[Biojava-l] GFF

[Matthew Pocock]

Hi.

We have been waging the feature-creation battle again today. It seems to
work at the moment, but is a bit string & brown-paper for long-term use.

The GFF code is now debugged (what I mean is that it works for my
example stript). To run it:

cd biojava-live/demos/gff
javac -classpath ../../xml.jar:../../biojava.jar GFFToFeatures.java
java -classpath ../../xml.jar:../../biojava.jar:. GFFToFeatures
varC4-2.dna varC4-2.gff

The output I get is pasted in below.

ps the SVM packages now build error free, so you should be able to build
the entire project without errors at all - just some pesky CORBA
deprication warnings!!!!

> java -fast64 -classpath ../../xml.jar:../../biojava.jar:.
GFFToFeatures varC4-2.dna varC4-2.gff
Loading sequences
Adding org.biojava.bio.seq.Feature$Template
Adding org.biojava.bio.seq.StrandedFeature$Template
Sequences:
        MAL4P2:BLASTX_991005
Loading gff
Features:
        MAL4P2:BLASTX_991005
        MAL4P2:BLASTX_991005
        MAL4P2:BLASTX_991005
        MAL4P2:BLASTX_991005
        MAL4P2:BLASTX_991005
        MAL4P2:BLASTX_991005
Adding features from gff to sequences
Printing out annotated sequences
        MAL4P2:BLASTX_991005
                Feature sequence hand_built (220982, 228657) -
                Feature intron hand_built (222317, 223158) -
                Feature exon hand_built (220982, 222316) -
                Feature exon hand_built (223159, 228657) -
                Feature coding_exon hand_built (220982, 222316) -
                Feature coding_exon hand_built (223159, 228657) -