Convert PAINT tool IBA XML to GAF

[dustine32]

The OFFICIAL ticket for this. Related to pantherdb/features-bugs#20 as that ticket is about formatting the input for this ticket's new code.

Currently being developed in https://github.com/dustine32/pthr_db_caller but will be hooked into the update pipeline to generate the release GAFs (and soon GPADs).

This should take the XML output from Anushya's PAINT tool IBA propagator and output to GAF 2.2 format:

$ format_xml_iba_to_gaf.py --file_xml PTHR12548.xml
UniProtKB	C3YJJ8	BRAFLDRAFT_207856	involved_in	GO:0006357	PMID:21873635	IBA	PANTHER:PTN000284480|WB:WBGene00001061|UniProtKB:Q14188|UniProtKB:Q14186|MGI:MGI:101934	P	Uncharacterized protein (Fragment)	UniProtKB:C3YJJ8|PTN001756489	protein	taxon:7739	20200808	GO_Central
UniProtKB	M4CZ83	M4CZ83	involved_in	GO:0006357	PMID:21873635	IBA	PANTHER:PTN000284480|WB:WBGene00001061|UniProtKB:Q14188|UniProtKB:Q14186|MGI:MGI:101934	P	Uncharacterized protein	UniProtKB:M4CZ83|PTN004368046	protein	taxon:51351	20200808	GO_Central
UniProtKB	F6ZPV4	TFDP1	enables	GO:0000981	PMID:21873635	IBA	PANTHER:PTN000284480|UniProtKB:Q14188|UniProtKB:Q14186	F	Uncharacterized protein	UniProtKB:F6ZPV4|PTN001394910	protein	taxon:9796	20200914	GO_Central
...

Also needed to be worked into here:

• Assemble together annotations from multiple input files (corresponding to PANTHER families)
• Split annotations by organism to write to separate files (e.g. gene_association.paint_pombase, gene_association.paint_other)
• Construct header
• Confirm the total output equals (to a sane degree) the GAFs currently coming out of createGAF.pl

[pgaudet]

Hi @dustine32
This is great! However I think the example above is GAF2.1, not 2.2? (I dont see the GP2term relations).

Thanks, Pascale

[dustine32]

@pgaudet Thanks for catching this! My bad, I was just so excited about my progress that these examples were pulled from the code I was developing. Unfortunately, that was before I plugged in the relation handling.

I updated the example lines to correct this!

[pgaudet]

I know! Sorry to be a pain ;) Le ven. 30 avr. 2021 à 8:03 PM, dustine32 ***@***.***> a écrit :

…

@pgaudet <https://github.com/pgaudet> Thanks for catching this! My bad, I was just so excited about my progress that these examples were pulled from the code I was developing. Unfortunately, that was before I plugged in the relation handling. I updated the example lines to correct this! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#52 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABEPWUBA66VDC6IMRW5SJ33TLLWFNANCNFSM432VJVOA> .