[Biojava-l] reading nib sequence files

Richard HOLLAND hollandr at gis.a-star.edu.sg
Sun Jan 23 21:48:44 EST 2005


It's a compressed binary format. I doubt BioJava would be able to read
it without a lot of effort as the current parser framework is set up for
text input only.

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 
> mark.schreiber at group.novartis.com
> Sent: Monday, January 24, 2005 10:11 AM
> To: baggott2 at llnl.gov
> Cc: biojava-l-bounces at portal.open-bio.org; biojava-l at biojava.org
> Subject: Re: [Biojava-l] reading nib sequence files
> 
> 
> In short, no.
> 
> Do you have a description of the format? It may not be too 
> hard to adapt 
> an existing parser.
> 
> - Mark
> 
> 
> 
> 
> 
> Dan Baggott <dan.baggott.work at gmail.com>
> Sent by: biojava-l-bounces at portal.open-bio.org
> 01/21/2005 07:02 AM
> Please respond to baggott2
> 
>  
>         To:     biojava-l at biojava.org
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] reading nib sequence files
> 
> 
> Does anyone hava any java code for reading from .nib nucleotide
> sequence files (ie what's used by the UCSC folks)?   I know Jim Kent
> et al. have some utilities (I think in C) for reading from nib files
> but am wondering about java...
> 
> Thanks,
> 
> Dan
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