[Biojava-l] reading nib sequence files

[Richard HOLLAND]

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   
 
---------------------------------------------
This email is confidential and may be privileged. If you are not the
intended recipient, please delete it and notify us immediately. Please
do not copy or use it for any purpose, or disclose its content to any
other person. Thank you.
---------------------------------------------


> -----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
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>