[Bioperl-l] problem with swissprot parsin

[Siddhartha Basu]

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