export submissions to GFF3 format

wurmlab / afra

Genome Annotation for the Masses

http://afra.sbcs.qmul.ac.uk

Apache License 2.0

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export submissions to GFF3 format #67

Closed hargup closed 9 years ago

hargup commented 9 years ago

[x] Change indentation to 2 spaces.
[x] Verify the generated GFF3 file using http://genometools.org/cgi-bin/gff3validator.cgi
[x] Handle more than one submission
[x] Handle more than one transcript in a single submission
[x] Create a black list of non standard subfeature type to ignore while exporting them.
[x] Fix the phase calculation
[x] Query Task and Submission to find out all the submission corresponding to a GFF given by the user from the database.
[x] Re-factor code to reduce redundancy.
[x] Calculate the end part for the ##sequence-region meta-data
[x] Rebase and clean up the history.
[x] Generate the names of the features on the client side.

yeban commented 9 years ago

You could use http://genometools.org/ to validate the generated GFF3.

yannickwurm commented 9 years ago

Looks like a good place for some automated testing too - cheers

yeban commented 9 years ago

Exporter shouldn't have to worry about giving features and subfeatures an appropriate name. Appropriate names should be assigned to features and subfeatures on the client side.

Exporter doesn't seem to take into account the fact that there might be multiple mRNA corresponding to a gene.

yeban commented 9 years ago

Should track genometools/genometools#514 regarding validation errors.

yeban commented 9 years ago

@hargup Generating names client side is now in master. Please could you rebase the PR on master and quickly verify if everything is good to merge?

yeban commented 9 years ago

@hargup Alternative splicing hasn't yet been taken into account.

hargup commented 9 years ago

@yeban have a look now.

yeban commented 9 years ago

Thanks a ton!