gmane.comp.lang.perl.bio.general

parsing result of CAP3 (ACE file)

-- 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
+---------------------------------------------+

headers

Joshua Udall | 3 Sep 17:38

Re: parsing result of CAP3 (ACE file)

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 --
>
>
>
>
> +---------------------------------------------+

(Continue reading)

headers

Jean-Marc FRIGERIO | 9 Sep 10:42

Re: parsing result of CAP3 (ACE file)

> > -- 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
> > +---------------------------------------------+
>
> 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).
>

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