[Bioperl-l] Problem with load_seqdatabase

albert vilella vilella at bio.ub.es
Wed Jun 4 15:53:58 EDT 2003


I've been trying to load a swissprot dataset into a biosql database
using load_seqdatabase.pl, but I get an error:

./load_seqdatabase.pl -host localhost -dbname biosql -dbuser root
-dbpass '*******' -namespace bioperl -format swiss

------------- EXCEPTION  -------------
MSG: swissprot stream with no ID. Not swissprot in my book
STACK Bio::SeqIO::swiss::next_seq
STACK toplevel ./load_seqdatabase.pl:386

Apparently, the next_seq subrutine gets stucked in the first entry while
parsing the ID field:


$line =~ /^ID\s+([^\s_]+)(_([^\s_]+))?\s+([^\s;]+);\s+([^\s;]+);/ ||
$self->throw("swissprot stream with no ID. Not swissprot in my book");


This is strange because I can read the same entry in the same file with:

#! /usr/bin/perl -w

use strict;
use Bio::SeqIO;
use Bio::Seq;

my $file = shift @ARGV;
my $in = Bio::SeqIO->new ( -file => $file,
			   -format => 'swiss');
my $seq = $in->next_seq();
print "Seq: ", $seq->accession_number(), " -- ", $seq->desc(), "\n\n";

Anybody experiencing similar problems? Any guess of what is happening?

Thanks in advance,

Albert Vilella
Molecular Evolution - Dept. Genetics
Universitat de Barcelona
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