[Bioperl-l] Need help in needle parser

[Khoiwal Tara]

Hi,
  I want to parse the output of needle.I tried but didn't able to get expected output.
   
  My code is as follows:
   
  #!/usr/local/bin/perl
   
  use strict;
use warnings;
use Bio::AlignIO;
  my $needleReport = $ARGV[0];
  
my $in = new Bio::AlignIO(-format => 'emboss',-file =>$needleReport);
   
  while(my $align = $in->next_aln()){
    print "Alignment Length:".$align->length()."\n";
  print "Percentage Identity:".$align->percentage_identity()."\n";
  print "Consensus string:".$align->consensus_string()."\n";
  print "Number of sequences:".$align->no_sequence()."\n";
  print "Number of residues:".$align->no_residues()."\n";
}

But it doesn't go inside the while loop.
  Pls help me.
  How to find the alignment position for the query sequence on the target sequence from the needle output?
  Where can i find the good documentation on needle parser and its usage?
  Good document on bioperl for beginners.
   
  Regards,
  Tara Khoiwal.

 			
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