diff --git a/orthofinder/scripts/get_orthologues.py b/orthofinder/scripts/get_orthologues.py
index 85786f60aea8ac39df7cbedb45b4bcd08cf76cfc..478c25e4edea6ea8ff5dfc4b5cf4e11329a8cce5 100755
--- a/orthofinder/scripts/get_orthologues.py
+++ b/orthofinder/scripts/get_orthologues.py
@@ -90,10 +90,11 @@ class OrthoGroupsSet(object):
self._extractor = idExtractor
self.clustersFN = clustersFilename_pairs
self.seqIDsEx = None
- self.ogs = self.OGs()
+ self.ogs = None
self.speciesToUse = util.GetSpeciesToUse(self.speciesIDsFN)
self.seqsInfo = util.GetSeqsInfo(orthofinderWorkingDir, self.speciesToUse)
self.fileInfo = util.FileInfo(inputDir=orthofinderWorkingDir, outputDir = orthofinderWorkingDir, graphFilename="")
+ self.id_to_og = None
def SequenceDict(self):
if self.seqIDsEx == None:
@@ -114,9 +115,18 @@ class OrthoGroupsSet(object):
return self._Spec_SeqIDs
def OGs(self):
- ogs = MCL.GetPredictedOGs(self.clustersFN)
- ogs = [[Seq(g) for g in og] for og in ogs if len(og) >= 4]
- return ogs
+ if self.ogs != None:
+ return self.ogs
+ self.ogs = MCL.GetPredictedOGs(self.clustersFN)
+ self.ogs = [[Seq(g) for g in og] for og in self.ogs if len(og) >= 4]
+ return self.ogs
+
+ def ID_to_OG_Dict(self):
+ if self.id_to_og != None:
+ return self.id_to_og
+ self.id_to_og = {g.ToString():iog for iog, og in enumerate(self.OGs()) for g in og}
+ return self.id_to_og
+
# ==============================================================================================================================
@@ -144,14 +154,15 @@ def lil_max(M):
# ASTRAL
def GetOGsToUse(ogSet):
- return range(100, min(10000, len(ogSet.ogs)))
+ return range(100, min(10000, len(ogSet.OGs())))
def CreateTaxaMapFile(ogSet, i_ogs_to_use, outputFN):
"""Get max number of sequences per species"""
sp_max = defaultdict(int)
+ ogs = ogSet.OGs()
for iog in i_ogs_to_use:
thisCount = defaultdict(int)
- for seq in ogSet.ogs[iog]:
+ for seq in ogs[iog]:
thisCount[seq.iSp] += 1
for iSp in thisCount:
sp_max[iSp] = max(sp_max[iSp], thisCount[iSp])
@@ -335,8 +346,9 @@ class DendroBLASTTrees(object):
def PrepareGeneTreeCommand(self):
cmds = []
- for iog in xrange(len(self.ogSet.ogs)):
- nTaxa = len(self.ogSet.ogs[iog])
+ ogs = self.ogSet.OGs()
+ for iog in xrange(len(ogs)):
+ nTaxa = len(ogs[iog])
cmds.append([" ".join(["fastme", "-i", self.distPat % iog, "-o", self.treesPatIDs % iog, "-w", "O"] + (["-s"] if nTaxa < 1000 else []))])
return cmds
@@ -364,7 +376,7 @@ class DendroBLASTTrees(object):
print( "-----------------------------------")
util.RunParallelOrderedCommandLists(self.nProcesses, [[cmd_spTree]] + cmds_geneTrees, qHideStdout = True)
seqDict = self.ogSet.Spec_SeqDict()
- for iog in xrange(len(self.ogSet.ogs)):
+ for iog in xrange(len(self.ogSet.OGs())):
self.RenameTreeTaxa(self.treesPatIDs % iog, self.treesPat % iog, seqDict, qFixNegatives=True)
self.RenameTreeTaxa(spTreeFN_ids, self.workingDir + "SpeciesTree_unrooted.txt", self.ogSet.SpeciesDict(), qFixNegatives=True)
#spTreeFN_ids = RunAstral(self.ogSet, self.treesPatIDs, self.workingDir)
diff --git a/orthofinder/scripts/orthologues_from_recon_trees.py b/orthofinder/scripts/orthologues_from_recon_trees.py
index 840eff48364d6715d3542e79646c557e0261f43c..dd3948735f25ea5d9e95f4aff32c5ea19e5a64b2 100644
--- a/orthofinder/scripts/orthologues_from_recon_trees.py
