[Bioperl-l] Bio::Index::Fasta return object problem

[Brian Osborne]

David,

Your loop doesn't look right to me. Try something like:

my @ids = qw( AC1111 B45455 );

foreach my $id (@ids) {
  my $seq = $inx->fetch($id); # Returns Bio::Seq object
  $out->write_seq($seq);#requires a valid Bio::PrimarySeqI object
}

Is your code derived from some example code?

Brian O.


-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of david vilanova
Sent: Monday, April 28, 2003 9:47 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Bio::Index::Fasta return object problem

Dear all,
I have some problems when I try to retreive sequences from an indexed file.
The Index::Fasta  seems to return a Bio::Seq object however the method
write_seq requires a valid Bio::PrimarySeqI object. How can I can go through
this problem.

Thanks
------------- EXCEPTION  -------------
MSG: Did not provide a valid Bio::PrimarySeqI object
STACK Bio::SeqIO::fasta::write_seq
/usr/local/psu/bioperl-live/Bio/SeqIO/fasta.pm:175
STACK toplevel fasta.pl:21


use Bio::Index::Fasta;
use strict;

my ($Index_File_Name,$Fasta_File) = @ARGV;
my $inx = Bio::Index::Fasta->new(
'-filename' => $Index_File_Name,
'-write_flag' => 1);
$inx->make_index($Fasta_File);

# Print out several sequences present in the index
# in Fasta format

my $out = Bio::SeqIO->new('-format' => 'Fasta','-fh' => \*STDOUT);

foreach my $id ($Index_File_Name) {
my $seq = $inx->fetch($id); # Returns Bio::Seq object
$out->write_seq($seq);#requires a valid Bio::PrimarySeqI object
}


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