Skip Menu |
 

This queue is for tickets about the bioperl CPAN distribution.

Report information
The Basics
Id: 44535
Status: resolved
Priority: 0/
Queue: bioperl

People
Owner: Nobody in particular
Requestors: gresham [...] cse.msstate.edu
Cc:
AdminCc:

Bug Information
Severity: (no value)
Broken in: (no value)
Fixed in: (no value)



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>
Download (untitled) / with headers
text/plain 956b
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,
This has now been fixed in bioperl svn and will be in 1.6.1. thanks!


This service is sponsored and maintained by Best Practical Solutions and runs on Perl.org infrastructure.

Please report any issues with rt.cpan.org to rt-cpan-admin@bestpractical.com.