def getAge(start,end,species,mytree,margin=50):
from StringIO import StringIO
from Bio import Phylo,AlignIO
from treetime import TreeAnc
myfasta=''
for spec in species.keys():
myfasta=myfasta+'>'+spec+'\nA'+str(''.join(species[spec][(start-margin-analysis_start):(end+margin-analysis_start)]))+'A\n'
my_aln = AlignIO.read(StringIO(myfasta), 'fasta')
ta = TreeAnc(tree=mytree, aln=my_aln, gtr='JC69')
ta.infer_ancestral_sequences(method = 'ml', infer_gtr=True, marginal=False)
seq=ta.get_reconstructed_alignment()
print 'ancestral seq inferred'
# for i in range(len(seq)):
# print seq[i].id+' '+seq[i].seq[(margin+1):(margin+1+end-start)]
Phylo.write(ta.tree, home+'/Annotation/Conservation/SEqAlign/test_'+id+'.nwk', 'newick')
mytreeAnnot=Phylo.read(home+'/Annotation/Conservation/SEqAlign/test_'+id+'.nwk', "newick")
AncestralSeq={}
for y in seq:
AncestralSeq[y.id]=str(y.seq[(margin+1):(margin+1+end-start)])
AppearedInCommonAncestor=['human','chimp','gorilla','orangutan','macaque','marmoset','tarsier','lemur','treeShrew','mouse','cow','elephant','opossum','platypus','chicken','frog','zebrafish','lamprey']
AppearedInCommonAncestorScientific=['hg19','panTro2','gorGor1','ponAbe2','rheMac2','calJac1','tarSyr1','micMur1','tupBel1','mm9','bosTau4','loxAfr3','monDom5','ornAna1','galGal3','xenTro2','danRer6','petMar1']
CommonAncestor=['hg19','NODE_0000044','NODE_0000043','NODE_0000042','NODE_0000040','NODE_0000039','NODE_0000038','NODE_0000036','NODE_0000035','NODE_0000028','NODE_0000018','NODE_0000013','NODE_0000011','NODE_0000010','NODE_0000007','NODE_0000006','NODE_0000001','NODE_0000000']
CommonAncestorName=['Humans','Chimpanzees','Gorillas','Orangutans','Gibbons','Monkeys','Tarsiers','Lemurs','Shrews','Rodents','Boroeutheria','Afroeutheria','Marsupials','Monotremes','Sauropsids','Amphibians','Vertebrates','Chordates']
PhyloGeneticDistance=[ mytreeAnnot.distance('hg19', CommonAncestor[i]) for i in range(0,len(CommonAncestor))]
verbose=4,
fill_overhangs=not params.keep_overhangs)
treeanc.infer_ancestral_sequences('ml',
infer_gtr=params.infer_gtr,
marginal=params.marginal)
###########################################################################
### OUTPUT and saving of results
###########################################################################
if params.infer_gtr:
print('\nInferred GTR model:')
print(treeanc.gtr)
outaln_name = '.'.join(
params.aln.split('/')[-1].split('.')[:-1]) + '_ancestral.fasta'
AlignIO.write(treeanc.get_reconstructed_alignment(), outaln_name, 'fasta')
# decorate tree with inferred mutations
terminal_count = 0
for n in treeanc.tree.find_clades():
if n.up is None:
continue
n.confidence = None
if n.is_terminal() and len(n.name) > 40:
n.name = n.name[:35] + '_%03d' % terminal_count
terminal_count += 1
if len(n.mutations):
n.comment = '&mutations="' + '_'.join(
[a + str(pos) + d for (a, pos, d) in n.mutations]) + '"'
# write tree to file
