def infer_tree_from_leaves(self, region, in_tree, leafseqs, naive_seq):
if 'dendropy' not in sys.modules:
import dendropy
dendropy = sys.modules['dendropy']
taxon_namespace = dendropy.TaxonNamespace()
with tempfile.NamedTemporaryFile() as tmpfile:
tmpfile.write('>%s\n%s\n' % ('naive', naive_seq))
for iseq in range(len(leafseqs)):
tmpfile.write(
'>t%s\n%s\n' % (iseq + 1, leafseqs[iseq])
) # NOTE the order of the leaves/names is checked when reading bppseqgen output
tmpfile.flush() # BEWARE if you forget this you are f****d
with open(os.devnull, 'w') as fnull:
out_tree = subprocess.check_output('./bin/FastTree -gtr -nt ' +
tmpfile.name,
shell=True,
stderr=fnull)
out_dtree = dendropy.Tree.get_from_string(
out_tree, 'newick', taxon_namespace=taxon_namespace)
out_dtree.reroot_at_node(
out_dtree.find_node_with_taxon_label('naive'),
update_bipartitions=True)
out_tree = out_dtree.as_string(schema='newick',
suppress_rooting=True)
in_height = treegenerator.get_mean_height(in_tree)
out_height = treegenerator.get_mean_height(out_tree)
base_width = 100
print ' %s trees:' % ('full sequence' if region == 'all' else region)
print ' %s' % utils.color('blue', 'input:')
print treegenerator.get_ascii_tree(in_tree,
extra_str=' ',
width=base_width)
print ' %s' % utils.color('blue', 'output:')
print treegenerator.get_ascii_tree(out_tree,
extra_str=' ',
width=int(base_width * out_height /
in_height))
in_dtree = dendropy.Tree.get_from_string(
in_tree, 'newick', taxon_namespace=taxon_namespace)
if self.args.debug:
print ' heights: %.3f %.3f' % (in_height,
out_height)
print ' symmetric difference: %d' % dendropy.calculate.treecompare.symmetric_difference(
in_dtree, out_dtree)
print ' euclidean distance: %f' % dendropy.calculate.treecompare.euclidean_distance(
in_dtree, out_dtree)
print ' r-f distance: %f' % dendropy.calculate.treecompare.robinson_foulds_distance(
in_dtree, out_dtree)
def infer_tree_from_leaves(self, region, in_tree, leafseqs):
with tempfile.NamedTemporaryFile() as tmpfile:
for iseq in range(len(leafseqs)):
tmpfile.write(
'>t%s\n%s\n' % (iseq + 1, leafseqs[iseq])
) # NOTE the order of the leaves/names is checked when reading bppseqgen output
tmpfile.flush() # BEWARE if you forget this you are f****d
with open(os.devnull, 'w') as fnull:
out_tree = subprocess.check_output('./bin/FastTree -gtr -nt ' +
tmpfile.name,
shell=True,
stderr=fnull)
in_height = treegenerator.get_mean_height(in_tree)
out_height = treegenerator.get_mean_height(out_tree)
base_width = 100
print ' %s trees: input/output' % region
print treegenerator.get_ascii_tree(in_tree,
extra_str=' ',
width=base_width)
print treegenerator.get_ascii_tree(out_tree,
extra_str=' ',
width=int(base_width * out_height /
in_height))
if 'dendropy' not in sys.modules:
import dendropy
in_dtree = sys.modules['dendropy'].Tree.get_from_string(
in_tree, 'newick')
out_dtree = sys.modules['dendropy'].Tree.get_from_string(
out_tree, 'newick')
if self.args.debug:
print ' heights: %.3f %.3f' % (in_height,
out_height)
print ' symmetric difference: %d' % in_dtree.symmetric_difference(
out_dtree)
print ' euclidean distance: %f' % in_dtree.euclidean_distance(
out_dtree)
print ' r-f distance: %f' % in_dtree.robinson_foulds_distance(
out_dtree)
def add_mutants(self, reco_event, irandom):
if self.args.mutation_multiplier is not None and self.args.mutation_multiplier == 0.: # some of the stuff below fails if mut mult is actually 0.
reco_event.final_seqs.append(
reco_event.recombined_seq) # set final sequnce in reco_event
reco_event.indelfos = [
indelutils.get_empty_indel()
for _ in range(len(reco_event.final_seqs))
]
return
# When generating trees, each tree's number of leaves and total depth are chosen from the specified distributions (a.t.m., by default n-leaves is from a geometric/zipf, and depth is from data)
# This chosen depth corresponds to the sequence-wide mutation frequency.
# In order to account for varying mutation rates in v, d, and j we simulate these regions separately, by appropriately rescaling the tree for each region.
