[Bioperl-l] bpindex/bpfetch work for me:

[Brian Osborne]

Ewan,

Perhaps it's an error specific for format = genbank?

~/programming/perl/Index>perl ~/bioperl-live/scripts/index/bpindex.PLS -dir
/home/bosborne/programming/perl/Index/ -fmt genbank testidx BAB68554.gb

~/programming/perl/Index>ls
total 34
   2 BAB68554.gb*     3 gbindex            1 mkGenbankIndex*     3 testidx
   3 faidx            1 mkFastaIndex*     14 test.fa*
   3 gbidx            1 mkFastaIndex~*     3 test.fa.idx

~/programming/perl/Index>perl ~/bioperl-live/scripts/index/bpfetch.PLS -dir
/home/bosborne/programming/perl/Index/ testidx:BAB68554
Database testidx in testidx:BAB68554 is not loadable. Skipping

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


Brian O.


-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Ewan Birney
Sent: Tuesday, February 25, 2003 9:49 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] bpindex/bpfetch work for me:


Brian -

bpindex and bpfetch work for me (branch-1-2)


[birney at riker scripts]$ perl -I ../ index/bpindex.pl test
~/src/wise2/test_data/pep.fa
[birney at riker scripts]$ perl -I ../ index/bpfetch.pl test:ROA1_HUMAN
>ROA1_HUMAN
SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT
YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL
RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL
SKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSG
DGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGG
SGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSS
SSSSYGSGRRF





What error are you getting?




-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney at ebi.ac.uk>.
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