[Bioperl-l] problem with swissprot parsin

[Brian Osborne]

Siddhartha,

Bio::DB::Flat::BinarySearch or Bio::DB::Flat::BDB? Also, please show your
code when you ask a question, it simplifies matters. For example, it would
tell me which module you used, which file format, and so on. It also helps
to attach the actual sequence files, or some smaller test file that shows
the same error. What happens occasionally is that a question will get
ignored for the simple reason that no one knows how to answer, there's not
enough information given in the letter.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Siddhartha Basu
Sent: Thursday, October 14, 2004 2:51 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] problem with swissprot parsin

Hi,
I have already described this problem in this mailing list but haven't
got anybodies attention yet. I had also asked the author of this module
but nothing back yet. Anyway i really could'nt figure out how to solve
this and so i am writing again. I have also tried by replacing the
swiss.pm module from the bioperl-live version. But the problem persists.
I understand that this is a maintained module and i am not getting
ignored because of maintenance issue.

I am trying to make a flat file index of swissprot/trembl files using
Bio::DB::Flat module. However, i am getting the following consistent
warnings during the indexing process.
======================================================================
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18676877.
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18676916.
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18676956.
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18677002.
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18677045.
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18677091.
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18677136.
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18677178.
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18677209.
Use of uninitialized value in substitution (s///) at
/usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <GEN1> line
18677249.
========================================================================
Though, the indexing get completed, i could'nt fetch any data from there
  as it does not return any seq obj.
I also get the same warnings when i try to read the swissprot file using
the Bio::SeqIO module.
I am using bioperl-1.4 and understand it has something to do with the
swissprot parser in Seq::IO module.
So, does any fix or solution available for this problem.

Thanks in  advance.

-siddhartha
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