[Bioperl-l] parsing ACE file

Florent Angly florent.angly at gmail.com
Thu Jan 24 17:06:29 EST 2008


That would be the module Bio::Assembly::IO::ace
It works fine as far as I know.
To parse an assembly, use Bio::Assembly::IO: 
http://doc.bioperl.org/bioperl-live/Bio/Assembly/IO.html
Regards,
Florent

Phillip San Miguel wrote:
> Stefano Ghignone wrote:
>> Dear All,
>>     dealing with an assembly .ace file and a list of contigs (from 
>> that assembly), how can I extract from the .ace file the read names 
>> forming each listed contig? Is there any module doing this job?
>>
>> Any suggestion about how to start is welcome...
>> Cheers
>>
>> Stefano
>>
>>   
> perl -ne 'next unless (/^(?:CO)|(?:RD)/);print' acefile.ace
>
> will give you a list of each the contigs followed by the reads in each 
> contig, if "acefile.ace" is a phrap ace file.
>
> There is a bioperl module for handling phrap ace file, but I'm not 
> sure what its current status is. Last time I looked (probably a couple 
> of years ago) it seemed to have been abandoned half-finished.
>



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