def merge_subalignments(self):
'''
Merge alignment subset extended alignments to get one extended
alignment for current placement subset.
'''
pp = self.placement_problem
_LOG.info("Merging sub-alignments for placement problem : %s." %
(pp.label))
''' First find fragments assigned to this placement problem'''
pp.fragments = pp.parent.fragments.get_soft_sub_alignment([])
for ap in pp.get_children():
pp.fragments.seq_names |= set(ap.fragments)
''' Then, gather a list of all alignments relevant to this placement
subset'''
fragfilesperap = dict()
for ap in pp.children:
assert isinstance(ap, SeppProblem)
''' Get all fragment chunk alignments for this alignment subset'''
aligned_files = [fp.get_job_result_by_name('hmmalign') for
fp in ap.children]
fragfilesperap[ap] = aligned_files
''' Now, build an extended alignment *per each fragment chunk*.
Simply merge all hmmalign results for fragment chunk numbered i'''
extendedAlignments = []
for i in range(0, self.root_problem.fragment_chunks):
extendedAlignment = ExtendedAlignment(pp.fragments.seq_names)
for ap in pp.children:
# _LOG.debug("Merging fragment chunks for subalignment : %s."
# %(ap.label))
if fragfilesperap[ap][i]:
ap_alg = ap.read_extendend_alignment_and_relabel_columns(
ap.jobs["hmmbuild"].infile, [fragfilesperap[ap][i]])
else:
ap_alg = ap.read_extendend_alignment_and_relabel_columns(
ap.jobs["hmmbuild"].infile, [])
_LOG.debug(
("Merging alignment subset into placement subset for "
"chunk %d: %s.") % (i, ap.label))
extendedAlignment.merge_in(ap_alg, convert_to_string=False)
'''Extended alignmnts have all fragments. remove the ones that
don't belong to thsi chunk'''
extendedAlignment.remove_missing_fragments()
extendedAlignment.from_bytearray_to_string()
extendedAlignments.append(extendedAlignment)
return extendedAlignments
def merge_subalignments(self):
'''
Merge alignment subset extended alignments to get one extended
alignment for current placement subset.
'''
pp = self.placement_problem
_LOG.info("Merging sub-alignments for placement problem : %s." %
(pp.label))
''' First find fragments assigned to this placement problem'''
pp.fragments = pp.parent.fragments.get_soft_sub_alignment([])
for ap in pp.get_children():
pp.fragments.seq_names |= set(ap.fragments)
''' Then, gather a list of all alignments relevant to this placement
subset'''
fragfilesperap = dict()
for ap in pp.children:
assert isinstance(ap, SeppProblem)
''' Get all fragment chunk alignments for this alignment subset'''
aligned_files = [
fp.get_job_result_by_name('hmmalign') for fp in ap.children
]
fragfilesperap[ap] = aligned_files
''' Now, build an extended alignment *per each fragment chunk*.
Simply merge all hmmalign results for fragment chunk numbered i'''
extendedAlignments = []
for i in range(0, self.root_problem.fragment_chunks):
extendedAlignment = ExtendedAlignment(pp.fragments.seq_names)
for ap in pp.children:
# _LOG.debug("Merging fragment chunks for subalignment : %s."
# %(ap.label))
if fragfilesperap[ap][i]:
ap_alg = ap.read_extendend_alignment_and_relabel_columns(
ap.jobs["hmmbuild"].infile, [fragfilesperap[ap][i]])
else:
ap_alg = ap.read_extendend_alignment_and_relabel_columns(
ap.jobs["hmmbuild"].infile, [])
_LOG.debug(
("Merging alignment subset into placement subset for "
"chunk %d: %s.") % (i, ap.label))
extendedAlignment.merge_in(ap_alg, convert_to_string=False)
'''Extended alignmnts have all fragments. remove the ones that
don't belong to thsi chunk'''
extendedAlignment.remove_missing_fragments()
extendedAlignment.from_bytearray_to_string()
extendedAlignments.append(extendedAlignment)
return extendedAlignments
