[Biojava-l] Improved GFF filtering

[Matthew Pocock]

Hi,

I've been tinkering with the GFF code in an effert to
make it easier to use. The result is a complete revamp
of the gff.GFFFilter demo application. You can use the
app to filter a gff stream or file to a stream or file
by any of the columns. If you prefix a value with !,
then this will match all lines that don't match that
value e.g. "-feature source" matches embl source lines
and "-feature !source" matches everything else.

The new usage looks something like this:

[mrp@localhost demos]$ java gff.GFFFilter
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 -)
    --source [!]s  source==s or source!=s
    --feature [!]f feature==f or feature!=f
    --seq [!]s     sequence==s or sequence!=s
    --frame [!]f   frame==f or frame!=f where f is one
of 0, 1, 2
    --strand [!]s  strand==s or strand!=s where s is
one of ., +, -
    --start [<>]x  start==x or start<x or start>x
    --end [<>]y    end==y or end<y or end>y
    --help         this help message

        at gff.GFFFilter.main(GFFFilter.java:64)

Matthew

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