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Fix minor bugs in GO-Elite: Mm MPhenoOntology and Hs WikiPathways parsing #35

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Fix minor bugs in GO-Elite: Mm MPhenoOntology and Hs WikiPathways parsing #35

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c7d723c
added '*.pyc' and 'mpmath/**/*.pyc' to .gitignore
warrenmcg Feb 25, 2017
db97bc2
fix bug that failed to recognize mm_symbols in updated HMD_Phenotype.…
warrenmcg Feb 25, 2017
b132f0b
change WikiPathway pathway values to UTF-8 encoding to prevent bug th…
warrenmcg Feb 27, 2017
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
@@ -1,2 +1,3 @@

mpmath/**/*.pyc
*.pyc
*.zip
4 changes: 2 additions & 2 deletions GeneSetDownloader.py
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Expand Up @@ -486,7 +486,7 @@ def importPhenotypeOntologyGeneAssociations():
t = string.split(data,'\t')
hs_symbol=t[0]; hs_entrez=t[1]; mm_symbol=t[2]; mgi=t[3]; pheno_ids=t[4]
if 'MP' not in pheno_ids:
try: pheno_ids = t[5]
try: mm_symbol=t[3]; mgi=t[4]; pheno_ids=t[5]
except Exception: pass
hs_symbol = string.lower(hs_symbol)
mm_symbol = string.lower(mm_symbol)
Expand Down Expand Up @@ -1243,4 +1243,4 @@ def buildAccessoryPathwayDatabases(selected_species,additional_resources,force):
additional_resources+=['miRNA Targets','GOSlim','Disease Ontology','Phenotype Ontology','KEGG','RVista Transcription Factor Sites']
additional_resources=['BioGRID']
buildAccessoryPathwayDatabases(selected_species,additional_resources,force)

3 changes: 2 additions & 1 deletion gene_associations.py
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Expand Up @@ -1349,7 +1349,7 @@ def __init__(self,system_name,geneID,pathway):
except Exception: null=[]
def GeneID(self): return str(self.geneID)
def System(self): return str(self.system_name)
def Pathway(self): return str(self.pathway)
def Pathway(self): return self.pathway ## Returning str() threw an error for non-ASCII characters in HsWikiPathways
def setGraphID(self,graphID): self.graphID = graphID
def setGroupID(self,groupid): self.groupid = groupid
def GraphID(self): return self.graphID
Expand Down Expand Up @@ -1396,6 +1396,7 @@ def exportWikiPathwayData(species_name,pathway_db,type):
values +=[wpd.Uniprot(), wpd.Unigene(), wpd.Refseq(), wpd.MOD(), wpd.Pubchem(), wpd.CAS(), wpd.Chebi()]
values = string.join(values,'\t')
values = string.replace(values,'\n','') ###Included by mistake
values = values.encode('UTF-8', 'replace') ## Need this line to prevent non-ASCII characters from HsWikiPathways throwing an error
export_data.write(values+'\n')
export_data.close()
#print 'WikiPathways data exported to:',export_dir
Expand Down