def main(ddir, rrange = None):
read_parameters(ddir)
tf = open("%s/tree" % (ddir))
t = newickToTree(tf.read())
root = "N1"
parent, children = findParentsAndChildren(t, root)
treestr = rootedTreeToStr(parent, children, root)
open("%s/tree.full" % (ddir), "w").write(treestr)
evidence_cpds = read_evidence_cpds("%s/%s" % (ddir, common.CPD_DIR))
internal_cpds = read_internal_cpds("%s/%s" % (ddir, common.TREE_CPD_FILE))
ef = open("%s/evidence" % (ddir))
evidence = read_evidence(ef)
model, observed_species, ancestors = build_model(t, evidence_cpds, internal_cpds)
naive_model, spec2, anc2 = build_naive_model(t, evidence_cpds)
blast_model, spec3, anc3 = build_blast_model(t, evidence_cpds, internal_cpds)
gtg_model, spec4, anc4 = build_gtg_model(t, evidence_cpds, internal_cpds)
complete_evidence(evidence, observed_species)
# compute posteriors
of = open("%s/reaction-scores" % (ddir), "w")
of.write("#Generated by \"%s\" on %s\n" % (" ".join(sys.argv), datetime.datetime.now()))
if rrange != None:
of.write("#Reaction range: %s\n" % (rrange))
compute_reaction_scores(model, naive_model,
blast_model, gtg_model, evidence,
observed_species, ancestors, of, rrange)
def main(ddir, rrange=None):
read_parameters(ddir)
tf = open("%s/tree" % (ddir))
t = newickToTree(tf.read())
root = "N1"
parent, children = findParentsAndChildren(t, root)
treestr = rootedTreeToStr(parent, children, root)
open("%s/tree.full" % (ddir), "w").write(treestr)
evidence_cpds = read_evidence_cpds("%s/%s" % (ddir, common.CPD_DIR))
internal_cpds = read_internal_cpds("%s/%s" % (ddir, common.TREE_CPD_FILE))
ef = open("%s/evidence" % (ddir))
evidence = read_evidence(ef)
model, observed_species, ancestors = build_model(t, evidence_cpds,
internal_cpds)
naive_model, spec2, anc2 = build_naive_model(t, evidence_cpds)
blast_model, spec3, anc3 = build_blast_model(t, evidence_cpds,
internal_cpds)
gtg_model, spec4, anc4 = build_gtg_model(t, evidence_cpds, internal_cpds)
complete_evidence(evidence, observed_species)
# compute posteriors
of = open("%s/reaction-scores" % (ddir), "w")
of.write("#Generated by \"%s\" on %s\n" %
(" ".join(sys.argv), datetime.datetime.now()))
if rrange != None:
of.write("#Reaction range: %s\n" % (rrange))
compute_reaction_scores(model, naive_model, blast_model, gtg_model,
evidence, observed_species, ancestors, of, rrange)
def read_tree(fn):
return tree.newickToTree(open(fn).read())
def read_tree(fn):
return tree.newickToTree(open(fn).read())