[Bioperl-l] bio-alignio-maf

Brian Osborne bosborne11 at verizon.net
Thu May 29 11:11:55 EDT 2008


Dave,

Try your script on some *maf files in the Bioperl package instead of  
test1.maf:

bioperl-live/t/data/bug2453.maf
bioperl-live/t/data/humor.maf

What is the result?


Brian O.



On May 29, 2008, at 4:10 AM, dave burt (RI) wrote:

> 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
> <test1.maf>_______________________________________________
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