Re: Bioinformatics: Slow Parsing of a Fasta File

in reply to Bioinformatics: Slow Parsing of a Fasta File

I've never used any BioPerl modules myself (so I cannot say anything about their performance in general), but half an hour for reading ~200MB sounds extremely long indeed. That makes me wonder if the file is maybe not stored locally, i.e. you're doing I/O with some remote share...

Could you check if running something functionally similar, but without Bio::SeqIO — in its most simple case

while (<>) {
    print if /^>/;
}
[download]

(or perl -ne "print if /^>/" Test.fasta as a one-liner) takes similarly long?

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