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

[david vilanova]

Hi brian,
doesn't work for me. Still give the same problem exception. I picked up the
code from the Bio::Index::Fasta module documentation which comes with the
last bioperl release and costumised a little bit.


> 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
> }
>
>
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