[Bioperl-guts-l] [Bug 1383] New: scripts/index/bpfetch.pl doesn't work

bugzilla-daemon at cvs.open-bio.org bugzilla-daemon at cvs.open-bio.org
Fri Feb 14 11:59:48 EST 2003


http://bugzilla.bioperl.org/show_bug.cgi?id=1383

           Summary: scripts/index/bpfetch.pl doesn't work
           Product: Bioperl
           Version: main-trunk
          Platform: PC
        OS/Version: Windows 2000
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Documentation
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: brian_osborne at cognia.com


I can create an index, in this called "gbindex", of a Genbank file using 
scripts/index/bpindex.pl. This index works with a one-liner like: perl -e 'use 
Bio::Index::GenBank; $idx = Bio::Index::GenBank->new(-filename=>"gbindex"); 
$seq = $idx->fetch("BAB68554"); print $seq->seq;'
MLTEDDKQLIQHVWEKVLEHQEDFGAEALERMFIVYPSTKTYFPHFDLHHDSEQIRHHGKKVVGALGDAVKHIDNLSATL
SELSNLHAYNLRVDPVNFKLLSHCFQVVLGAHLGREYTPQVQVAYDKFLAAVSAVLAEKYR.

However, a command like:
~/bioperl-live/scripts/index/bpfetch.pl -dir . gbindex:BAB68554

Gives:

Database gbindex in gbindex:BAB68554 is not loadable. Skipping

Error Can't locate object method "_type_and_version" via package "Bio::Index::Ge
nBank" at /usr/lib/perl5/site_perl/5.8.0/Bio/Index/Abstract.pm line 406.

Brian O.



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