def merge_results(self):
''' TODO: implement this
'''
assert isinstance(self.root_problem,SeppProblem)
'''Generate single extended alignment'''
fullExtendedAlignment = self.root_problem.get_children()[0].jobs["pplacer"].get_attribute("full_extended_alignment_object")
for pp in self.root_problem.get_children()[1:]:
extended_alignment = pp.jobs["pplacer"].get_attribute("full_extended_alignment_object")
fullExtendedAlignment.merge_in(extended_alignment,convert_to_string=True)
self.results = fullExtendedAlignment
mergeinput = []
'''Append main tree to merge input'''
mergeinput.append("%s;" %(self.root_problem.subtree.compose_newick(labels = True)))
jsons = []
for pp in self.root_problem.get_children():
assert isinstance(pp,SeppProblem)
if (pp.get_job_result_by_name("pplacer") is None):
continue
'''Append subset trees and json locations to merge input'''
mergeinput.append("%s;\n%s" %(pp.subtree.compose_newick(labels = True),
pp.get_job_result_by_name("pplacer")))
mergeinput.append("")
mergeinput.append("")
meregeinputstring = "\n".join(mergeinput)
mergeJsonJob = MergeJsonJob()
mergeJsonJob.setup(meregeinputstring,
self.get_output_filename("placement.json"))
mergeJsonJob.run()
def merge_results(self):
''' TODO: implement this
'''
assert isinstance(self.root_problem,SeppProblem)
'''Generate single extended alignment'''
fullExtendedAlignment = self.root_problem.get_children()[0].jobs["pplacer"].get_attribute("full_extended_alignment_object")
for pp in self.root_problem.get_children()[1:]:
extended_alignment = pp.jobs["pplacer"].get_attribute("full_extended_alignment_object")
fullExtendedAlignment.merge_in(extended_alignment,convert_to_string=True)
self.results = fullExtendedAlignment
mergeinput = []
'''Append main tree to merge input'''
mergeinput.append("%s;" %(self.root_problem.subtree.compose_newick(labels = True)))
jsons = []
for pp in self.root_problem.get_children():
assert isinstance(pp,SeppProblem)
if (pp.get_job_result_by_name("pplacer") is None):
continue
'''Append subset trees and json locations to merge input'''
mergeinput.append("%s;\n%s" %(pp.subtree.compose_newick(labels = True),
pp.get_job_result_by_name("pplacer")))
mergeinput.append("")
mergeinput.append("")
meregeinputstring = "\n".join(mergeinput)
mergeJsonJob = MergeJsonJob()
mergeJsonJob.setup(meregeinputstring,
self.get_output_filename("placement.json"))
mergeJsonJob.run()
def merge_results(self):
assert isinstance(self.root_problem, SeppProblem)
'''Generate single extended alignment'''
fullExtendedAlignment = ExtendedAlignment(
self.root_problem.fragments.keys())
# self.root_problem.get_children()[0].jobs[get_placement_job_name(0)]\
# .get_attribute("full_extended_alignment_object")
for pp in self.root_problem.get_children():
for i in range(0, self.root_problem.fragment_chunks):
extended_alignment = pp.jobs[
get_placement_job_name(i)].get_attribute(
"full_extended_alignment_object")
fullExtendedAlignment.merge_in(
extended_alignment, convert_to_string=True)
self.results = fullExtendedAlignment
mergeinput = []
'''Append main tree to merge input'''
mergeinput.append(
"%s;" % (self.root_problem.subtree.compose_newick(labels=True)))
for pp in self.root_problem.get_children():
assert isinstance(pp, SeppProblem)
for i in range(0, self.root_problem.fragment_chunks):
if (pp.get_job_result_by_name(
get_placement_job_name(i)) is None):
continue
'''Append subset trees and json locations to merge input'''
mergeinput.append(
"%s;\n%s" % (
pp.subtree.compose_newick(labels=True),
pp.get_job_result_by_name(get_placement_job_name(i))))
mergeinput.append("")
mergeinput.append("")
meregeinputstring = "\n".join(mergeinput)
mergeJsonJob = MergeJsonJob()
mergeJsonJob.setup(meregeinputstring,
self.get_output_filename("placement.json"))
mergeJsonJob.run()
def testMerge(self):
sys.argv = [sys.argv[0]]
stdindata = open(get_data_path("tmp/tempmerge")).read()
# write path of seppJsonMerger.jar into configuration
setattr(sepp.config.options(), 'jsonmerger', Namespace(
path=get_data_path("../../../tools/merge/seppJsonMerger.jar")))
