def test003():
print "** Test 003 **"
# Tree remapping
whole_tree = newick.tree.parseTree("((((scer,spar),smik),sbay),scas);")
sub_tree = newick.tree.parseTree("((scer,smik),scas);")
# Name nodes on whole tree
newick.tree.labelInternalNodes(whole_tree)
if False:
# Only need to do this if you want more/other data.
# Load the genes
load_fxn = biofile.getIDFunction("vanilla")
cdna_dicts = {}
geneutil.readGenomesFromFile(os.path.expanduser("~/research/data/scerevisiae/saccharomyces-files.txt"), os.path.expanduser("~/bio/genomes"), cdna_dicts, 1, load_fxn)
align_dict = pickle.load(file(os.path.expanduser("~/research/data/scerevisiae/scer-ortholog-alignments.p"),'r'))
(nal, spec_orf_list, protal) = align_dict["YBR177C"]
aligned_seqs = {}
for xi in range(len(spec_orf_list)):
(spec,orf) = spec_orf_list[xi]
gene = cdna_dicts[spec][orf]
prot = protal[xi]
aligned_gene = muscle.alignGeneFromProtein(gene, prot)
aligned_seqs[spec] = aligned_gene
print aligned_seqs
seq_dict = {'spar': 'ATGTCAGAAGTTTCGAAATGGCCAGCTATCAACCCGTTCCATTGGGGATACAATGGTACTGTTTCACATGTCGTCGGTGAAAATGGTTCCATCAAACTAAATTTAAAAGACAACAAGGAACAGGTTGAATTTGACGAGTTCGTTAACAAATATGTCCCAACGTTGAAGAATGGTGCTCAATTTAAATTGAGTCCTTACTTGTTCACAGGTATTTTGCAAACCCTGTACTTAAATGCTGCTGATTTCTCTAAGAAATTTCCTGTATTCTACGGCAGAGAAATTGTCAAATTCTCGGATAATGGAGTTTGTACCGCTGACTGGCTCATGGATTCCTGGAAGAAGGATTACAAACTCGATCAAAGTACTATGGGTTTCGATAAGAAAAAATTTGGTGAAGACGAGAAGGAGACGCATCCAGAAGGGTGGCCTCGTTTACAACCACGTACAAGGTATCTGAAGGATAATGAATTGGAAAATGTAAGGGAGGTTGATCTGCCCTTAGTAGTTATCCTACATGGTCTTGCTGGTGGTAGTCATGAGCCTATCATAAGATCTCTTGCTGAAAACCTCTCTCGG------AGTGGGAGATTTCAAGTGGTGGTACTAAATACTAGAGGCTGTGCACGTTCTAAAATTACAACCAGAAATTTATTTACGGCTTACCACACAATGGATATTCGTGAATTTTTGCAAAGAGAAAAGGAGAGATATCCAAATAGAAAATTATACGCTGTGGGATGCTCCTTCGGTGCTACGATGTTGGGAAACTATCTGGGAGAAGAAGGCGATAAATCTCCTTTATCTGCAGCTGCTACCCTGTGCAACCCTTGGGATCTTCTCCTTTCGGCACTTAGAATGACCGAGGATTGGTGGTCAAAGACTTTATTTTCCAAAAATATTGCCCAATTCTTAACAAGAACTGTTCAAGTTAATATGGGTGAACTAGGAGTTCCAAATGGCTCCCGTCCTGACCATCCTCCCACAGTCAAGAATCCATCTTACTATATGTTCACACCTGAAAATCTAATAAAGGCAAAAAGCTTTAAATCGAGTCTGGAATTTGATGAATTGTACACTGCGCCTGCTTTAGGCTTCCCAAATGCTATGGAATATTATAAAGCGGCCAGCTCAATAAGCAGAGTTGATACAATTCGGGTTCCTACTCTAGTTATCAATTCAAGGGATGATCCTGTTGTCGGCCCGGATCAA---CCTTACTCAATCGTGGAAAAAAATCCTCGTGTTTTGTATTGTAGAACCGACTTAGGAGGTCATTTAGCTTACCTAGATAAAGACAATAATTCGTGGGCTACCAAGGCGATTGCAGAATTCTTTACTAAGTTTGATGAATTAGTTGTA', \
