[Bioperl-l] problem parsing SwissProt Records

[Anand Venkatraman]

Hi Suddartha,

I think this problem occurs because of:

[a] In your SwissProt Record, if you look around line 
(say 10-20 lines before) 18676877, you would find that
there should be a line that should have started with
RA, but in some records, it starts with RG. And this
is because of the SwissProt or UniProt file format, if
RG comes then RA doesn't and vice-versa.

A note on the abbreviations
RA : Reference authors
RG: Reference group

And as regards the complaints, when there is no RA
annotation, then the script doen't find something that
gets stored in the "$au" variable of the "swiss.pm"
module.

Hope it helps.

Anand


-----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
_______________________________________________
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l


		
_______________________________
Do you Yahoo!?
Declare Yourself - Register online to vote today!
http://vote.yahoo.com