[Biojava-l] Phrap output

[mark.schreiber at novartis.com]

Hi -

The classes in org.biojava.bio.program.phred might do what you need 
although they are more for reading phd files. They may give you a starting 
point though.

- Mark





Avinash Kewalramani <avinash at lanl.gov>
Sent by: biojava-l-bounces at portal.open-bio.org
06/16/2005 03:34 AM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        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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