ORF GFF file filter for summary

[jgluck]

We would like the ability to provide a gff formatted file of ORFS and have results filtered so that only those misassemblies which overlap orfs are reported.

[jgluck]

@cmhill Question.

Currently I wait for summary.gff to be created. I then run through summary.gff and create orf_filtered_summary.gff which contains only those lines which overlapped orfs from a provided sorted gff formatted file of ORFS.

Do you have a different vision for this output, or do you think that this is fine? If orfs exist I have to add columns to the table file. That's all that's left now.

[cmhill-zz]

Make sure the reported ORF misassemblies are the intersection between the misassembly and the ORF in question. You are going to have cases where a misassembled region might span 10kb, and there might be multiple ORFs within that region.

The big thing is adding the columns to the table. You're going to have modify generate_summary_table in pipeline.py.

[jgluck]

Almost done. Testing it on NOT Carsonella. I'm making the assumption that the orfs and the current summary are in the same order. I believe this is incorrect. I should probably be sorting both.

[jgluck]

@cmhill I just pushed the changes to a new branch called "orf-filter" I didn't want to pollute the current code base. If you open pipeline.py and search for "orf" it should show up.

The lines in question are: https://github.com/jgluck/VALET/blob/orf-filter/src/py/pipeline.py#L181-L195