[Bioperl-l] bio-alignio-maf

Chris Fields cjfields at uiuc.edu
Thu May 29 14:48:28 EDT 2008


If this is MAF output from biomart we should probably try to support  
it directly.  I'll try to take a look at it.

chris

On May 29, 2008, at 11:46 AM, dave burt (RI) wrote:

> 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>_______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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