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

Frédéric Sapet frederic.sapet at gmail.com
Thu Aug 25 09:24:08 EDT 2011


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
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