| Subject: | BioPerl and GBrowse |
| Date: | Tue, 24 Mar 2009 15:58:05 -0500 |
| To: | <bug-bioperl [...] rt.cpan.org> |
| From: | "Cathy Gresham" <gresham [...] cse.msstate.edu> |
BioPerl version 1.6.0
Gbrowse version 1.69
Perl version 5.8.8
Suse Linux version 10 sp2
When calling BioPerl from Gbrowse noticed errors on some certain tags.
Tracked it down to tags with a strand value of '.'
Looked in
/usr/lib/perl/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
It was not recognizing a strand value of .
It only recognized values of +, -, null, 1, or -1 or 0
I added the strand eq '.' after the '' line so that the procedure would no longer throw an error.
my @args = (-name => $name,
-strand => $strand eq '+' ? 1
:$strand eq '-' ? -1
:$strand eq '' ? 0
:$strand eq '.' ? 0
:$strand == 1 ? 1
:$strand == -1 ? -1
:0,
-attributes => $attributes,