[Bioperl-l] bio-alignio-maf

dave burt (RI) dave.burt at roslin.ed.ac.uk
Thu May 29 12:46:10 EDT 2008


Brain
 
- good idea ! worked fine
 
- the problem was traced to the header line
 
- should be 
 
##maf version=1 scoring=zero
 
- and not the following, which is included in the biomart downloaded file
 
##maf version=1
#Tue Apr 29 16:49:45 2008
#The start coordinate is a zero-based number.
#For segments in the negative strand, the start
#is relative to the end of the chromosome. Please, refer to
#http://genome.ucsc.edu/FAQ/FAQformat#format5 for a
#description of this file format.
 
simple solution - usually is 99% of time
 
many thanks for the clues
 
Dave
 
 

________________________________

From: Brian Osborne [mailto:bosborne11 at verizon.net]
Sent: Thu 29/05/2008 16:11
To: dave burt (RI)
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] bio-alignio-maf



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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