'smik': 'ATGTCAGAAGTTTCGAAATGGCCAGCTATCAACCCATTCCATTGGGGATACAATGGTACTGTTTCGCATGTTGTCGGTGAAAATGGTTCCATGAAACTAGGTTTAAAAGATAACAAGGAACAGATTGAATTTGATCAGTTCGTTAACAAATATGTTCCAAGTTTGAAGAATGGTGCTCACTTCAAATTGAGTCCTTACTTGTTCACAGGTATTTTACAAACGTTGTACTTAAACGCTGCAGACTTCTCGAAGAAATTTCCTGTATTTTATGGCAGAGAAATTATCAAATTCTCCGATAATGGAGTTTGCACCGCTGATTGGGTTATGAGCTCCTGGAAGAGGGATTACAAACTCAATCAAAGTACCATGAGCTTTGATAAAAGCAAATTCGACGGAGACGAAAAAGCGACGCATCCAGAAGGATGGCCTCGTTTACAACCACGTACAAGATATTTGAAGGATAATGAGTTAGAGGAGCTCAGAGAAATTGAGCTCCCCTTAGTAGTCATTTTGCATGGACTTGCCGGTGGCAGTCATGAACCGATCATAAGATCTCTTGCTGAAAACCTGTCTCGC------AGCGGGAAATTTCAAGTGGTGGTGCTAAATACCAGAGGTTGTGCACGCTCCAAAATTACAACCAGGAACTTATTCACGGCTTACCACACAATGGATATCCGTGAATTTTTGCAAAGAGAAAATCAAAGACATCCAAACAGAAAGTTATACGCTGTAGGATGTTCTTTTGGTGCCACCATGTTGGGGAATTATCTCGGTGAAGAAGGTGATAAATCACCTTTATCTGCAGCTGCTACCTTATGCAATCCTTGGGACCTTCTCCTTTCAGCGCTTAGAATGACCGAGGATTGGTGGTCAAAAACTTTATTTTCCAAAAATATTGCACAGTTTTTAACAAGAACCGTTCAAGTTAACATGGGTGAACTAGGAGTCCCAAACGGCTCTCATCCCGACCATCCTCCTACAGTAAAAAATCCATCCTACTATATGTTCACCCCTGAAAATTTAATAAAGGCAAAACACTTCAAATCGAGTCTGGAATTCGATGAATTGTATACTGCACCTGCTTTAGGCTTTCCAAATGCAATGGAGTATTATAAAGCAGCTAGCTCAATAAACAGAGTTGCTACAATTAAGGTTCCTACTTTAGTTATCAATTCTAGAGATGATCCTGTTGTCGGCCCAGATCAG---CCTTATTCAATTGTAGAAAAAAACCCTCGTATTTTGTATTGCGGAACCGATTTAGGGGGCCATTTAGCCTACCTAGATAATGACAATAACTCATGGGCAACTAAGGCGATTGCAGAATTCTTTACTAAATTTGATCAACTGGTTGTA', \
'scas': 'ATGGCTTCACAATCAACATATCCACTCATTAAACCATGGAATTGGGGGTATCACGGAACCGTGACCCAAATTACCAGTAAGGAAGGTACTGTACTCATTCCATTAAAGGACAACAAAGAGGGTATTCCATTAGCAGAATTAGTTTCAAAGAATGTCCCTAGTTTAAAGGATGGTGCTAAGTTTGAGTTGAAACCTTTTTTATTCACTGGTATTTTACAAACTCTGTACCTTGGCGCAGCTGACTTTTCTAAGAAATTCCAAGTCTTTTATGGTAGAGAAATTGTGGAATTCTCAGATACTGGTGTATGTACTGCCGATTGGGTAATGCCATCTTGGAAGCAAAAATATAACTTTAATGAGAAAACATCAACTTTTGACAAGAAAGCATTCGACCTGGACGAAAAAGAAACACATCCAGACAATTGGCCTCGTTTGCAACCTCGTACCAGATACTTAAATGAAAAAGAAATGACGACTATCCACGAGGATGACAGACCATTGGTTGTTTGTTGTCATGGGTTAGCTGGTGGCTCTCACGAACCAATTATCAGATCATTGACTGAAAATCTATCTAAGGTTGGTAATGGGAAATTCCAAGTGGTTGTCCTAAATACTCGTGGCTGTGCACGTTCTAAGATTACTACTCGTAACCTATTTACTGCTTTCCATACTATGGATCTACGTGAATTTGTCAACAGAGAACACCAAAAACATCCTAACAGAAAGATTTATGCCGTTGGATTTTCATTCGGGGGTACAATGTTAGCAAATTATTTAGGAGAAGAAGGTGATAAAACTCCAATTGCATCTGCTGCAGTGTTATGTAACCCGTGGGATATGGTATTATCCGGTATGAAAACGAGAGATGATTTTTGGACAAGAACGCTATTTGCTAAGAATATTACAGATTTCTTGACTAGAATGGTTAAAGTTAATATGGCAGAATTGGAATCTCCAGATGGTTCTAAGCCTGATCACATCCCAACAGTGAAAAATCCATCTTATTATACATTTACCCAAGAAAATTTGGCAAAAGCCAAGGATTTTAAATTAATATCTGACTTTGATGACGTATTTACTGCACCTGCATTGGGTTTCAAAAACGCATTGGAGTACTACGCTGCAGCTGGGTCCATTAACAGACTACCTAATATTAAGATTCCTTTATTAGTTATCAATTCCACTGATGATCCAGTTGTTGGGCCGGATCCAATCCCAAACCATATCATAGATTCAAACAACCACCTACTGCTATGTGAAACCGATATCGGTGGCCATTTGGCATATTTGGATAAAAATAATGATTCATGGTCAACGAACCAAATCGCCAATTATTTCGACAAATTTGATGAAGTGGCATTA', \
'sbay': 'ATGTCAGAAGTTTCAAAGTGGCCAGCTATTAACCCATTTCATTGGGGGTACAACGGTACAGTTTCACATGTCGTTGGTGGTAATGGTTCTGTGAAGTTAAGCTTGAAGAGCGATAAGGAGCAAGTCGAGTTTGATACGTTTGTTAATAAATATGTCCCGATTCTGAAAAACGGGGCCCATTATAAACTAAGTCCCTACTTGTTCACAGGTATTTTACAAACCCTATACTTGAACGCTGCTGATTTCTCAAAGAAATTTCCCGTATTTTATGGTAGAGAAATCGTCAAGTTCTCGGATGACGGTGTCTGTACTGCTGATTGGGTCATGAACTCTTGGGAAAAGGAATATGATTTCGACCAAAAGACTATGAAATTTGATACGAAGAAGTTTGGCGACGACGAAAAGGCGACGCACCCAGAAGGATGGCCTCGTTTACAACCACGTACGAGGTACCTCAGGGACGAAGAGTTGGAAGAACAGAGAAAAGTAGATCTTCCCCTAGTTATCATCCTCCATGGTCTTGCCGGAGGCAGTCATGAACCAATCATAAGATCCCTAACTGAGAACTTGTCTCGTATCGGCAATGGGAGATTCCAAGTCGTGGTGCTAAACACGAGAGGCTGTGCACGTTCTAAAATCACCACTAGAAACCTATTCACAGCTTACCACACAATGGATATCCGTGAGTTCTTGCAAAGGGAAAAAGAAAGATATCCAAACAGAAAATTATACACTGTAGGGTGCTCTTTCGGGGCTACCATGTTAGCAAACTATTTGGGTGAAGAAGGTGACAAATCACCTGTATCTGCTGCTGTTACGTTATGTAATCCTTGGGATCTTCTTCTTTCGGCACTTAGAATGACTGAAGACTGGTGGTCAAAAACTTTGTTTTCTAAAAATATTGCCCAATTTTTAACAAGAACCGTTCAAGTTAACATGGGCGAATTAGGTGTTCCAAATGGCTCTCGTCCTGACCATACACCTACAGTTAAAAATCCATCTTACTATAAGTTCACACCTGAGAATTTGATGAAGGCAAAGCGCTTTAAGTCGAGTCTCGAATTCGATGAGCTGTACACTGCACCAGCTTTGGGCTTCCCGAATGCTATGGAATATTATAAATCAGCTAGTTCAATCAACAGGGCTGATAAAATCAAGGTTCCTACTTTAGTAATCAATTCTAGAGATGATCCTGTTGTTGGCCCAGACCAA---CCTTATTCATTTGTGGAGAAGAACCCTAATATACTATTCTGTAGAACCGACCTAGGTGGCCATTTAGCCTACCTAGATAGCAACAATGATTCGTGGGTTACAAAGGCGATTTCCGAGTTCTTGAATAAGTTTGAGGAGTTAGTGTTA',
'scer': 'ATGTCAGAAGTTTCCAAATGGCCAGCAATCAACCCATTCCATTGGGGATACAATGGTACAGTTTCGCATATTGTCGGTGAAAATGGTTCCATTAAACTCCATTTAAAAGACAACAAGGAGCAAGTTGATTTTGACGAGTTCGCTAACAAATATGTCCCAACGTTGAAGAATGGTGCCCAATTCAAATTGAGTCCTTACTTGTTCACAGGTATTTTGCAAACTTTGTACTTAGGTGCTGCTGATTTCTCTAAGAAATTTCCTGTATTCTACGGCAGGGAAATTGTCAAATTCTCGGATGGTGGAGTTTGCACCGCTGACTGGCTCATAGATTCATGGAAAAAGGATTATGAATTCGATCAAAGTACTACGAGCTTTGATAAAAAAAAATTTGATAAAGACGAGAAGGCGACACATCCAGAAGGATGGCCTCGTTTACAACCACGTACAAGGTACCTGAAAGATAATGAGTTGGAAGAACTACGGGAGGTTGATCTACCCCTAGTAGTTATTCTACATGGTCTTGCTGGTGGTAGTCATGAGCCGATTATAAGATCTCTTGCTGAAAACCTGTCTCGC------AGTGGGAGATTTCAAGTGGTCGTCCTAAATACCAGAGGTTGTGCACGTTCCAAAATTACCACCAGAAATTTATTTACAGCTTATCACACAATGGATATTCGCGAGTTTTTGCAAAGAGAAAAGCAAAGACATCCAGATAGAAAACTATACGCTGTGGGATGCTCTTTTGGTGCTACGATGCTGGCAAACTATCTGGGAGAAGAGGGCGATAAATCACCTTTATCCGCAGCTGCTACTTTGTGCAATCCTTGGGATCTTCTCCTTTCAGCAATTAGGATGAGCCAGGATTGGTGGTCAAGAACTTTATTTTCCAAAAATATTGCGCAATTCTTAACAAGAACCGTTCAGGTTAATATGGGTGAATTAGGAGTTCCAAATGGCTCTCTCCCCGATCATCCTCCCACAGTCAAGAATCCATCTTTCTATATGTTCACGCCTGAAAATCTAATAAAGGCAAAGAGCTTTAAATCGACCCGGGAATTTGATGAAGTGTACACTGCGCCTGCTTTAGGCTTCCCAAATGCTATGGAGTATTATAAAGCGGCCAGCTCAATAAACAGAGTTGATACAATTCGGGTTCCTACCCTTGTTATCAATTCCAGGGATGATCCTGTTGTCGGCCCAGATCAA---CCATACTCAATCGTGGAAAAGAATCCTCGTATTTTGTATTGTAGAACCGATTTAGGTGGTCATTTAGCTTACCTAGATAAAGACAACAACTCGTGGGCTACCAAGGCAATTGCAGAATTTTTCACTAAGTTTGATGAATTAGTCGTA'}
seq_labels = [x.name for x in sub_tree.leaves]
seqs = [seq_dict[k] for k in seq_labels]
# Run PAML
opts = paml.CodeML.FMutSel_F_options
opts["RateAncestor"] = "1"
cm = paml.CodeML("codon", opts)
cm.loadSequences(seqs, seq_labels, str(sub_tree))
cm.run()
cm.putBranchRatesOnTree(seq_labels, sub_tree, label="rate")
cm.putAncestralSequencesOnTree(seq_labels, sub_tree, label="sequence")
# Now remap the tree.
whole_node_dict = dict([(x.name, x) for x in whole_tree.nodes])
sub_node_dict = dict([(x.name, x) for x in sub_tree.nodes])
sub_names = [x.name for x in sub_tree.leaves]
#print whole_node_dict["scer"].getMostRecentCommonAncestor(whole_node_dict["smik"]).name
newick.tree.mapLabelsOntoSubtree(whole_tree, sub_tree)
for i in range(len(sub_names)-1):
for j in range(i+1, len(sub_names)):
s1 = sub_names[i]
s2 = sub_names[j]
sub_mrca = sub_node_dict[s1].getMostRecentCommonAncestor(sub_node_dict[s2])
mrca = whole_node_dict[s1].getMostRecentCommonAncestor(whole_node_dict[s2])
assert sub_mrca.name == mrca.name
shutil.rmtree(cm.tmpdir)
def test003():
print "** Test 003 **"
# Tree remapping
whole_tree = newick.tree.parseTree("((((scer,spar),smik),sbay),scas);")
sub_tree = newick.tree.parseTree("((scer,smik),scas);")
# Name nodes on whole tree
newick.tree.labelInternalNodes(whole_tree)
if False:
