[Bioperl-l] phrap ace format parser?

[Peter Kos]

Brian,

If you think that your coding style is understandable for a third 
party user, then I would be interested in your code if you don't mind 
sending me off-list. I am just writing a RemoveContigs.pl and later 
perhaps some other stuff which allows me modifying the database 
without reassembly.
Not Bioperl compliant either; I am sorry for that.
I am not sure if I could use (bits of ?) your code  but it may be 
worthy to take a look and perhaps give it a try.

Regards
Peter

On Saturday, July 27, 2002 1:00 AM, Brian Desany 
[SMTP:bdesany@bcm.tmc.edu] wrote:
>
> >Does any know whether there is bioperl module to parse from or
> >to  phrap
> >ace output file? BTW, does anyone know the documentation of
> >this ace format?
>
> Documentation can be found at http://www.phrap.org, it's part of 
the
> consed
> documentation.
>
> I have cobbled together a module that parses Ace files, but it's
> not
> "bioperl-compliant" yet, in that coding style isn't up to snuff and
> there's
> site-specific code in it.
>
> I can send it to you off-list if you like, or you can wait until I
> get
> around to bioperl-ifying it (I don't have a timeframe for that).
>
> -Brian.
> --------------------------------------------
> Brian A. Desany, Ph.D.
> Dictyostelium Genome Sequencing Project
> Baylor College of Medicine
> bdesany@bcm.tmc.edu
> (713)798-5639
> http://www.dictygenome.org
> --------------------------------------------

..................................................................  
..........
Peter B. Kos, Ph.D.
Molecular Microbiology and Genetics Lab.
Research Institute of Innovative Technology for the Earth (RITE)
9-2 Kizugawadai, Kizu-cho, Soraku-gun,
Kyoto 619-0292 JAPAN
Phone: +81-774-75-2308
Fax: +81-774-75-2321
E-mail: kos@rite.or.jp