[Biojava-l] Another GFF utility

Schreiber, Mark mark.schreiber@agresearch.co.nz
Wed, 16 Oct 2002 09:00:26 +1300

Haven't had a chance to test them yet but I use GFF <em>a lot</em> so
I'm sure to find them useful.

- Mark

> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
> Sent: Tuesday, 15 October 2002 10:39 p.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Another GFF utility
> Hi,
> I've written another GFF utility. gff.GFFMask allows
> you to filter features in one file depending of if
> they hit features in another file.
> Are these kinds of utilities usefull to anyone?
> Matthew
> C:\devel\biojava-live\demos>java -classpath 
> .;../ant-build/biojava.jar gff.GFFMa sk Exception in thread 
> "main" java.lang.Exception: Use: GFFToFeatures [options]
>     --infile in            read gff from file named in
> (stdin if absent or -)
>     --outfile out          write gff to file named out
> (stdout if absent or -)
>     --maskfile mask        read the masking gff from
> file named mask (stdin if absent or -)
>     --mode contain|overlap features should either be
> totaly contained within or overlap the mask
>     --hits accept|reject   features hitting the mask
> will be accepted or rejected
>     --use_seq_names y|n    mask hits should count only
> if seq names match if y
>         at gff.GFFMask.main(GFFMask.java:41)
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