def build_scaffolds(adjacencies, perm_container, debug_output,
correct_distances):
"""
Assembles scaffolds wrt to inferred adjacencies
"""
if debug_output:
logger.debug("Building scaffolds")
contigs, contig_index = _make_contigs(perm_container)
scaffolds = _extend_scaffolds(adjacencies, contigs, contig_index,
correct_distances)
num_contigs = sum([len(s.contigs) for s in scaffolds])
logger.debug("%d contigs were joined into %d scaffolds", num_contigs,
len(scaffolds))
if debugger.debugging and debug_output:
links_out = os.path.join(debugger.debug_dir, "scaffolder.links")
output_links(scaffolds, links_out)
contigs_out = os.path.join(debugger.debug_dir,
"scaffolder_contigs.txt")
output_permutations(perm_container.target_perms, contigs_out)
perms_out = os.path.join(debugger.debug_dir,
"scaffolder_scaffolds.txt")
output_scaffolds_premutations(scaffolds, perms_out)
return scaffolds
def merge_scaffolds(big_scaffolds, small_scaffolds, perm_container, rearrange):
"""
Merges scaffold sets from different iterations. If rearrangements are allowed,
tries to keep some small-scale rearrangements from the weaker scaffold set.
"""
logger.info("Merging two iterations")
#synchronizing scaffolds to the same permutations
big_updated = _update_scaffolds(big_scaffolds, perm_container)
small_updated = _update_scaffolds(small_scaffolds, perm_container)
if rearrange:
projector = RearrangementProjector(big_updated, small_updated, True)
new_adj = projector.project()
big_rearranged = build_scaffolds(new_adj, perm_container, False, False)
else:
big_rearranged = big_updated
merged_scf = _merge_scaffolds(big_rearranged, small_updated)
merged_scf = _merge_consecutive_contigs(merged_scf)
if debugger.debugging:
links_out = os.path.join(debugger.debug_dir, "merged.links")
output_links(merged_scf, links_out)
perms_out = os.path.join(debugger.debug_dir, "merged_scaffolds.txt")
output_scaffolds_premutations(merged_scf, perms_out)
return merged_scf
def merge_scaffolds(big_scaffolds, small_scaffolds, perm_container, rearrange, ancestral = False):
"""
Merges scaffold sets from different iterations. If rearrangements are allowed,
tries to keep some small-scale rearrangements from the weaker scaffold set.
"""
logger.info("Merging two iterations")
#synchronizing scaffolds to the same permutations
big_updated = _update_scaffolds(big_scaffolds, perm_container, ancestral=ancestral)
small_updated = _update_scaffolds(small_scaffolds, perm_container, ancestral=ancestral)
if rearrange:
projector = RearrangementProjector(big_updated, small_updated, True)
new_adj = projector.project()
big_rearranged = build_scaffolds(new_adj, perm_container, False, False, ancestral=ancestral)
else:
big_rearranged = big_updated
merged_scf = _merge_scaffolds(big_rearranged, small_updated)
merged_scf = _merge_consecutive_contigs(merged_scf)
if debugger.debugging:
links_out = os.path.join(debugger.debug_dir, "merged.links")
output_links(merged_scf, links_out)
perms_out = os.path.join(debugger.debug_dir, "merged_scaffolds.txt")
output_scaffolds_premutations(merged_scf, perms_out)
return merged_scf
def build_scaffolds(adjacencies, perm_container, debug_output=True,
correct_distances=True, ancestral=False):
"""
Assembles scaffolds wrt to inferred adjacencies
"""
if debug_output:
logger.info("Building scaffolds")
if not ancestral:
contigs, contig_index = _make_contigs(perm_container)
else:
contigs, contig_index = _make_contigs(perm_container, ancestral=ancestral)
scaffolds = _extend_scaffolds(adjacencies, contigs, contig_index,
correct_distances)
num_contigs = sum(map(lambda s: len(s.contigs), scaffolds))
logger.debug("{0} contigs were joined into {1} scaffolds"
.format(num_contigs, len(scaffolds)))
if debugger.debugging and debug_output:
links_out = os.path.join(debugger.debug_dir, "scaffolder.links")
output_links(scaffolds, links_out)
contigs_out = os.path.join(debugger.debug_dir, "scaffolder_contigs.txt")
output_permutations(perm_container.target_perms, contigs_out)
perms_out = os.path.join(debugger.debug_dir, "scaffolder_scaffolds.txt")
output_scaffolds_premutations(scaffolds, perms_out)
return scaffolds
def build_scaffolds(adjacencies,
perm_container,
debug_output=True,
correct_distances=True,
ancestral=False):
"""
Assembles scaffolds wrt to inferred adjacencies
"""
if debug_output:
logger.info("Building scaffolds")
if not ancestral:
contigs, contig_index = _make_contigs(perm_container)
else:
contigs, contig_index = _make_contigs(perm_container,
ancestral=ancestral)
scaffolds = _extend_scaffolds(adjacencies, contigs, contig_index,
correct_distances)
num_contigs = sum(map(lambda s: len(s.contigs), scaffolds))
logger.debug("{0} contigs were joined into {1} scaffolds".format(
num_contigs, len(scaffolds)))
if debugger.debugging and debug_output:
links_out = os.path.join(debugger.debug_dir, "scaffolder.links")
output_links(scaffolds, links_out)
contigs_out = os.path.join(debugger.debug_dir,
"scaffolder_contigs.txt")
output_permutations(perm_container.target_perms, contigs_out)
perms_out = os.path.join(debugger.debug_dir,
"scaffolder_scaffolds.txt")
output_scaffolds_premutations(scaffolds, perms_out)
return scaffolds