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

[Chris Fields]

Could you archive the files and attach them to a bug report (you can  
mark it as an enhancement request).  We can take a look.

http://bugzilla.open-bio.org/

chris

On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote:

> Chris et al. -
>
> A student and I have written code to do this - write ace files as  
> well as
> parse them one entry at a time.  In trying to use the Assembly::IO  
> as it was
> in 1.5, we ran into problems with large ace files containing many  
> entries
> because of file handle limit issues with the inherited implementation
> DB_File.  Our implementation simply reads one contig at a time  
> instead of
> first trying to slurp the whole ace into memory.  I'm happy to add  
> it to
> Bioperl, but I am not sure how to do it.  If I sent *.pm files to  
> someone,
> could they help me get it into bioperl?  It may not be perfect  
> either, but
> it should be a good start.
>
> Josh
>
> On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields <cjfields at illinois.edu>  
> wrote:
>
>> 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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>
>
>
> -- 
> Joshua Udall
> Assistant Professor
> 295 WIDB
> Plant and Wildlife Science Dept.
> Brigham Young University
> Provo, UT 84602
> 801-422-9307
> Fax: 801-422-0008
> USA
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