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Re: Bioinformatics: Slow Parsing of a Fasta File

by almut (Canon)
on Jul 27, 2010 at 19:25 UTC ( #851593=note: print w/replies, xml ) Need Help??

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 /^>/; }

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

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Re^2: Bioinformatics: Slow Parsing of a Fasta File
by Anonymous Monk on Jul 28, 2010 at 06:38 UTC
    The code perl -ne "print if /^>/" test.fasta works just quite quickly.

    I am reading this file from the same folder that the program is in... While not wanting to resort to a regex to extract the sequences and their header information I believe this is going to be my only way through!

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