mergeJsonJob = MergeJsonJob()
mergeJsonJob.setup(stdindata.replace(
'data/tmp/pplacer.extended',
os.path.dirname(get_data_path("tmp/tempmerge")) +
'/pplacer.extended'), get_data_path("tmp/mergedfile"))
mergeJsonJob.run()
def merge_results(self):
assert isinstance(self.root_problem, SeppProblem)
'''Generate single extended alignment'''
fullExtendedAlignment = ExtendedAlignment(
self.root_problem.fragments.keys())
# self.root_problem.get_children()[0].jobs[get_placement_job_name(0)]\
# .get_attribute("full_extended_alignment_object")
for pp in self.root_problem.get_children():
for i in range(0, self.root_problem.fragment_chunks):
extended_alignment = pp.jobs[get_placement_job_name(
i)].get_attribute("full_extended_alignment_object")
fullExtendedAlignment.merge_in(extended_alignment,
convert_to_string=True)
self.results = fullExtendedAlignment
mergeinput = []
'''Append main tree to merge input'''
mergeinput.append(
"%s;" % (self.root_problem.subtree.compose_newick(labels=True)))
for pp in self.root_problem.get_children():
assert isinstance(pp, SeppProblem)
for i in range(0, self.root_problem.fragment_chunks):
if (pp.get_job_result_by_name(get_placement_job_name(i)) is
None):
continue
'''Append subset trees and json locations to merge input'''
mergeinput.append(
"%s;\n%s" %
(pp.subtree.compose_newick(labels=True),
pp.get_job_result_by_name(get_placement_job_name(i))))
mergeinput.append("")
mergeinput.append("")
meregeinputstring = "\n".join(mergeinput)
mergeJsonJob = MergeJsonJob()
mergeJsonJob.setup(meregeinputstring,
self.get_output_filename("placement.json"))
mergeJsonJob.run()
def testMerge(self):
sys.argv = [sys.argv[0]]
stdindata = open("data/tmp/tempmerge").read()
mergeJsonJob = MergeJsonJob()
mergeJsonJob.setup(stdindata, "data/tmp/mergedfile")
mergeJsonJob.run()
def merge_results(self):
assert isinstance(self.root_problem, SeppProblem)
'''Generate single extended alignment'''
fullExtendedAlignment = ExtendedAlignment(
self.root_problem.fragments.keys())
# self.root_problem.get_children()[0].jobs[get_placement_job_name(0)]\
# .get_attribute("full_extended_alignment_object")
for pp in self.root_problem.get_children():
for i in range(0, self.root_problem.fragment_chunks):
extended_alignment = pp.jobs[get_placement_job_name(
i)].get_attribute("full_extended_alignment_object")
fullExtendedAlignment.merge_in(extended_alignment,
convert_to_string=True)
self.results = fullExtendedAlignment
# IF only one placement subset, no need to go to java
if len(self.root_problem.get_children()) == 1:
import json
mergeinput = []
for pp in self.root_problem.get_children():
assert isinstance(pp, SeppProblem)
for i in range(0, self.root_problem.fragment_chunks):
if (pp.get_job_result_by_name(get_placement_job_name(i)) is
None):
continue
'''Append subset trees and json locations to merge input'''
with open(
pp.get_job_result_by_name(
get_placement_job_name(i))) as f:
mergeinput.append(json.load(f))
_LOG.info(
"There are %d fragment chunks on a single placement subset"
% len(mergeinput))
result = mergeinput[0]
for i in range(1, len(mergeinput)):
result["placements"] = result["placements"] + mergeinput[i][
"placements"]
with open(self.get_output_filename("placement.json"), 'w') as f:
json.dump(result, f, sort_keys=True, indent=4)
else:
mergeinput = []
'''Append main tree to merge input'''
mergeinput.append(
"%s;" %
(self.root_problem.subtree.compose_newick(labels=True)))
for pp in self.root_problem.get_children():
assert isinstance(pp, SeppProblem)
for i in range(0, self.root_problem.fragment_chunks):
if (pp.get_job_result_by_name(get_placement_job_name(i)) is
None):
continue
'''Append subset trees and json locations to merge input'''
mergeinput.append(
"%s;\n%s" %
(pp.subtree.compose_newick(labels=True),
pp.get_job_result_by_name(get_placement_job_name(i))))
mergeinput.append("")
mergeinput.append("")
meregeinputstring = "\n".join(mergeinput)
_LOG.debug(mergeinput)
mergeJsonJob = MergeJsonJob()
mergeJsonJob.setup(meregeinputstring,
self.get_output_filename("placement.json"))
mergeJsonJob.run()