# i.e.: here we get the sequence-wide mute freq from the tree, and rescale it by the repertoire-wide ratios from data (which are stored in the tree file).
# looks like e.g.: (t2:0.003751736951,t1:0.003751736951):0.001248262937;v:0.98,d:1.8,j:0.87, where the newick trees has branch lengths corresponding to the whole sequence (i.e. the weighted mean of v, d, and j)
# NOTE a.t.m (and probably permanently) the mean branch lengths for each region are the same for all the trees in the file, I just don't have a better place to put them while I'm passing from TreeGenerator to here than at the end of each line in the file
treefostr = self.treeinfo[random.randint(
0,
len(self.treeinfo) - 1
)] # per-region mutation info is tacked on after the tree... sigh. kind of hackey but works ok.
assert treefostr.count(';') == 1
isplit = treefostr.find(';') + 1
chosen_tree = treefostr[:isplit] # includes semi-colon
mutefo = [rstr for rstr in treefostr[isplit:].split(',')]
mean_total_height = treegenerator.get_mean_height(chosen_tree)
regional_heights = {
} # per-region height, including <self.args.mutation_multiplier>
for tmpstr in mutefo:
region, ratio = tmpstr.split(':')
assert region in utils.regions
ratio = float(ratio)
if self.args.mutation_multiplier is not None: # multiply the branch lengths by some factor
ratio *= self.args.mutation_multiplier
regional_heights[region] = mean_total_height * ratio
scaled_trees = {
r: treegenerator.rescale_tree(chosen_tree, regional_heights[r])
for r in utils.regions
}
if self.args.debug:
print ' chose tree with total height %f' % treegenerator.get_mean_height(
chosen_tree)
print ' regional trees rescaled to heights: %s' % (' '.join([
'%s %.3f (expected %.3f)' %
(region, treegenerator.get_mean_height(
scaled_trees[region]), regional_heights[region])
for region in utils.regions
]))
print treegenerator.get_ascii_tree(chosen_tree, extra_str=' ')
n_leaves = treegenerator.get_n_leaves(chosen_tree)
cmdfos = []
for region in utils.regions:
simstr = reco_event.eroded_seqs[region]
if region == 'd':
simstr = reco_event.insertions[
'vd'] + simstr + reco_event.insertions['dj']
cmdfos.append(
self.prepare_bppseqgen(simstr,
scaled_trees[region],
n_leaves,
reco_event.genes[region],
reco_event,
seed=irandom))
utils.run_cmds(
[cfo for cfo in cmdfos if cfo is not None],
sleep=False) # shenanigan is to handle zero-length regional seqs
mseqs = {}
for ireg in range(
len(utils.regions)
): # NOTE kind of sketchy just using index in <utils.regions> (although it just depends on the loop immediately above a.t.m.)
if cmdfos[ireg] is None:
mseqs[utils.regions[ireg]] = [
'' for _ in range(n_leaves)
] # return an empty string for each leaf node
else:
mseqs[utils.regions[ireg]] = self.read_bppseqgen_output(
cmdfos[ireg], n_leaves)
assert len(reco_event.final_seqs) == 0
for iseq in range(n_leaves):
seq = mseqs['v'][iseq] + mseqs['d'][iseq] + mseqs['j'][iseq]
seq = reco_event.revert_conserved_codons(
seq, debug=self.args.debug
) # if mutation screwed up the conserved codons, just switch 'em back to what they were to start with
reco_event.final_seqs.append(
seq) # set final sequnce in reco_event
reco_event.final_codon_positions.append(
copy.deepcopy(reco_event.post_erosion_codon_positions)
) # separate codon positions for each sequence, because of shm indels
self.add_shm_indels(reco_event)
reco_event.setline(
irandom
) # set the line here because we use it when checking tree simulation, and want to make sure the uids are always set at the same point in the workflow
self.check_tree_simulation(mean_total_height, regional_heights,
scaled_trees, mseqs, reco_event)
if self.args.debug:
utils.print_reco_event(reco_event.line, extra_str=' ')