+++ b/orthofinder/scripts/orthologues_from_recon_trees.py
@@ -109,17 +109,21 @@ def multiply(specmin, specmax, matrixDir):
product = M.dot(M.transpose())
return product, M
-def WriteOrthologues(resultsDir, spec1, spec2, orthologues, speciesDict, sequenceDict):
+def WriteOrthologues(resultsDir, spec1, spec2, orthologues, ogSet):
+ speciesDict = ogSet.SpeciesDict()
+ id_to_og = ogSet.ID_to_OG_Dict()
+ sequenceDict = ogSet.SequenceDict()
d1 = resultsDir + "Orthologues_" + speciesDict[str(spec1)] + "/"
d2 = resultsDir + "Orthologues_" + speciesDict[str(spec2)] + "/"
with open(d1 + '%s__v__%s.csv' % (speciesDict[str(spec1)], speciesDict[str(spec2)]), 'wb') as outfile1, open(d2 + '%s__v__%s.csv' % (speciesDict[str(spec2)], speciesDict[str(spec1)]), 'wb') as outfile2:
writer1 = csv.writer(outfile1)
writer2 = csv.writer(outfile2)
- writer1.writerow((speciesDict[str(spec1)], speciesDict[str(spec2)]))
- writer2.writerow((speciesDict[str(spec2)], speciesDict[str(spec1)]))
+ writer1.writerow(("Orthogroup", speciesDict[str(spec1)], speciesDict[str(spec2)]))
+ writer2.writerow(("Orthogroup", speciesDict[str(spec2)], speciesDict[str(spec1)]))
for genes1, genes2 in orthologues:
- writer1.writerow((", ".join([sequenceDict["%d_%d" % (spec1, o)] for o in genes1]), ", ".join([sequenceDict["%d_%d" % (spec2, o)] for o in genes2])))
- writer2.writerow((", ".join([sequenceDict["%d_%d" % (spec2, o)] for o in genes2]), ", ".join([sequenceDict["%d_%d" % (spec1, o)] for o in genes1])))
+ og = "OG%07d" % id_to_og["%d_%d" % (spec1, genes1[0])]
+ writer1.writerow((og, ", ".join([sequenceDict["%d_%d" % (spec1, o)] for o in genes1]), ", ".join([sequenceDict["%d_%d" % (spec2, o)] for o in genes2])))
+ writer2.writerow((og, ", ".join([sequenceDict["%d_%d" % (spec2, o)] for o in genes2]), ", ".join([sequenceDict["%d_%d" % (spec1, o)] for o in genes1])))
def GetOrthologues(orig_matrix, orig_matrix_csc, index):
orthologues = orig_matrix.getrowview(index).nonzero()[1]
@@ -140,7 +144,8 @@ def find_all(matrix, orig_matrix):
orthologues.append((orthologuesSp1, orthologuesSp2))
return orthologues
-def species_find_all(speciesDict, sequenceDict, matrixDir, resultsDir):
+def species_find_all(ogSet, matrixDir, resultsDir):
+ speciesDict = ogSet.SpeciesDict()
# Calls multiply and find_all on each species pair, and appends the numbers from find_all's output to the relevant csv lists.
speciesIDs = sorted(map(int, speciesDict.keys()))
nspecies = len(speciesIDs)
@@ -151,7 +156,7 @@ def species_find_all(speciesDict, sequenceDict, matrixDir, resultsDir):
if index1 >= index2: continue
product, M = multiply(index1, index2, matrixDir)
orthologues = find_all(product, M)
- WriteOrthologues(resultsDir, speciesIDs[index2], speciesIDs[index1], orthologues, speciesDict, sequenceDict)
+ WriteOrthologues(resultsDir, speciesIDs[index2], speciesIDs[index1], orthologues, ogSet)
def get_orthologue_lists(ogSet, resultsDir, dlcparResultsDir, workingDir):
# -> Matrices
@@ -164,6 +169,6 @@ def get_orthologue_lists(ogSet, resultsDir, dlcparResultsDir, workingDir):
one_to_one_efficient(orthodict, genenumbers, speciesLabels, iSpecies, matrixDir)
# -> csv files
- species_find_all(ogSet.SpeciesDict(), ogSet.SequenceDict(), matrixDir, resultsDir)
+ species_find_all(ogSet, matrixDir, resultsDir)