[Biojava-l] Another GFF utility
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.
> -----Original Message-----
> From: Matthew Pocock [mailto:email@example.com]
> Sent: Tuesday, 15 October 2002 10:39 p.m.
> To: firstname.lastname@example.org
> Subject: [Biojava-l] Another GFF utility
> 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?
> 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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