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Adds avg read length in the output header with run the -t rel_ab_w_re…
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…ad_stats option
abmiguez committed Sep 1, 2023
1 parent 048cd23 commit 8f7de07
Showing 1 changed file with 3 additions and 0 deletions.
3 changes: 3 additions & 0 deletions metaphlan/metaphlan.py
Original file line number Diff line number Diff line change
@@ -1429,6 +1429,9 @@ def main():
outf.write('#{}\n'.format(pars['index']))
outf.write('#{}\n'.format(' '.join(sys.argv)))
outf.write('#{} reads processed\n'.format(n_metagenome_reads))

if pars['t'] == 'rel_ab_w_read_stats':
outf.write('#Average read length {}\n'.format(avg_read_length))

if not CAMI_OUTPUT:
outf.write('#' + '\t'.join((pars["sample_id_key"], pars["sample_id"])) + '\n')

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