[Bioperl-l] Re(2): Status of assembly modules

[Lee Katz]

I figured it out (I haven't tested much though).

To whoever works on Assembly::IO::ace.pm:
I changed a regular expression on line 231 because the contig object was not
initializing properly.  For some reason the 454 ace file had adopted the
reference assembly's ID and therefore there was a GI number followed by a
pipe.  The pipe was not captured with \w+.  I think that the regex will be
safe with \s(\S+)\s.

 if (/^CO\s(\S+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!
#if (/^CO\s(\w+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!

On Thu, Nov 18, 2010 at 12:04 PM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 3
> Date: Wed, 17 Nov 2010 22:20:03 -0500
> From: Lee Katz <lskatz at gatech.edu>
> Subject: Re: [Bioperl-l] Status of assembly modules
> To: bioperl-l at lists.open-bio.org
> Message-ID:
>        <AANLkTi=aFAnYrEXj3D4joZeYwxRT971M_ZYR0uFJOrxc at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I have read on the BioPerl site that a 454 ace is not standardized due to
> its coordinate system.  How can I convert it to the standard ace file?
>
> When I run this code either by using contig or assembly objects, I get an
> error.
> Can't call method "get_consensus_sequence" on an undefined value at
> Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.
>
>    sub _newblerAceToAce($args){
>      my($self,$args)=@_;
>      my
>
> $ace454=Bio::Assembly::IO->new(-file=>$args{ace454Path},-format=>"ace",-variant=>'454');
>      my
> $ace=Bio::Assembly::IO->new(-file=>">$args{acePath}",-format=>"ace");
>      #while(my $contig=$ace454->next_contig){
>      while(my $scaffold=$ace454->next_assembly){
>        print Dumper $scaffold;
>      }
>      return $args{acePath};
>    }
>



-- 
Lee Katz
http://leeskatz.com