def is_fragmented_ref_fake_translocation(align1, align2, ref_lens):
# Check whether translocation is caused by fragmented reference and thus should be marked Fake misassembly
# Return inconsistency value if translocation is fake or None if translocation is real
# !!! it is assumed that align1.ref != align2.ref
# assert align1.ref != align2.ref, "Internal QUAST bug: is_fragmented_ref_fake_translocation() " \
# "should be called only if align1.ref != align2.ref"
if align1.ref == align2.ref:
return False
if qconfig.check_for_fragmented_ref:
if qconfig.is_combined_ref and not is_same_reference(align1.ref, align2.ref):
return False
if all([d <= qconfig.fragmented_max_indent for d in __get_border_gaps(align1, align2, ref_lens)]):
return True
return False
def get_score(score, aligns, ref_lens, is_cyclic, uncovered_len, seq, region_struct_variations, penalties):
if len(aligns) > 1:
align1, align2 = aligns[-2], aligns[-1]
is_fake_translocation = is_fragmented_ref_fake_translocation(align1, align2, ref_lens)
overlaped_len = max(0, align1.end() - align2.start() + 1)
if len(aligns) > 2: # does not affect score and uncovered but it is important for further checking on set correctness
exclude_internal_overlaps(aligns[-3], align1)
reduced_len = exclude_internal_overlaps(align1, align2) # reduced_len is for align1 only
# check whether the set is still correct, i.e both alignments are rather large
if min(align1.len2, align2.len2) < max(qconfig.min_cluster, qconfig.min_alignment):
return None, None
added_len = get_added_len(aligns, aligns[-1])
uncovered_len -= (added_len - reduced_len)
score += score_single_align(align2, ctg_len=added_len) - score_single_align(align1, ctg_len=reduced_len)
is_extensive_misassembly, aux_data = is_misassembly(align1, align2, seq, ref_lens, is_cyclic, region_struct_variations,
is_fake_translocation)
if is_extensive_misassembly:
misassembly_penalty = penalties['extensive']
if align1.ref != align2.ref:
if qconfig.is_combined_ref and not is_same_reference(align1.ref, align2.ref):
misassembly = Misassembly.INTERSPECTRANSLOCATION
else:
misassembly = Misassembly.TRANSLOCATION
elif abs(aux_data["inconsistency"]) > qconfig.extensive_misassembly_threshold:
misassembly = Misassembly.RELOCATION
score -= float(abs(aux_data["inconsistency"])) / ref_lens[align1.ref]
else:
misassembly = Misassembly.INVERSION
score -= misassembly - Misassembly.INVERSION
elif aux_data['is_sv']:
misassembly_penalty = 0
elif abs(aux_data['inconsistency']) > qconfig.MAX_INDEL_LENGTH and not aux_data['is_scaffold_gap']:
misassembly_penalty = penalties['local']
elif aux_data['is_scaffold_gap']:
misassembly_penalty = penalties['scaffold']
else:
misassembly_penalty = 0
overlap_penalty = min(overlaped_len * penalties['overlap_multiplier'], misassembly_penalty)
score -= (misassembly_penalty + overlap_penalty)
else:
score += score_single_align(aligns[-1])
uncovered_len -= aligns[-1].len2
return score, uncovered_len
def process_misassembled_contig(sorted_aligns, cyclic, aligned_lengths, region_misassemblies, ref_lens, ref_aligns,
ref_features, contig_seq, references_misassemblies, region_struct_variations,
misassemblies_matched_sv, ca_output, is_ambiguous=False):
misassembly_internal_overlap = 0
prev_align = sorted_aligns[0]
cur_aligned_length = prev_align.len2
is_misassembled = False
contig_is_printed = False
indels_info = IndelsInfo()
contig_aligned_length = 0 # for internal debugging purposes
for i in range(len(sorted_aligns) - 1):
next_align = sorted_aligns[i + 1]
is_fake_translocation = is_fragmented_ref_fake_translocation(prev_align, next_align, ref_lens)
cur_aligned_length -= exclude_internal_overlaps(prev_align, next_align, i, ca_output)
