[Bioperl-l] Bio::Index::Fasta foreach loop

[Ann Hedley]

Hi

I've used Bio::Index::Fasta to make the index $inxdc from a fasta file. 
 I now want a  loop to to examine each sequence in turn.

This script prints the correct sequence...

  my $seqdc = $inxdc->fetch("CEC00023");
  print $seqdc->seq;

... so the index file is OK, but how do I put that in a loop for each 
sequence $id?

Any ideas much appreciated

Many Thanks
Ann


#!/usr/bin/perl -w

use strict;
use Bio::Index::Fasta; # using fasta file format

##########get decoder seqs into $idxdc 
#########################################

  my $Index_File_name = shift;
  my $filedc = "/home/user1/alldc5.fsa";
  my $inxdc = Bio::Index::Fasta->new( -filename   => $filedc . ".idx",
                                    -write_flag => 1 );
  # pass a reference to the critical function to the Bio::Index object
  $inxdc->id_parser(\&get_id);
  # make the index
  $inxdc->make_index($filedc);

###########print sequence and length for all 
seqs###############################

foreach $inxdc($id)        #????????????
{
  my $seqdc = $inxdc->fetch("$id");
  print $seqdc->seq;
  print " length is ",$seqdc->length(), ", decoder\n";
}


#########################################################################

# here is where the retrieval key is specified
  sub get_id
  {
     my $header = shift;
     $header =~ /^>(CEC\d{5})/;
     $1;
  }