[Bioperl-l] fasta35 and fasta36 parsing support in BioPerl

Chris Fields cjfields at illinois.edu
Thu Aug 25 12:34:40 EDT 2011


Frederic,

The best place to post this is to our bug server:

  http://redmine.open-bio.org

Attach all relevant data for the bug, this really helps us to diagnose the issue.

chris

On Aug 25, 2011, at 8:24 AM, Frédéric Sapet wrote:

> Hello
> I have tried to parse a fasta35 report file using BioPerl, in order to
> produce a valid HTML file.
> It seems to work well, but there's a small issue with homology string
> in the report.
> Please find in joined files, a test script.
> 
> After that, I have tried to parse a fasta36 file, but this seems to be
> not supported yet: here is the error thrown :
> 
> Uncaught exception from user code:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Unrecognized alignment line (3) '>--'
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /home/bga/bioinfo/fsapet/BioPerlLive/lib/perl5/Bio/Root/Root.pm:472
> STACK: Bio::SearchIO::fasta::next_result
> /home/bga/bioinfo/fsapet/BioPerlLive/lib/perl5/Bio/SearchIO/fasta.pm:1061
> STACK: ./test.pl:36
> -----------------------------------------------------------
> at /usr/lib/perl5/site_perl/5.10.0/Error.pm line 184
> Error::throw('Bio::Root::Exception', 'Unrecognized alignment line (3)
> \'>--\'') called at
> /home/bga/bioinfo/fsapet/BioPerlLive/lib/perl5/Bio/Root/Root.pm line
> 472
> Bio::Root::Root::throw('Bio::SearchIO::fasta=HASH', 'Unrecognized
> alignment line (3) \'>--\'') called at
> /home/bga/bioinfo/fsapet/BioPerlLive/lib/perl5/Bio/SearchIO/fasta.pm
> line 1061
> Bio::SearchIO::fasta::next_result('Bio::SearchIO::fasta=HASH') called
> at ./test.pl line 36
> 
> Thank you
> 
> Fred
> <FastaBioPerl.tar.bz2>_______________________________________________
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