Convert PAINT tool IBA XML to GAF

dustine32 commented 3 years ago

The OFFICIAL ticket for this. Related to https://github.com/pantherdb/features-bugs/issues/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 commented 3 years ago

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 commented 3 years ago

@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 commented 3 years ago

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!

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pantherdb / fullgo_paint_update

Convert PAINT tool IBA XML to GAF #52