Bioperl-guts: Proposed simple fix for Bugs #132, #133, #204
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 :
OS: Irix 6.4
Submission from: smtp.genelogic.com (188.8.131.52)
The Seq.pm module's out_fasta method generates a fasta line which looks
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:
Submission from: bush215.cshl.org (184.108.40.206)
Tried to retrieve GenPept ID ( CAB11162.1)
mistakingly using GenBank.pm module and
the following fatal error occurred:
Can't call method "seq" on an undefined value
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.
Throw an exception if $stream->next_seq() returns undef instead of
returning the undef.
Do this for both GenBank and GenPept.
Center for Human Genetics
Duke University Medical Center
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