excel-tab') writer.writeheader() for b in bracken_abundances: - adjusted_fraction_total_reads = float(b['new_est_reads']) / float(total_reads) - b['fraction_total_reads'] = '{:.5f}'.format(adjusted_fraction_total_reads) + b['total_reads'] = total_reads + kraken_adjusted_fraction_total_reads = float(b['kraken_assigned_reads']) / float(total_reads) + b['kraken_fraction_total_reads'] = '{:.6f}'.format(kraken_adjusted_fraction_total_reads) + bracken_adjusted_fraction_total_reads = float(b['new_est_reads']) / float(total_reads) + b['bracken_fraction_total_reads'] = '{:.6f}'.format(bracken_adjusted_fraction_total_reads) writer.writerow(b) if __name__ == '__main__':