[Bioperl-l] parsing result of CAP3 (ACE file)

Joshua Udall jaudall at gmail.com
Wed Sep 3 11:38:08 EDT 2008


Laurent -

I have modified modules that will do it as I recently ran into problems with
the DB_FILE module in Assembly::IO.  In addition, the current version of
cap3 seems to put a contig length where a pad length is expected (based on
the Ace format description).  The modules I have will parse the ace file
contig-by-contig rather than having the entire assembly slurped into memory
(or a tied hash) all at once.  You are welcome to them if you are interested
and I'd like to get them in Bioperl at some point.  Bascially, there are
three files - a modified Contig.pm, ContigIO.pm, and a modified ace.pm (in a
ContigIO directory).

Josh

On Wed, Sep 3, 2008 at 7:04 AM, Laurent Manchon <lmanchon at univ-montp2.fr>wrote:

> -- Hi,
>
> Is somebody have a piece of code to parse result of CAP3 assembly program
> which
> format is ACE ?
> I need to retrieve the alignment from this file.
>
> thank you,
> Laurent --
>
>
>
>
> +---------------------------------------------+
>  Laurent Manchon
>  Email: lmanchon at univ-montp2.fr
> +---------------------------------------------+
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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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