# Only need to do this if you want more/other data.
# Load the genes
load_fxn = biofile.getIDFunction("vanilla")
cdna_dicts = {}
geneutil.readGenomesFromFile(
os.path.expanduser(
"~/research/data/scerevisiae/saccharomyces-files.txt"),
os.path.expanduser("~/bio/genomes"), cdna_dicts, 1, load_fxn)
align_dict = pickle.load(
file(
os.path.expanduser(
"~/research/data/scerevisiae/scer-ortholog-alignments.p"),
'r'))
(nal, spec_orf_list, protal) = align_dict["YBR177C"]
aligned_seqs = {}
for xi in range(len(spec_orf_list)):
(spec, orf) = spec_orf_list[xi]
gene = cdna_dicts[spec][orf]
prot = protal[xi]
aligned_gene = muscle.alignGeneFromProtein(gene, prot)
aligned_seqs[spec] = aligned_gene
print aligned_seqs
seq_dict = {'spar': 'ATGTCAGAAGTTTCGAAATGGCCAGCTATCAACCCGTTCCATTGGGGATACAATGGTACTGTTTCACATGTCGTCGGTGAAAATGGTTCCATCAAACTAAATTTAAAAGACAACAAGGAACAGGTTGAATTTGACGAGTTCGTTAACAAATATGTCCCAACGTTGAAGAATGGTGCTCAATTTAAATTGAGTCCTTACTTGTTCACAGGTATTTTGCAAACCCTGTACTTAAATGCTGCTGATTTCTCTAAGAAATTTCCTGTATTCTACGGCAGAGAAATTGTCAAATTCTCGGATAATGGAGTTTGTACCGCTGACTGGCTCATGGATTCCTGGAAGAAGGATTACAAACTCGATCAAAGTACTATGGGTTTCGATAAGAAAAAATTTGGTGAAGACGAGAAGGAGACGCATCCAGAAGGGTGGCCTCGTTTACAACCACGTACAAGGTATCTGAAGGATAATGAATTGGAAAATGTAAGGGAGGTTGATCTGCCCTTAGTAGTTATCCTACATGGTCTTGCTGGTGGTAGTCATGAGCCTATCATAAGATCTCTTGCTGAAAACCTCTCTCGG------AGTGGGAGATTTCAAGTGGTGGTACTAAATACTAGAGGCTGTGCACGTTCTAAAATTACAACCAGAAATTTATTTACGGCTTACCACACAATGGATATTCGTGAATTTTTGCAAAGAGAAAAGGAGAGATATCCAAATAGAAAATTATACGCTGTGGGATGCTCCTTCGGTGCTACGATGTTGGGAAACTATCTGGGAGAAGAAGGCGATAAATCTCCTTTATCTGCAGCTGCTACCCTGTGCAACCCTTGGGATCTTCTCCTTTCGGCACTTAGAATGACCGAGGATTGGTGGTCAAAGACTTTATTTTCCAAAAATATTGCCCAATTCTTAACAAGAACTGTTCAAGTTAATATGGGTGAACTAGGAGTTCCAAATGGCTCCCGTCCTGACCATCCTCCCACAGTCAAGAATCCATCTTACTATATGTTCACACCTGAAAATCTAATAAAGGCAAAAAGCTTTAAATCGAGTCTGGAATTTGATGAATTGTACACTGCGCCTGCTTTAGGCTTCCCAAATGCTATGGAATATTATAAAGCGGCCAGCTCAATAAGCAGAGTTGATACAATTCGGGTTCCTACTCTAGTTATCAATTCAAGGGATGATCCTGTTGTCGGCCCGGATCAA---CCTTACTCAATCGTGGAAAAAAATCCTCGTGTTTTGTATTGTAGAACCGACTTAGGAGGTCATTTAGCTTACCTAGATAAAGACAATAATTCGTGGGCTACCAAGGCGATTGCAGAATTCTTTACTAAGTTTGATGAATTAGTTGTA', \
'smik': 'ATGTCAGAAGTTTCGAAATGGCCAGCTATCAACCCATTCCATTGGGGATACAATGGTACTGTTTCGCATGTTGTCGGTGAAAATGGTTCCATGAAACTAGGTTTAAAAGATAACAAGGAACAGATTGAATTTGATCAGTTCGTTAACAAATATGTTCCAAGTTTGAAGAATGGTGCTCACTTCAAATTGAGTCCTTACTTGTTCACAGGTATTTTACAAACGTTGTACTTAAACGCTGCAGACTTCTCGAAGAAATTTCCTGTATTTTATGGCAGAGAAATTATCAAATTCTCCGATAATGGAGTTTGCACCGCTGATTGGGTTATGAGCTCCTGGAAGAGGGATTACAAACTCAATCAAAGTACCATGAGCTTTGATAAAAGCAAATTCGACGGAGACGAAAAAGCGACGCATCCAGAAGGATGGCCTCGTTTACAACCACGTACAAGATATTTGAAGGATAATGAGTTAGAGGAGCTCAGAGAAATTGAGCTCCCCTTAGTAGTCATTTTGCATGGACTTGCCGGTGGCAGTCATGAACCGATCATAAGATCTCTTGCTGAAAACCTGTCTCGC------AGCGGGAAATTTCAAGTGGTGGTGCTAAATACCAGAGGTTGTGCACGCTCCAAAATTACAACCAGGAACTTATTCACGGCTTACCACACAATGGATATCCGTGAATTTTTGCAAAGAGAAAATCAAAGACATCCAAACAGAAAGTTATACGCTGTAGGATGTTCTTTTGGTGCCACCATGTTGGGGAATTATCTCGGTGAAGAAGGTGATAAATCACCTTTATCTGCAGCTGCTACCTTATGCAATCCTTGGGACCTTCTCCTTTCAGCGCTTAGAATGACCGAGGATTGGTGGTCAAAAACTTTATTTTCCAAAAATATTGCACAGTTTTTAACAAGAACCGTTCAAGTTAACATGGGTGAACTAGGAGTCCCAAACGGCTCTCATCCCGACCATCCTCCTACAGTAAAAAATCCATCCTACTATATGTTCACCCCTGAAAATTTAATAAAGGCAAAACACTTCAAATCGAGTCTGGAATTCGATGAATTGTATACTGCACCTGCTTTAGGCTTTCCAAATGCAATGGAGTATTATAAAGCAGCTAGCTCAATAAACAGAGTTGCTACAATTAAGGTTCCTACTTTAGTTATCAATTCTAGAGATGATCCTGTTGTCGGCCCAGATCAG---CCTTATTCAATTGTAGAAAAAAACCCTCGTATTTTGTATTGCGGAACCGATTTAGGGGGCCATTTAGCCTACCTAGATAATGACAATAACTCATGGGCAACTAAGGCGATTGCAGAATTCTTTACTAAATTTGATCAACTGGTTGTA', \
'scas': 'ATGGCTTCACAATCAACATATCCACTCATTAAACCATGGAATTGGGGGTATCACGGAACCGTGACCCAAATTACCAGTAAGGAAGGTACTGTACTCATTCCATTAAAGGACAACAAAGAGGGTATTCCATTAGCAGAATTAGTTTCAAAGAATGTCCCTAGTTTAAAGGATGGTGCTAAGTTTGAGTTGAAACCTTTTTTATTCACTGGTATTTTACAAACTCTGTACCTTGGCGCAGCTGACTTTTCTAAGAAATTCCAAGTCTTTTATGGTAGAGAAATTGTGGAATTCTCAGATACTGGTGTATGTACTGCCGATTGGGTAATGCCATCTTGGAAGCAAAAATATAACTTTAATGAGAAAACATCAACTTTTGACAAGAAAGCATTCGACCTGGACGAAAAAGAAACACATCCAGACAATTGGCCTCGTTTGCAACCTCGTACCAGATACTTAAATGAAAAAGAAATGACGACTATCCACGAGGATGACAGACCATTGGTTGTTTGTTGTCATGGGTTAGCTGGTGGCTCTCACGAACCAATTATCAGATCATTGACTGAAAATCTATCTAAGGTTGGTAATGGGAAATTCCAAGTGGTTGTCCTAAATACTCGTGGCTGTGCACGTTCTAAGATTACTACTCGTAACCTATTTACTGCTTTCCATACTATGGATCTACGTGAATTTGTCAACAGAGAACACCAAAAACATCCTAACAGAAAGATTTATGCCGTTGGATTTTCATTCGGGGGTACAATGTTAGCAAATTATTTAGGAGAAGAAGGTGATAAAACTCCAATTGCATCTGCTGCAGTGTTATGTAACCCGTGGGATATGGTATTATCCGGTATGAAAACGAGAGATGATTTTTGGACAAGAACGCTATTTGCTAAGAATATTACAGATTTCTTGACTAGAATGGTTAAAGTTAATATGGCAGAATTGGAATCTCCAGATGGTTCTAAGCCTGATCACATCCCAACAGTGAAAAATCCATCTTATTATACATTTACCCAAGAAAATTTGGCAAAAGCCAAGGATTTTAAATTAATATCTGACTTTGATGACGTATTTACTGCACCTGCATTGGGTTTCAAAAACGCATTGGAGTACTACGCTGCAGCTGGGTCCATTAACAGACTACCTAATATTAAGATTCCTTTATTAGTTATCAATTCCACTGATGATCCAGTTGTTGGGCCGGATCCAATCCCAAACCATATCATAGATTCAAACAACCACCTACTGCTATGTGAAACCGATATCGGTGGCCATTTGGCATATTTGGATAAAAATAATGATTCATGGTCAACGAACCAAATCGCCAATTATTTCGACAAATTTGATGAAGTGGCATTA', \
