for newCognateID in range(1,numCognates + 1):
multi = MSA("cognates/" + phylName + "/" + familyName + "/" + str(conceptID - 3) + "." + str(newCognateID) + ".msq",merge_vowels=False,unique_seqs=False)
cognateLangs = [nameToID[taxon] - langs[0] for taxon in multi.taxa]
#cognateLangs = [int(lexdict[IDList[0]][0]) - langs[0] for IDList in etym_dict[cognateID] if IDList != 0]
#print "cognate set " + str(cognateID) + " - cognate langs: " + str(cognateLangs)
if len(cognateLangs) > 1: #cognate sets of size 1 are useless
cognateGuideTree = subGuideTree(familyGuideTree,cognateLangs)
#print("\nAligning cognate " + str(cognateID) + ":")
#print " cognate langs = " + str(cognateLangs)
#printTree(cognateGuideTree,0,names=[germanicNameTable[lang] for lang in cognateLangs])
cognateNameTable = [nameTable[lang] for lang in cognateLangs]
tree_mtx = convert.newick.nwk2guidetree(str(cognateGuideTree))
multi.prog_align(model=internal_asjp,gop=-4,scale=0.9,guide_tree=tree_mtx)
#print(multi)
cons = get_consensus(multi, cognateGuideTree, recon_alg="sankoff_parsimony", gaps=True, classes=False, rep_weights = rep_weights, local = "gap")
cognateParsimony = 0.0
#aggregate the parsimony value
for i in range(len(cognateGuideTree.reconstructed)):
cognateParsimony += min(cognateGuideTree.sankoffTable[i].values())
familyParsimony += cognateParsimony
print("Reconstructed proto-" + familyName + " word for concept " + str(conceptID - 3) + ":\t" + cons + "\twith average parsimony " + str(cognateParsimony / len(cognateLangs)))
#PRINT OUT RECONSTRUCTION STEPS IN A TREE VISUALIZATION
if graphicalOutput:
outputTree = Tree()
outputTree.add_face(TextFace(str("".join(cognateGuideTree.reconstructed))), column=0, position = "branch-right")
if (IDList != 0):
[langID, word, entry, langName] = lexdict[IDList[0]][:4]
entry_msq_file.write(langName + "\t" + entry + "\n")
entry_msq_file.close()
cognateLangs = [int(lexdict[IDList[0]][0]) - langs[0] for IDList in etym_dict[cognateID] if IDList != 0]
if len(cognateLangs) > 1: #cognate sets of size 1 are useless
cognateGuideTree = subGuideTree(germanicGuideTree,cognateLangs)
print("\nAligning cognate " + str(cognateID) + ":")
print " cognate langs = " + str(cognateLangs)
printTree(cognateGuideTree,0,names=[germanicNameTable[lang] for lang in cognateLangs])
multi = MSA("./cognate" + str(cognateID) + ".msq",merge_vowels=True,unique_seqs=False)
tree_mtx = convert.newick.nwk2guidetree(str(cognateGuideTree))
multi.prog_align(model=sca,gop=-4,scale=0.9,guide_tree=tree_mtx)
print(multi)
#old version of call had taxa=[str(i) for i in range(len(langs))]
cons = get_consensus(multi, cognateGuideTree, gaps=True, classes=False)
print("Reconstructed proto word for concept " + str(conceptID - 3) + ":\t" + cons)
#print("\nDetermining and counting sound changes at the edges of the guide tree, and cascading them to the supertrees:")
for node in cognateGuideTree.postorder():
if not hasattr(node, "recon_changes"):
node.recon_changes = {}
if not node.isRoot():
for i in range (0,len(node.reconstructed)):
#if node.reconstructed[i] != node.Parent.reconstructed[i]:
change = (node.Parent.reconstructed[i], node.reconstructed[i])
origNode = node
while origNode != None:
if not hasattr(origNode, "recon_changes"):
origNode.recon_changes = {}
if change not in origNode.recon_changes.keys():
origNode.recon_changes[change] = 1
if len(cognateLangs) > 1: #cognate sets of size 1 are useless
cognateGuideTree = subGuideTree(germanicGuideTree, cognateLangs)
print("\nAligning cognate " + str(cognateID) + ":")
print " cognate langs = " + str(cognateLangs)
printTree(cognateGuideTree,
0,
names=[germanicNameTable[lang] for lang in cognateLangs])
multi = MSA("./cognate" + str(cognateID) + ".msq",
merge_vowels=True,
unique_seqs=False)
tree_mtx = convert.newick.nwk2guidetree(str(cognateGuideTree))
multi.prog_align(model=sca, gop=-4, scale=0.9, guide_tree=tree_mtx)
print(multi)
#old version of call had taxa=[str(i) for i in range(len(langs))]
cons = get_consensus(multi,
cognateGuideTree,
gaps=True,
classes=False)
print("Reconstructed proto word for concept " +
str(conceptID - 3) + ":\t" + cons)
#print("\nDetermining and counting sound changes at the edges of the guide tree, and cascading them to the supertrees:")
for node in cognateGuideTree.postorder():
if not hasattr(node, "recon_changes"):
node.recon_changes = {}
if not node.isRoot():
for i in range(0, len(node.reconstructed)):
#if node.reconstructed[i] != node.Parent.reconstructed[i]:
change = (node.Parent.reconstructed[i],
node.reconstructed[i])
origNode = node
while origNode != None:
if not hasattr(origNode, "recon_changes"):