is_extensive_misassembly, aux_data = is_misassembly(prev_align, next_align, contig_seq, ref_lens,
cyclic, region_struct_variations, is_fake_translocation)
inconsistency = aux_data["inconsistency"]
distance_on_contig = aux_data["distance_on_contig"]
misassembly_internal_overlap += aux_data["misassembly_internal_overlap"]
cyclic_moment = aux_data["cyclic_moment"]
ca_output.icarus_out_f.write(prev_align.icarus_report_str() + '\n')
ca_output.stdout_f.write('\t\t\tReal Alignment %d: %s\n' % (i+1, str(prev_align)))
ref_aligns.setdefault(prev_align.ref, []).append(prev_align)
ca_output.coords_filtered_f.write(str(prev_align) + '\n')
if aux_data["is_sv"]:
ca_output.stdout_f.write('\t\t\t Not a misassembly (structural variation of the genome) between these two alignments\n')
ca_output.icarus_out_f.write('fake: not a misassembly (structural variation of the genome)\n')
misassemblies_matched_sv += 1
elif aux_data["is_scaffold_gap"] and abs(inconsistency) > qconfig.extensive_misassembly_threshold:
ca_output.stdout_f.write('\t\t\t Incorrectly estimated size of scaffold gap between these two alignments: ')
ca_output.stdout_f.write('gap length difference = ' + str(inconsistency) + '\n')
region_misassemblies.append(Misassembly.SCAFFOLD_GAP)
ca_output.icarus_out_f.write('fake: scaffold gap size wrong estimation' + '\n')
elif is_extensive_misassembly:
is_misassembled = True
aligned_lengths.append(cur_aligned_length)
contig_aligned_length += cur_aligned_length
cur_aligned_length = 0
if not contig_is_printed:
ca_output.misassembly_f.write(prev_align.contig + '\n')
contig_is_printed = True
ca_output.misassembly_f.write('Extensive misassembly (')
ca_output.stdout_f.write('\t\t\t Extensive misassembly (')
if prev_align.ref != next_align.ref: # it is not a Fake translocation, because is_extensive_misassembly is True
if qconfig.is_combined_ref and \
not is_same_reference(prev_align.ref, next_align.ref): # if chromosomes from different references
region_misassemblies.append(Misassembly.INTERSPECTRANSLOCATION)
ref1, ref2 = get_ref_by_chromosome(prev_align.ref), get_ref_by_chromosome(next_align.ref)
references_misassemblies[ref1][ref2] += 1
references_misassemblies[ref2][ref1] += 1
ca_output.stdout_f.write('interspecies translocation')
ca_output.misassembly_f.write('interspecies translocation')
ca_output.icarus_out_f.write('interspecies translocation')
else:
region_misassemblies.append(Misassembly.TRANSLOCATION)
ca_output.stdout_f.write('translocation')
ca_output.misassembly_f.write('translocation')
ca_output.icarus_out_f.write('translocation')
elif abs(inconsistency) > qconfig.extensive_misassembly_threshold:
region_misassemblies.append(Misassembly.RELOCATION)
msg = 'relocation, inconsistency = ' + str(inconsistency) + \
(' [linear representation of circular genome]' if cyclic_moment else '')
ca_output.stdout_f.write(msg)
ca_output.misassembly_f.write(msg)
ca_output.icarus_out_f.write(msg)
else: #if strand1 != strand2:
region_misassemblies.append(Misassembly.INVERSION)
ca_output.stdout_f.write('inversion')
ca_output.misassembly_f.write('inversion')
ca_output.icarus_out_f.write('inversion')
ca_output.stdout_f.write(') between these two alignments\n')
ca_output.misassembly_f.write(') between %s %s and %s %s' % (prev_align.s2, prev_align.e2, next_align.s2, next_align.e2) + '\n')
ca_output.icarus_out_f.write('\n')
ref_features.setdefault(prev_align.ref, {})[prev_align.e1] = 'M'
ref_features.setdefault(next_align.ref, {})[next_align.e1] = 'M'
else:
reason_msg = "" + (" [linear representation of circular genome]" if cyclic_moment else "") + \
(" [fragmentation of reference genome]" if prev_align.ref != next_align.ref else "")
if inconsistency == 0 and cyclic_moment:
