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

[Tomso.Daniel]

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.   

At this point the program terminates.

What I would like to do is either fix the problem or ignore the
problem.  I've got to find a way to get the program to keep running!

Any help would be greatly appreciated!  I'm trying to get something
together for a one-on-one with the boss tomorrow, so a quick fix (i.e.
a way to ignore the exception) would be great for now.

If possible, please cc a copy of the response directly to this address
(tomso@niehs.nih.gov), since I've just subscribed and I may not get
things sorted out with the list right away.

Thanks again,

DT

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Daniel J. Tomso
Laboratory of Computational Biology and Risk Analysis
National Institute of Environmental Health Sciences

(919) 541-2872                           tomso@niehs.nih.gov
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