[Bioperl-l] parsing ACE file

Phillip San Miguel pmiguel at purdue.edu
Thu Jan 24 14:06:35 EST 2008


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.

-- 
Phillip


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