[Bioperl-l] bio-alignio-maf

dave burt (RI) dave.burt at roslin.ed.ac.uk
Thu May 29 04:10:31 EDT 2008


Dear All,

Testing a simple script

#!/bin/perl.exe

use strict;
use warnings;
use Bio::AlignIO;

my $alignment_file = "test1.maf";

printf STDERR "%s\n", $alignment_file;
	
my $alignio = Bio::AlignIO->new( -file => $alignment_file, -format =>
'maf');

while(my $aln = $alignio->next_aln()){
   my $match_line = $aln->match_line;

   print $aln, "\n";

   print $aln->length, "\n";
   print $aln->no_residues, "\n";
   print $aln->is_flush, "\n";
   print $aln->no_sequences, "\n";

   $aln->splice_by_seq_pos(1);

   print $aln->consensus_string(60), "\n";
   print $aln->get_seq_by_pos(1)->seq, "\n";
   print $aln->match_line(), "\n";

   print "\n";
 }

exit();

Note: test1.maf is attached

Problem: the while loop is never enetered - any ideas?

Dave
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