[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...
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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