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

[Abhishek Pratap]

Ok .. Sure in case we do write something which eventually I will have to :)
I will fwd it.

@Russel:

I feel to get info for specific the current method is very slow as it tries
to store the info for all contigs into memory. Such info could be memory
intensive specially with the next gen data coming from 454 sequencers. I
think we should grep to the contig/s of itnerest and then create a record
for it. Please correct me if I am wrong.

Thanks,
-Abhi

On Tue, Jan 6, 2009 at 3:52 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
>>>>
>>> =======================================================================
>>> Attention: The information contained in this message and/or attachments
>>> from AgResearch Limited is intended only for the persons or entities
>>> to which it is addressed and may contain confidential and/or privileged
>>> material. Any review, retransmission, dissemination or other use of, or
>>> taking of any action in reliance upon, this information by persons or
>>> entities other than the intended recipients is prohibited by AgResearch
>>> Limited. If you have received this message in error, please notify the
>>> sender immediately.
>>> =======================================================================
>>>
>>>
>>
>>
>> --
>> -----------------------------
>> 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
>>
>
>


-- 
-----------------------------
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