[Bioperl-l] bioperl-AlignIO problems parsing fasta files

[Jason Stajich]

[replying to myself]

although if you are trying to just read a sequence not an alignment  
then you want to use Bio::SeqIO.

See the copious help on the HOWTO page at bioperl website including a  
sequence and feature howto and beginner's guide.
  http://bioperl.org/wiki/HOWTOs

-jason
On May 5, 2006, at 9:21 AM, Jason Stajich wrote:

> Space after the > is causing the problem since we infer the ID as the
> everything after the '>' BEFORE the first whitespace.  Get rid of the
> space.
>    $ perl -i.backup -p -e 's/^>\s+/>/' YOURFASALNFILE
>
> On May 4, 2006, at 7:00 PM, Gloria Rendon wrote:
>
>> contents of the input file has a single sequence:
>>
>>> gi|90108701|pdb|2AHZ|B Chain B, K+ Complex Of The Nak Channel
>> MLSFLLTLKRMLRACLRAWKDKEFQVLFVLTILTLISGTIFYSTVEGLRPIDALYFSVVTLTTVGDGNF 
>> S
>> PQTDFGKIFTILYIFIGIGLVFGFIHKLAVNVQLPSILSN
>> ------------------------------------------
>> this is the script that tries to parse it:
>>
>> use Bio::AlignIO;
>> my $inseq = Bio::AlignIO->new(-format => 'fasta',
>>                            -file   => 'test.fasta');
>> while( my $aln = $inseq->next_aln ) {
>>      print "name: ", $aln->displayname;
>>      print "length: ", $aln->length;
>>      print "\n";
>> }
>>
>> ------------------------------------------
>> and this is the result of running that script on winxp
>>
>> D:\msa\NAK MUTANTS>perl parseFasta.pl
>>
>>
>> ------------- EXCEPTION  -------------
>> MSG: No sequence with name []
>> STACK Bio::SimpleAlign::displayname
>> C:/Perl/site/lib/Bio/SimpleAlign.pm:2047
>> STACK toplevel parseFasta.pl:11
>>
>> --------------------------------------
>> D:\msa\NAK MUTANTS>
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12/
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/