[Bioperl-l] [Bioperl-guts-l] [Bug 1544] New: Trouble dissecting problem Bio::SeqIO (fwd)

[Jason Stajich]

It is just a warning because the tag line doesn't wrap the way the parser
expects it to - it isn't a big deal.  If you don't want to see the
warnings you can set -verbose => -1 when you instantiate a
Bio::DB::GenBank.

my $db = Bio::DB::GenBank(-verbose => -1);


-jason
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Thu, 23 Oct 2003 09:24:59 -0400
From: bugzilla-daemon at portal.open-bio.org
To: bioperl-guts-l at bioperl.org
Subject: [Bioperl-guts-l] [Bug 1544] New: Trouble dissecting problem
    Bio::SeqIO

http://bugzilla.bioperl.org/show_bug.cgi?id=1544

           Summary: Trouble dissecting problem Bio::SeqIO
           Product: Bioperl
           Version: 1.2 branch
          Platform: PC
               URL: http://www.smd.qmul.ac.uk/gc/homepages/dbuchan/
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::SeqIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: d.w.a.buchan at qmul.ac.uk


I assume this is a problem with Bio::SeqIO but may be a problem with
Bio::DB::GenBank (but I doubt it). Currently I'm trying to download a file
~67,000 est from genbank, however upon trying to download and output some of the
records bioperl throws the following error (depending on the est record)

-------------------- WARNING ---------------------
MSG: trouble dissecting
"IPISGKPLPKVTLSRDGVPLKATMRFNTEITAENLTINLKESVTADAGRYEITAANSSGTTKAFINI VVLDRPGPPT
GPVVISDITEESVTLKWEPPKYDGGSQVTNYILLKRETSTAVWTEVSATVARTMMKVMKL ... ;, mRNA
sequence." into chunks of 66 chars or less - this tag won't print right
---------------------------------------------------

or

-------------------- WARNING ---------------------
MSG: trouble dissecting
"TGTTACCAATCTGAAGTGGGAGCGGCCGCATTGCTTTTTTTTTTTTTTTTTTTTTTTT T 3'];
double-stranded cDNA was ligated to Eco RI adaptors (Pharmacia),  digested with
Not I and cloned into the Not I and Eco RI sites of  the modified pT7T3 vector.
Library is normalized, and was constructed  by Bento Soares and M.Fatima
Bonaldo."" into chunks of 57 chars or less - this tag won't print right
---------------------------------------------------

In exchange it prints outputs nothing.  Unfortunately I can't give specific
accession numbers as I'm using the get_stream_by_id() method.  Although I will
gladly foward the file of accessions that I'm using and the script I'm using to
do this.

The perl version I'm using is 5.8.0, the Bio version I'm using is 1.2.3 both
running in RedHat 8.  We are experiencing the same problem when trying to
accomplish the same task on a Sun Solaris 8 machine



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