[Biojava-l] Error parsing GFF3 file

[Scooter Willis]

Phillip

I think it is complaining about the negative location (-1864985,746). Is
this a circular genome? That seems to be a rather large sequence segment and
I think it is correct to complain about the negative location. We tried to
plan ahead on circular genomes and genes that cross the boundary begin/end
boundary and at the same time not have the programmer brain explode trying
to handle all the combinations that exist.  It gets really fun when you have
a negative strand.

One of the challenges of a valid gff3 file is that you can make sure
ontology is correct and the file format is correct but when you try and
bring it all together to do something with the data(turn it into a protein)
you need to check harder.

If this is a valid location can you send me the gff3 segment and the DNA
sequence that describes the features and I will see what I can do to make it
work without previous reference to head exploding. Let me know what the end
goal is on parsing gff3 file and what is missing when you try and map to a
GeneSequence/ProteinSequence.

Thanks

Scooter

On Fri, Dec 31, 2010 at 12:07 PM, Philipp Comans <philipp.comans at mytum.de>wrote:

> Hello everyone,
>
> I am trying to parse the file available here:
> ftp://ftp.jgi-psf.org/pub/JGI_data/Amphimedon_queenslandica/annotation/Aqu1.gff3.gz
> with the following commands:
>
> import java.util.Iterator;
>
> import org.biojava3.genome.parsers.gff.FeatureI;
> import org.biojava3.genome.parsers.gff.FeatureList;
> import org.biojava3.genome.parsers.gff.GFF3Reader;
>
> public class GFFReader3 {
>
>        public static void main(String[] args) throws Exception {
>
>                FeatureList features = (FeatureList)
> GFF3Reader.read("/Users/philipp/Dropbox/IDP/JGI_data/annotation/Smiles.gff3");
>                Iterator<FeatureI> featureIterator = features.iterator();
>
>                FeatureI currentFeature = null;
>
>                while (featureIterator.hasNext()) {
>                        currentFeature = featureIterator.next();
>                        System.out.println(currentFeature);
>                }
>
>        }
>
> }
>
> The error I get is:
> 31.12.2010 18:05:10 org.biojava3.genome.parsers.gff.GFF3Reader read
> INFO: Gff.read(): Reading
> /Users/philipp/Dropbox/IDP/JGI_data/annotation/Aqu1.gff3
> Exception in thread "main" java.lang.IllegalArgumentException: Improper
> location parameters: (-1864985,746)
>        at org.biojava3.genome.parsers.gff.Location.<init>(Location.java:75)
>        at org.biojava3.genome.parsers.gff.Location.union(Location.java:258)
>        at
> org.biojava3.genome.parsers.gff.FeatureList.add(FeatureList.java:49)
>        at
> org.biojava3.genome.parsers.gff.GFF3Reader.read(GFF3Reader.java:59)
>        at GFFReader3.main(GFFReader3.java:11)
>
> I find this very strange because the file is a valid GFF document according
> to
> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online
>
> Is this a bug or am I doing something wrong?
> Thanks for your help, I wish you a happy New Year!
>
> Philipp
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