[Bioperl-l] Re (3): Status of assembly modules

[Florent Angly]

Hi Lee,

I am familiar with the assembly code. Could you file bug reports for 
these two issues on http://bugzilla.open-bio.org/ and include a files to 
reproduce the problems?

The issue in parsing the 'CO' line appears easy to fix. The issue about 
your 454 contigs may be harder. You have few contigs, but I am assuming 
that they contain many reads. When you're done putting up the bug 
reports, give me the links to them and I'll try to see what I can do 
about fixing the issues.

Florent

PS/ What version of BioPerl are you using? It would be good to make sure 
that the issues are present in the development version.



On 11/12/10 09:53, Lee Katz wrote:
> I am wondering if there is a way to optimize the BioPerl code for Assembly
> IO.  Specifically, when I convert a 2.2 MB genome (~200 contigs) from a 454
> ace file to a regular ace file, it takes a few hours to get through 30
> contigs using the code below (I estimate more than a day to get through all
> of it).
>
> Is there a way to optimize it?  To convert a sequence file to another format
> at most would take a minute and therefore converting an ace on the magnitude
> of hours or days is too much.  I wish I understood bioperl better but I
> think the best I can do is issue a challenge or a feature request:  who can
> speed up Assembly::IO::ace?
>
> # convert a Newbler ace to a standard ace
> 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");
> #output ace
>    my $numContigs=`grep -c ^CO $$args{ace454Path}`+0;
>    logmsg "Converting $$args{ace454Path} (454-ace) to $$args{acePath} (ace).
> $numContigs contigs total.";
>    while(my $contig=$ace454->next_contig){
>      logmsg "Finished with ".$contig->id ." out of $numContigs";
>      $ace->write_contig($contig);
>    }
>    return $$args{acePath};
> }
>
>
> Message: 3
>
> Date: Mon, 22 Nov 2010 15:18:10 -0500
>
> From: Lee Katz<lskatz at gatech.edu>
>
> Subject: [Bioperl-l] Re(2): Status of assembly modules
>
> To: bioperl-l at lists.open-bio.org
>
> Message-ID:
>
>         <AANLkTi=JShCLsHDxHK4eeWD3Da=vWmRkGN2rkuLwCjxn at mail.gmail.com>
>
> Content-Type: text/plain; charset=UTF-8
>
>
> 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};
>>     }
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