From 2b8d59025896f915b1f5ba2eb60c4e902c181bb5 Mon Sep 17 00:00:00 2001 From: Chris Rosenthal Date: Wed, 5 Jun 2024 11:25:07 -0700 Subject: [PATCH] Fixed bug on unseekable stdin object --- taxtastic/subcommands/named.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/taxtastic/subcommands/named.py b/taxtastic/subcommands/named.py index 2925a7b..06a5471 100644 --- a/taxtastic/subcommands/named.py +++ b/taxtastic/subcommands/named.py @@ -58,11 +58,11 @@ def action(args): tax = Taxonomy(engine, schema=args.schema) if args.seq_info: seq_info = csv.DictReader(args.seq_info) + fieldnames = seq_info.fieldnames + seq_info = list(seq_info) tax_ids = (i['tax_id'] for i in seq_info) named = tax.is_valid(tax_ids, no_rank=not args.ranked) - args.seq_info.seek(0) - seq_info = csv.DictReader(args.seq_info) - out = csv.DictWriter(args.outfile, fieldnames=seq_info.fieldnames) + out = csv.DictWriter(args.outfile, fieldnames=fieldnames) out.writeheader() out.writerows(i for i in seq_info if i['tax_id'] in named) else: