Bioperl-guts: Proposed simple fix for Bugs #132, #133, #204

Jason Stajich
Tue, 11 Apr 2000 12:21:36 -0400 (EDT)

The following are proposed fixes to small Bugs in bioperl.  They will be
applied to the 06-branch and the main trunk.  I will wait 1 day to see if
anyone has any problems with these fixes. 
Bug #132 - reads as follows :
Module: SeqIO::GCG
Version: 1.3
OS: Irix 6.4
Submission from: (
The module's out_fasta method generates a fasta line which looks

>$self->{id} $self->{desc}

But the SeqIO::GCG stores strings with newlines in the description field,
the fasta output invalid.

This is a problem when a seq is printed in the fasta module so
will just strip out newlines from the desc field before printing in the
SeqIO::fasta module's write_seq function
Bug #133 - reads as follows:
Module:  Bio::DB::GenBank
Version: 0.05.1
Submission from: (

Tried to retrieve GenPept ID ( CAB11162.1)
mistakingly using module and 
the following fatal error occurred:

Can't call method "seq" on an undefined value
at /usr/lib/perl5/site_perl/5.005/Bio/SeqIO/Fasta.
pm line 191.

Comments: "Should we throw an exception when we can't find a sequence.
           Perhaps nicer than a null..."

This fixes the second part of Bug 204 as well.

in get_Seq_by_id
Throw an exception if $stream->next_seq() returns undef instead of
returning the undef.

Do this for both GenBank and GenPept.


Jason Stajich
Center for Human Genetics
Duke University Medical Center

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