'sbay': 'ATGTCAGAAGTTTCAAAGTGGCCAGCTATTAACCCATTTCATTGGGGGTACAACGGTACAGTTTCACATGTCGTTGGTGGTAATGGTTCTGTGAAGTTAAGCTTGAAGAGCGATAAGGAGCAAGTCGAGTTTGATACGTTTGTTAATAAATATGTCCCGATTCTGAAAAACGGGGCCCATTATAAACTAAGTCCCTACTTGTTCACAGGTATTTTACAAACCCTATACTTGAACGCTGCTGATTTCTCAAAGAAATTTCCCGTATTTTATGGTAGAGAAATCGTCAAGTTCTCGGATGACGGTGTCTGTACTGCTGATTGGGTCATGAACTCTTGGGAAAAGGAATATGATTTCGACCAAAAGACTATGAAATTTGATACGAAGAAGTTTGGCGACGACGAAAAGGCGACGCACCCAGAAGGATGGCCTCGTTTACAACCACGTACGAGGTACCTCAGGGACGAAGAGTTGGAAGAACAGAGAAAAGTAGATCTTCCCCTAGTTATCATCCTCCATGGTCTTGCCGGAGGCAGTCATGAACCAATCATAAGATCCCTAACTGAGAACTTGTCTCGTATCGGCAATGGGAGATTCCAAGTCGTGGTGCTAAACACGAGAGGCTGTGCACGTTCTAAAATCACCACTAGAAACCTATTCACAGCTTACCACACAATGGATATCCGTGAGTTCTTGCAAAGGGAAAAAGAAAGATATCCAAACAGAAAATTATACACTGTAGGGTGCTCTTTCGGGGCTACCATGTTAGCAAACTATTTGGGTGAAGAAGGTGACAAATCACCTGTATCTGCTGCTGTTACGTTATGTAATCCTTGGGATCTTCTTCTTTCGGCACTTAGAATGACTGAAGACTGGTGGTCAAAAACTTTGTTTTCTAAAAATATTGCCCAATTTTTAACAAGAACCGTTCAAGTTAACATGGGCGAATTAGGTGTTCCAAATGGCTCTCGTCCTGACCATACACCTACAGTTAAAAATCCATCTTACTATAAGTTCACACCTGAGAATTTGATGAAGGCAAAGCGCTTTAAGTCGAGTCTCGAATTCGATGAGCTGTACACTGCACCAGCTTTGGGCTTCCCGAATGCTATGGAATATTATAAATCAGCTAGTTCAATCAACAGGGCTGATAAAATCAAGGTTCCTACTTTAGTAATCAATTCTAGAGATGATCCTGTTGTTGGCCCAGACCAA---CCTTATTCATTTGTGGAGAAGAACCCTAATATACTATTCTGTAGAACCGACCTAGGTGGCCATTTAGCCTACCTAGATAGCAACAATGATTCGTGGGTTACAAAGGCGATTTCCGAGTTCTTGAATAAGTTTGAGGAGTTAGTGTTA',
'scer': 'ATGTCAGAAGTTTCCAAATGGCCAGCAATCAACCCATTCCATTGGGGATACAATGGTACAGTTTCGCATATTGTCGGTGAAAATGGTTCCATTAAACTCCATTTAAAAGACAACAAGGAGCAAGTTGATTTTGACGAGTTCGCTAACAAATATGTCCCAACGTTGAAGAATGGTGCCCAATTCAAATTGAGTCCTTACTTGTTCACAGGTATTTTGCAAACTTTGTACTTAGGTGCTGCTGATTTCTCTAAGAAATTTCCTGTATTCTACGGCAGGGAAATTGTCAAATTCTCGGATGGTGGAGTTTGCACCGCTGACTGGCTCATAGATTCATGGAAAAAGGATTATGAATTCGATCAAAGTACTACGAGCTTTGATAAAAAAAAATTTGATAAAGACGAGAAGGCGACACATCCAGAAGGATGGCCTCGTTTACAACCACGTACAAGGTACCTGAAAGATAATGAGTTGGAAGAACTACGGGAGGTTGATCTACCCCTAGTAGTTATTCTACATGGTCTTGCTGGTGGTAGTCATGAGCCGATTATAAGATCTCTTGCTGAAAACCTGTCTCGC------AGTGGGAGATTTCAAGTGGTCGTCCTAAATACCAGAGGTTGTGCACGTTCCAAAATTACCACCAGAAATTTATTTACAGCTTATCACACAATGGATATTCGCGAGTTTTTGCAAAGAGAAAAGCAAAGACATCCAGATAGAAAACTATACGCTGTGGGATGCTCTTTTGGTGCTACGATGCTGGCAAACTATCTGGGAGAAGAGGGCGATAAATCACCTTTATCCGCAGCTGCTACTTTGTGCAATCCTTGGGATCTTCTCCTTTCAGCAATTAGGATGAGCCAGGATTGGTGGTCAAGAACTTTATTTTCCAAAAATATTGCGCAATTCTTAACAAGAACCGTTCAGGTTAATATGGGTGAATTAGGAGTTCCAAATGGCTCTCTCCCCGATCATCCTCCCACAGTCAAGAATCCATCTTTCTATATGTTCACGCCTGAAAATCTAATAAAGGCAAAGAGCTTTAAATCGACCCGGGAATTTGATGAAGTGTACACTGCGCCTGCTTTAGGCTTCCCAAATGCTATGGAGTATTATAAAGCGGCCAGCTCAATAAACAGAGTTGATACAATTCGGGTTCCTACCCTTGTTATCAATTCCAGGGATGATCCTGTTGTCGGCCCAGATCAA---CCATACTCAATCGTGGAAAAGAATCCTCGTATTTTGTATTGTAGAACCGATTTAGGTGGTCATTTAGCTTACCTAGATAAAGACAACAACTCGTGGGCTACCAAGGCAATTGCAGAATTTTTCACTAAGTTTGATGAATTAGTCGTA'}
seq_labels = [x.name for x in sub_tree.leaves]
