[Bioperl-l] Default output format for Bio::SeqIO?

Phillip San Miguel pmiguel at purdue.edu
Mon Jan 3 16:48:48 UTC 2011


The following:

perl -e 'use Bio::SeqIO; $out = new Bio::SeqIO()'

results in:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unknown format given or could not determine it []
STACK: Error::throw
STACK: Bio::Root::Root::throw 
/usr/local/lib/perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::SeqIO::new /usr/local/lib/perl/5.10.0/Bio/SeqIO.pm:383
STACK: -e:1
-----------------------------------------------------------

suggesting there is no default SeqIO format. Is that correct? If so, 
should the useful example script, bp_extract_feature_seq.pl, be updated 
so it will not error out from relying on a default format assumption?

-- 
Phillip




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