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Running SWORD on gzipped fasta

Open alcooj opened this issue 6 years ago • 2 comments

Good morning, Robert.

I was wondering if there is a way to run SWORD on input fasta database target files that are compressed (*.fa.gz). I've tried process substitution to read the fa.gz database file using zcat, and it returns "No alignments found." Otherwise, running SWORD on the decompressed database file works. Is there a way to avoid the need to decompress *.fa.gz target files?

Thanks.

alcooj avatar Jun 12 '18 12:06 alcooj

Hello, SWORD parses the database several times so it can't read streams. I would have to refactor the code to enable compressed files but haven't got the time at the moment. Is it crucial for you to use compressed files?

Best regards, Robert

rvaser avatar Jun 12 '18 13:06 rvaser

Not really. It's more of a space-saving issue as some of the reference database files I work with are large. For now, I'll then just have to work with the decompressed databases.

I appreciate the quick reply and thanks again!

alcooj avatar Jun 12 '18 14:06 alcooj