seqs = [seq_dict[k] for k in seq_labels]
# Run PAML
opts = paml.CodeML.FMutSel_F_options
opts["RateAncestor"] = "1"
cm = paml.CodeML("codon", opts)
cm.loadSequences(seqs, seq_labels, str(sub_tree))
cm.run()
cm.putBranchRatesOnTree(seq_labels, sub_tree, label="rate")
cm.putAncestralSequencesOnTree(seq_labels, sub_tree, label="sequence")
# Now remap the tree.
whole_node_dict = dict([(x.name, x) for x in whole_tree.nodes])
sub_node_dict = dict([(x.name, x) for x in sub_tree.nodes])
sub_names = [x.name for x in sub_tree.leaves]
#print whole_node_dict["scer"].getMostRecentCommonAncestor(whole_node_dict["smik"]).name
newick.tree.mapLabelsOntoSubtree(whole_tree, sub_tree)
for i in range(len(sub_names) - 1):
for j in range(i + 1, len(sub_names)):
s1 = sub_names[i]
s2 = sub_names[j]
sub_mrca = sub_node_dict[s1].getMostRecentCommonAncestor(
sub_node_dict[s2])
mrca = whole_node_dict[s1].getMostRecentCommonAncestor(
whole_node_dict[s2])
assert sub_mrca.name == mrca.name
shutil.rmtree(cm.tmpdir)
parser.add_option("-d", "--dict-out", dest="score_dict_fname", type="string", default=None, help="score dictionary output filename")
parser.add_option("-s", "--scores-out", dest="score_fname", type="string", default="vanilla", help="format of ID in FASTA entry")
parser.add_option("-p", "--pseudocount", dest="pseudocount", type="float", default=0.0, help="pseudocount to be added to all frequencies")
(options, args) = parser.parse_args()
in_fname = args[0]
info_outs = util.OutStreams(sys.stdout)
data_outs = util.OutStreams()
# Start up output
if not options.out_fname is None:
outf = file(options.out_fname, 'w')
data_outs.addStream(outf)
else:
data_outs.addStream(sys.stdout)
formatFxn = biofile.getIDFunction(options.format)
cdna_dict = biofile.readFASTADict(in_fname, formatFxn)
calc = Calculator()
calc.initializeFromSequences(cdna_dict.values(), options.pseudocount)
syn_dict = calc.getCodonSYNScores()
syn_opt_codons = []
for aa in translate.degenerateAAs():
codons = translate.getCodonsForAA(aa, rna=False)
best_syn_codon = sorted([(syn_dict[c],c) for c in codons])[-1][1]
syn_opt_codons.append(best_syn_codon)
data_outs.write("# Read {0}\n#{1:d} sequences, {2:d} codons, {3:d} nucleotides\n".format(in_fname, len(cdna_dict.keys()), int(sum(calc.codon_freq.values())), int(sum(calc.nucleotide_freq.values()))))
data_outs.write("# syn_scores = {0!s}\n".format(syn_dict))
data_outs.write("# SYN opt codons = {0!s}\n".format(sorted(syn_opt_codons)))
data_outs.write("{0!s}".format(calc))
if not options.score_dict_fname is None:
