[Bioperl-l] a query on Obtaining UniProt sequences

Anand Venkatraman bioperlanand at yahoo.com
Thu May 3 20:09:18 UTC 2007


I am using Bioperl 1.4 and I am trying to obtain protein sequences for specific Uniprot records.

For some records (ROA1_HUMAN), it prints the correct sequence, but  it first prints the warning "Use of uninitialized value in substitution (s///) at /usr/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line 855, <STREAM> line 43." 

For other records (BOLA_HAEIN), it prints the correct sequence (without any warnings).

Here is the code:
#!/usr/bin/perl -w
use strict;
use Bio::Perl;
use Bio::DB::SwissProt;

my $sp = new Bio::DB::SwissProt;

#my $seq_object  = $sp->get_Seq_by_id('ROA1_HUMAN');
my $seq_object  = $sp->get_Seq_by_id('BOLA_HAEIN');

my $sequence_as_a_string = $seq_object->seq();
print "$sequence_as_a_string\n";

 Is there something I need to fix.

Thanks in advance for the help.

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