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Re: fasta file

by pvaldes (Chaplain)
on Sep 27, 2011 at 08:59 UTC ( #928050=note: print w/replies, xml ) Need Help??

in reply to fasta file

You could also wrote this

if(/^>/) {

instead this:

if($_ =~ />/) {

That's a little more precise for your case probably

personally I prefer this more compact form also, but this is a matter of style only

if(/^>/) {$seq = $_} else {$accession{$seq} .= $_}
if you want in any case to write the same like this, I suggest that you consider indent your code
if($_ =~ />/) { $seq = $_; } else { $accession{$seq} .= $_; }

AND last but not least, don't try to reinvent the wheel, I strongly suggest you to take a look to the bioperl modules, specially the modules related with managing fasta files

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[stevieb]: do you have input coming in that you're parsing? if so, update the question. Also add an example of *exactly* what your desired output should look like given an example input
[stevieb]: valgrind doesn't catch a deep internal segfault issue :( sigh

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