[Biojava-l] Phrap output

[mark.schreiber at novartis.com]

If your going to follow the event based parsing model (which I strongly 
reccomend you do), I would make a Format implementation (possibly extended 
if you need more methods) and fire your events at something like the 
SimpleAssemblyBuilder object (again possibly extended if you need it to do 
more).

- Mark





"Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
Sent by: biojava-l-bounces at portal.open-bio.org
06/16/2005 09:41 AM

 
        To:     "Avinash Kewalramani" <avinash at lanl.gov>
        cc:     biojava-l at biojava.org, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        RE: [Biojava-l] Phrap output


Nope, nothing exists yet for reading Phrap/ACE. If you do end up writing
your own parser, it'd be really great if you could contribute it to the
project too.

The way the BioJava file parsers work removes the need for an
XML-translation step. File parsers read file, then fire events to
listeners, eg. you could fire an event that says 'add another sequence',
or one that says 'assembly finished'. The listener uses the events to
construct the appropriate objects. When writing the file back out again
the same events are generated, and another listener receives them and
writes out the corresponding bits of file.

You'd also have to decide how to represent the assembly once it is in
memory. The interface org.biojava.seq.Assembly might be a good starting
point.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> Avinash Kewalramani
> Sent: Thursday, June 16, 2005 3:35 AM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] Phrap output
> 
> 
> Hi
> 
> I need store some information from an ace assembly file(which 
> is Phrap 
> plain text output). To do this I will have to write my own parses to 
> parse this complicated text file.
> 
> Is there any class In bioJava or anywhere else which does 
> this.The best 
> scenario would be if some code converts this file to xml output which 
> can be easily parsed
> 
> I have looked around a bit in Biojava and elsewhere and couldn't find 
> anything for this. I dont want to use Perl(BioPerl probably has this)
> 
> Thanks
> 
> -- 
> ----------------------------------------------------------------------
> Avinash Kewalramani
> Technical Lead-Genome Informatics Group
> Bioscience Division
> Los Alamos National Laboratory 
> Los Alamos, NM 87545
> 
> Phone: 505-664-0527
> Cell:  816-213-1908
> E-mail:  avinash at lanl.gov
> ----------------------------------------------------------------------
> 
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