[Bioperl-guts-l] [Bug 3022] New: Regexp forget while parsing withrefm references

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Mar 5 05:54:43 EST 2010


http://bugzilla.open-bio.org/show_bug.cgi?id=3022

           Summary: Regexp forget while parsing withrefm references
           Product: BioPerl
           Version: 1.6 branch
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Keywords: Bioperl
          Severity: minor
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: tuco at pasteur.fr


Hi,

I discovered that 'references' from withrefm enzyme format is not well parsed.
Actually it is, but it remains the local line separator as the last references
into the array of references as shown below :

'_references' => [
                                                                               
 [
                                                                               
   'Seurinck, J., van Montagu, M., Unpublished observations.',
                                                                               
   '<1>'
                                                                               
 ]
                                                                              
],

Here is the diff from Bio::Restriction::IO::withrefm fixing the problem:

diff Bio/Restriction/IO/withrefm.pm `perldoc -l Bio::Restriction::IO::withrefm`
174c174
<         my ($refs) = $entry =~ /<8>(.+)<1>/s;
---
>         my ($refs) = $entry =~ /<8>(.+)/s;

Can someone fix it?

Thanks
Regards

Emmanuel


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