Beefy Boxes and Bandwidth Generously Provided by pair Networks
more useful options
 
PerlMonks  

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?


Comment on Re: Bioinformatics: Slow Parsing of a Fasta File
Select or Download Code
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!

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://851593]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others having an uproarious good time at the Monastery: (19)
As of 2015-07-02 17:08 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    The top three priorities of my open tasks are (in descending order of likelihood to be worked on) ...









    Results (44 votes), past polls