cjfields
commented
8 years ago Original Redmine Comment Author Name: Frederic Sapet Original Date: 2011-08-25T13:21:09Z
my BioPerl version :
perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,“\n”’ 1.0069
perl -MBio::SeqIO -e ‘printf “%vd\n”, $Bio::SeqIO::VERSION’ 49.46.48.48.54.57
Author Name: Frederic Sapet (Frederic Sapet) Original Redmine Issue: 3281, https://redmine.open-bio.org/issues/3281 Original Date: 2011-08-25 Original Assignee: Bioperl Guts
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(0x11df2c8)’, ‘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(0x11df2c8)’) called at ./test.pl line 36
Thank you
Fred