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Planteome / planteome-annotation-data

This is a place to discuss issues around the Planteome annotation data and store useful scripts etc.
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Formats of the association files in our database- not all are GAF 2.0 #6

Closed cooperl09 closed 6 years ago

cooperl09 commented 7 years ago

@elserj and I have been looking into the formats of the association files in our database- not all are GAF 2.0. Of the 195 assoc files we have in svn (not including ones in test directories), 33 of them are not labeled as gaf-version: 2.0. One is 2.1 So, there are 31 files that we have to be updated to 2.0. @elserj could you post the list?

elserj commented 7 years ago

eo-associations/eo_gene_Oryza_Gramene.assoc eo-associations/eo_protein_Oryza_Gramene.assoc eo-associations/eo_qtl_Oryza_Gramene.assoc go-associations/go_geneproduct_Prunus_persica_GDR.assoc po-associations/po_anatomy_gene_oryza_gramene.assoc po-associations/po_anatomy_gene_physcomitrella_gramene.assoc po-associations/po_anatomy_gene_Picea_jaiswallab.assoc po-associations/po_anatomy_germplasm_Arabidopsis_NASC.assoc po-associations/po_anatomy_protein_Gossypium_AgBase.assoc po-associations/po_anatomy_qtl_oryza_gramene.assoc po-associations/po_gene_Arabidopsis_PPPP.assoc po-associations/po_gene_G.max_PPPP.assoc po-associations/po_gene_M.truncatula_PPPP.assoc po-associations/po_gene_S.lycopersicum_PPPP.assoc po-associations/po_gene_Z.mays_PPPP.assoc po-associations/po_germplasm_S.chmielewskii_sgn.assoc po-associations/po_germplasm_S.lycopersicum_sgn.assoc po-associations/po_germplasm_S.melongena_sgn.assoc po-associations/po_germplasm_S.pennellii_sgn.assoc po-associations/po_growth_gene_oryza_gramene.assoc po-associations/po_growth_protein_Gossypium_AgBase.assoc po-associations/po_growth_qtl_oryza_gramene.assoc po-associations/po_qtl_glycine_SoyBase.assoc to-associations/to_gene_G.max_PPPP.assoc to-associations/to_gene_M.truncatula_PPPP.assoc to-associations/to_gene_Oryza_Gramene.assoc to-associations/to_gene_O.sativa_PPPP.assoc to-associations/to_gene_S.lycopersicum_PPPP.assoc to-associations/to_gene_Z.mays_PPPP.assoc to-associations/to_protein_Oryza_Gramene.assoc to-associations/to_qtl_Gramene.assoc

elserj commented 6 years ago

This was done on Aug 4 with svn revision 835. Must have forgot to close the ticket.