ca_output.stdout_f.write('\t\t\t Not a misassembly' + reason_msg + ' between these two alignments\n')
ca_output.icarus_out_f.write('fake: not a misassembly' + reason_msg + '\n')
elif inconsistency == 0 and prev_align.ref != next_align.ref: # is_fragmented_ref_fake_translocation is True, because is_extensive_misassembly is False
ca_output.stdout_f.write('\t\t\t Not a misassembly' + reason_msg + ' between these two alignments\n')
region_misassemblies.append(Misassembly.FRAGMENTED)
ca_output.icarus_out_f.write('fake: not a misassembly' + reason_msg + '\n')
elif abs(inconsistency) <= qconfig.MAX_INDEL_LENGTH and \
count_ns_and_not_ns_between_aligns(contig_seq, prev_align, next_align)[1] <= qconfig.MAX_INDEL_LENGTH:
ns_number, not_ns_number = count_ns_and_not_ns_between_aligns(contig_seq, prev_align, next_align)
if inconsistency == 0:
ca_output.stdout_f.write(('\t\t\t Stretch of %d mismatches between these two alignments (number of Ns: %d)' %
(not_ns_number, ns_number)) + reason_msg + '\n')
indels_info.mismatches += not_ns_number
ca_output.icarus_out_f.write('indel: stretch of mismatches' + reason_msg + '\n')
else:
indel_length = abs(inconsistency)
indel_class = 'Indel (<= 5bp)' if indel_length <= qconfig.SHORT_INDEL_THRESHOLD else 'Indel (> 5bp)'
indel_type = 'insertion' if inconsistency < 0 else 'deletion'
mismatches = max(0, not_ns_number - indel_length)
ca_output.stdout_f.write(('\t\t\t %s between these two alignments: %s of length %d; %d mismatches (number of Ns: %d)')
% (indel_class, indel_type, indel_length, mismatches, ns_number) + reason_msg + '\n')
indels_info.indels_list.append(indel_length)
if indel_type == 'insertion':
indels_info.insertions += indel_length
else:
indels_info.deletions += indel_length
indels_info.mismatches += mismatches
ca_output.icarus_out_f.write('indel: ' + indel_class.lower() + reason_msg + '\n')
else:
if qconfig.strict_NA:
aligned_lengths.append(cur_aligned_length)
contig_aligned_length += cur_aligned_length
cur_aligned_length = 0
if distance_on_contig < 0:
#There is an overlap between the two alignments, a local misassembly
ca_output.stdout_f.write('\t\t\t Overlap between these two alignments (local misassembly).')
elif distance_on_contig > 0:
#There is a small gap between the two alignments, a local misassembly
ca_output.stdout_f.write('\t\t\t Gap between these two alignments (local misassembly).')
elif inconsistency < 0:
ca_output.stdout_f.write('\t\t\t Overlap between these two alignments (local misassembly).')
else:
ca_output.stdout_f.write('\t\t\t Gap between these two alignments (local misassembly).')
ca_output.stdout_f.write(' Inconsistency = ' + str(inconsistency) + reason_msg + '\n')
ca_output.icarus_out_f.write('local misassembly' + reason_msg + '\n')
region_misassemblies.append(Misassembly.LOCAL)
prev_align = next_align
cur_aligned_length += prev_align.len2 - (-distance_on_contig if distance_on_contig < 0 else 0)
#Record the very last alignment
i = len(sorted_aligns) - 1
ca_output.stdout_f.write('\t\t\tReal Alignment %d: %s' % (i + 1, str(next_align)) + '\n')
ca_output.icarus_out_f.write(next_align.icarus_report_str() + '\n')
ref_aligns.setdefault(next_align.ref, []).append(next_align)
ca_output.coords_filtered_f.write(str(next_align) + '\n')
aligned_lengths.append(cur_aligned_length)
contig_aligned_length += cur_aligned_length
assert contig_aligned_length <= len(contig_seq), "Internal QUAST bug: contig aligned length is greater than " \
"contig length (contig: %s, len: %d, aligned: %d)!" % \
(sorted_aligns[0].contig, contig_aligned_length, len(contig_seq))
return is_misassembled, misassembly_internal_overlap, references_misassemblies, indels_info, misassemblies_matched_sv
