def LoadAssociation(self, line):
#header line
if line[0] == "#":
return False
cols = line.split("\t")
success = False
geneA = int(cols[1])
geneB = int(cols[2])
name = "biogrid:%s" % (cols[0])
cantContinue = False
taxA = cols[15].strip()
taxB = cols[16].strip()
if taxA == taxB and taxA == "9606":
if geneA not in self.biosettings.regions.genes:
self.missing.add(geneA)
cantContinue = True
if geneB not in self.biosettings.regions.genes:
self.missing.add(geneB)
cantContinue = True
if not cantContinue:
groupID = self.biosettings.NextID()
pathway = Pathway(self.groupID, groupID, name, "")
pathway.AddGene(geneA)
pathway.AddGene(geneB)
pathway.Commit(self.biosettings)
self.biosettings.RelatePathways(self.groupID, groupID, cols[12].strip(), "")
success = True
#else:
# print "Unknown tax ID: ", taxA, taxB
else:
print "Unable to find one or more genes (%s, %s) in %s total genes" % (geneA, geneB, len(self.biosettings.regions.genes))
return success
def Commit(self, groupTypeID, biosettings): #First, we'll add ourselves to the groups table pathway = Pathway(groupTypeID, self.groupID, self.term_id, self.description) #Next, add our associations to the association table for association in self.associations: pathway.AddGene(association[0]) #finally, we can add the various groups. If we have no parents, we can set ourselves as our own parent (since we don't have any root) parentCount = len(self.parents) for parent in self.parents: biosettings.RelatePathways(parent, self.groupID, self.parents[parent][0], self.parents[parent][1]) if parentCount == 0: biosettings.RelatePathways(groupTypeID, self.groupID, "", "") pathway.Commit(biosettings)
def LoadAssociation(self, line):
cols = line.split("\t")
success = False
if len(cols[0].split(":")) > 1:
idA = cols[0].split(":") #type:id
idB = cols[1].split(":")
geneA = None
geneB = None
acceptableTypes = ["uniprotkb"]
taxA = cols[9].split(":")[-1].strip()
taxB = cols[10].split(":")[-1].strip()
idLookup = BuildLookup(cols[13])
if taxA == taxB and taxA == "9606(H**o sapiens)":
#we can also attempt to id a gene using columns 4 & 5
if idA[0] in acceptableTypes:
ids = self.biosettings.regions.AliasToGeneID([idA[1]])
if len(ids) == 1:
geneA = list(ids)[0]
elif len(ids) == 0:
self.missingUni = idA[1]
else:
self.ambiguousUni = idA[1]
if idB[0] in acceptableTypes:
ids = self.biosettings.regions.AliasToGeneID([idB[1]])
if len(ids) == 1:
geneB = list(ids)[0]
elif len(ids) == 0:
self.missingUni = idB[1]
else:
self.ambiguousUni = idB[1]
if geneA != None and geneB != None and geneA != geneB:
groupID = self.biosettings.NextID()
if idLookup["mint"] in self.observedIDs:
print "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
print thisdoesnt.exit
self.observedIDs.add(idLookup["mint"])
pathway = Pathway(self.groupID, groupID, idLookup["mint"], "")
pathway.AddGene(geneA)
pathway.AddGene(geneB)
pathway.Commit(self.biosettings)
self.biosettings.RelatePathways(self.groupID, groupID, "mint", "")
success = True
#else:
# print "Unknown tax ID: ", taxA, taxB
return success
def LoadAssociation(self, line):
cols = line.split("\t")
words = cols[0].split("|")
dipA = words[0].strip()
uniA = words[len(words) - 1][10:]
words = cols[1].split("|")
dipB = words[0].strip()
uniB = words[len(words) - 1][10:]
taxA = cols[9][6:]
taxB = cols[10][6:]
comment = cols[6]
name = cols[13]
success = False
if taxA == taxB:
idsA = self.biosettings.regions.AliasToGeneID([uniA])
idsB = self.biosettings.regions.AliasToGeneID([uniB])
if len(idsA) == 1 and len(idsB) == 1:
geneA = list(idsA)[0]
geneB = list(idsB)[0]
if geneA != geneB:
groupID = self.biosettings.NextID()
pathway = Pathway(self.groupID, groupID, name, comment)
pathway.AddGene(geneA)
pathway.AddGene(geneB)
pathway.Commit(self.biosettings)
self.biosettings.RelatePathways(self.groupID, groupID,
"PFAM", "")
success = True
else:
if len(idsA) == 0:
self.missingUni.add(uniA)
else:
self.ambiguousUni.add(uniA)
if len(idsB) == 0:
self.missingUni.add(uniB)
else:
self.ambiguousUni.add(uniB)
else:
print >> sys.stdout, "Misaligned Taxonomy (%s), %s %s : %s" % (
name, taxA, taxB, comment)
return success
def LoadPathway(self, groupID, remotePathway): definition = remotePathway['definition'] entryID = remotePathway['entry_id'] genes = set() # geneIDs identified with pathway failedInsertions = 0 geneCount = 0 print "\n\nPathway(%s): %s - %s" % (groupID, entryID, definition) #because this could timeout, let's make sure it doesn't just faile doContinue = False while not doContinue: #try remoteGeneList = self.srv.get_genes_by_pathway(entryID) doContinue = True for geneHSA in remoteGeneList: gene = geneHSA[4:] geneIDs = self.biosettings.regions.AliasToGeneID([gene]) if len(geneIDs) == 0: print "-----(%s, %s)\tUnable to recognize gene" % (gene, geneHSA) failedInsertions+=1 elif len(geneIDs) != 1: failedInsertions+=1 print "-----(%s,%s)\tUnable to disambiguate gene ID (%s distinct ids) " % (gene, geneHSA, len(geneIDs)) else: genes.add(geneIDs[0]) if len(genes) > 0: pathway = Pathway(self.groupID, groupID, entryID[5:], definition) for geneID in genes: pathway.AddGene(geneID) geneCount+=1 pathway.Commit(self.biosettings) self.biosettings.RelatePathways(self.groupID, groupID, "", "") print "Genes Identified: %s\nGenes unable to be inserted: %s\nTotal genes associated : %s" % (geneCount, failedInsertions, len(genes))