[Bioperl-l] Help with error handling (unable to load sequence in Bio::SeqIO)

[Hilmar Lapp]

"Tomso.Daniel" wrote:
> 
> Greetings.
> 
> This is my first post to the list!
> 
> I've got a perl program that is retrieving and processing a list of
> GenBank sequences.  It is retrieving by accession.
> 
> The problem is that some of the sequences seem to have errors that
> Bio::Seq doesn't like.  The basic process is this:
> 
> retrieve seq
> store as local file
> 
> and later . . .
> 
> open file
> read a seq with next_seq()
> 
> I presume the crash occurs at this point, as the file seems to
> retrieve properly.  Furthermore, the overall code is good, since the
> error is only associated with a few sequences (most process fine).
> 
> The error message that is generated is this:
> 
> ------------------- WARNING ---------------------
> MSG: unable to parse location successfully out of
> complement(join(complement(204
> 79..20643), ignoring feature (seqid=AL136324)
> ---------------------------------------------------
> Can't call method "location" on an undefined value at
> /usr/lib/perl5/site_perl/5
> .6.0/Bio/SeqIO/FTHelper.pm line 136, <GEN55> line 161.
> 

That's a known bug that's already been fixed. I assume you're running
Bioperl 0.7, not the development trunk.

It points again to the urgent need for a point release ... The only
problem is that at present I don't even have time to answer all emails
I should answer ... Well, I'll try to get a release out of the door
next week. If you don't want to wait, you can download from the
anonymous CVS server. Specify -r branch-07 to cvs checkout in order to
get the latest stable branch, but you can also try the main trunk (the
bug you encountered should be fixed in both).

	Hilmar
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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