[Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl

[Chris Fields]

Not at this time (write_assembly is not implemented).  If you come up  
with code to do so let us know (patches are always welcome).

chris

On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote:

> Thanks that helped.
>
> Any method to write Ace files ?
>
> Thanks,
> -Abhi
>
> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell <
> Russell.Smithies at agresearch.co.nz> wrote:
>
>> Here's how I've been doing it:
>>
>>
>> my $infile = "454Contigs.ace";
>> my $parser = new Bio::Assembly::IO(-file   => $infile ,-format =>  
>> "ace") or
>> die $!;
>> my $assembly = $parser->next_assembly;
>>
>> # to work with a named contig
>> my @wanted_id = ("Contig100");
>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!;
>>
>> #get the consensus
>> my $consensus = $contig->get_consensus_sequence();
>>
>> #get the consensus qualities
>> my @quality_values  = @{$contig->get_consensus_quality()->qual()};
>>
>> hope this helps,
>>
>> Russell
>>
>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap
>>> Sent: Tuesday, 6 January 2009 6:43 p.m.
>>> To: bioperl-l at lists.open-bio.org
>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl
>>>
>>> Hi All
>>>
>>> I am looking for some code to parse the ACE file format. I have  
>>> big ACE
>>> files which I would like to trim based on the user defined Contig  
>>> name
>>> and
>>> specific region and write out the output to another fresh ACE file.
>>>
>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of  
>>> slow.
>>> Any
>>> other alternative or suggestions.
>>>
>>> Thanks All,
>>> -Abhi
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> -----------------------------
>>> Abhishek Pratap
>>> Bioinformatics Software Engineer
>>> Institute for Genome Sciences
>>> School of Medicine, Univ of Maryland
>>> 801, W. Baltimore Street, Baltimore, MD 21209
>>> Ph: (+1)-410-706-2296
>>> www.igs.umaryland.edu/
>>>
>>> Chair
>>> RSG-Worldwide
>>> ISCB-Student Council
>>> http://iscbsc.org/rsg
>>>
>>> www.bioinfosolutions.com
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> = 
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>
>
>
> -- 
> -----------------------------
> Abhishek Pratap
> Bioinformatics Software Engineer
> Institute for Genome Sciences
> School of Medicine, Univ of Maryland
> 801, W. Baltimore Street, Baltimore, MD 21209
> Ph: (+1)-410-706-2296
> www.igs.umaryland.edu/
>
> Chair
> RSG-Worldwide
> ISCB-Student Council
> http://iscbsc.org/rsg
>
> www.bioinfosolutions.com
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