def create_mismatches_plot(assembly, window_size, ref_len, root_dir, output_dir): assembly_label = qutils.label_from_fpath_for_fname(assembly.fpath) nucmer_dirpath = join(root_dir, '..', 'contigs_reports') nucmer_fpath = join(create_nucmer_output_dir(nucmer_dirpath), assembly_label) _, _, _, _, used_snps_fpath = get_nucmer_aux_out_fpaths(nucmer_fpath) if not exists(used_snps_fpath): return None mismatches_fpath = join(output_dir, assembly_label + '.mismatches.txt') mismatch_density_by_chrom = defaultdict(lambda : [0] * (ref_len // window_size + 1)) for line in open_gzipsafe(used_snps_fpath): chrom, contig, ref_pos, ref_nucl, ctg_nucl, ctg_pos = line.split('\t') if ref_nucl != '.' and ctg_nucl != '.': mismatch_density_by_chrom[chrom][int(ref_pos) // window_size] += 1 with open(mismatches_fpath, 'w') as out_f: for chrom, density_list in mismatch_density_by_chrom.items(): start, end = 0, 0 for i, density in enumerate(density_list): if density == 0: end = (i + 1) * window_size else: if end: out_f.write('\t'.join([chrom, str(start), str(end), '0']) + '\n') out_f.write('\t'.join([chrom, str(i * window_size), str(((i + 1) * window_size)), str(density)]) + '\n') start = (i + 1) * window_size end = None out_f.write('\t'.join([chrom, str(start), str(end), '0']) + '\n') return mismatches_fpath
def merge_gffs(gffs, out_path): '''Merges all GFF files into a single one, dropping GFF header.''' out_file = open_gzipsafe(out_path, 'w') out_file.write('##gff-version 3\n') for gff_path in gffs: with open(gff_path) as gff_file: out_file.writelines(itertools.islice(gff_file, 2, None)) out_file.close() return out_path
def parse_gff(gff_path): gff_file = open_gzipsafe(gff_path) r = csv.reader(list(filter(lambda l: not l.startswith("#"), gff_file)), delimiter='\t') for index, _source, type, start, end, score, strand, phase, extra in r: if type != 'mRNA': continue # We're only interested in genes here. attrs = dict(kv.split("=") for kv in extra.split(";")) yield index, attrs.get('Name'), int(start), int(end), strand gff_file.close()
def get_genes_from_file(fpath, feature): if not fpath or not os.path.exists(fpath): # it is already checked in quast,py, so we need no more notification #print ' Warning! ' + feature + '\'s file not specified or doesn\'t exist!' return [] genes_file = open_gzipsafe(fpath, 'r') genes = [] line = genes_file.readline().rstrip() while line == '' or line.startswith('#'): line = genes_file.readline().rstrip() genes_file.seek(0) if fpath.endswith('bed') or fpath.endswith('bed.gz'): genes = parse_bed(genes_file) elif txt_pattern_gi.match(line) or txt_pattern.match(line): genes = parse_txt(genes_file) elif gff_pattern.match(line): genes = parse_gff(genes_file, feature) elif ncbi_start_pattern.match(line): try: genes = parse_ncbi(genes_file) except ParseException: exc_type, exc_value, _ = sys.exc_info() logger.warning('Parsing exception ' + exc_value) logger.warning(fpath + ' was skipped') genes = [] else: logger.warning( 'Incorrect format of ' + feature + '\'s file! GFF, NCBI and the plain TXT format accepted. See manual.' ) logger.warning(fpath + ' was skipped') genes_file.close() return genes
def get_genes_from_file(fpath, feature): if not fpath or not os.path.exists(fpath): # it is already checked in quast,py, so we need no more notification #print ' Warning! ' + feature + '\'s file not specified or doesn\'t exist!' return [] genes_file = open_gzipsafe(fpath, 'r') genes = [] line = genes_file.readline().rstrip() while line == '' or line.startswith('#'): line = genes_file.readline().rstrip() genes_file.seek(0) if fpath.endswith('bed') or fpath.endswith('bed.gz'): genes = parse_bed(genes_file) elif txt_pattern_gi.match(line) or txt_pattern.match(line): genes = parse_txt(genes_file) elif gff_pattern.match(line): genes = parse_gff(genes_file, feature) elif ncbi_start_pattern.match(line): try: genes = parse_ncbi(genes_file) except ParseException: exc_type, exc_value, _ = sys.exc_info() logger.warning('Parsing exception ' + exc_value) logger.warning(fpath + ' was skipped') genes = [] else: logger.warning('Incorrect format of ' + feature + '\'s file! GFF, NCBI and the plain TXT format accepted. See manual.') logger.warning(fpath + ' was skipped') genes_file.close() return genes
def add_genes_to_gff(genes, gff_fpath, prokaryote): gff = open_gzipsafe(gff_fpath, 'w') if prokaryote: if qconfig.metagenemark: gff.write('##gff out for MetaGeneMark\n') else: gff.write('##gff out for GeneMarkS PROKARYOTIC\n') else: gff.write('##gff out for GeneMark-ES EUKARYOTIC\n') gff.write('##gff-version 3\n') for id, gene in enumerate(genes): gff.write('%s\tGeneMark\tgene\t%d\t%d\t.\t%s\t.\tID=%d\n' % (gene.contig, gene.start, gene.end, gene.strand, id + 1)) if gene.seq: gff.write('##Nucleotide sequence:\n') for i in range(0, len(gene.seq), 60): gff.write('##' + gene.seq[i:i + 60] + '\n') if gene.protein: gff.write('##Protein sequence:\n') for i in range(0, len(gene.protein), 60): gff.write('##' + gene.protein[i:i + 60] + '\n') gff.write('\n') gff.close()
def add_genes_to_gff(genes, gff_fpath, prokaryote): gff = open_gzipsafe(gff_fpath, 'w') if prokaryote: if qconfig.meta: gff.write('##gff out for MetaGeneMark\n') else: gff.write('##gff out for GeneMarkS PROKARYOTIC\n') else: gff.write('##gff out for GeneMark-ES EUKARYOTIC\n') gff.write('##gff-version 3\n') for id, gene in enumerate(genes): gff.write('%s\tGeneMark\tgene\t%d\t%d\t.\t%s\t.\tID=%d\n' % (gene.contig, gene.start, gene.end, gene.strand, id + 1)) if gene.seq: gff.write('##Nucleotide sequence:\n') for i in range(0, len(gene.seq), 60): gff.write('##' + gene.seq[i:i + 60] + '\n') if gene.protein: gff.write('##Protein sequence:\n') for i in range(0, len(gene.protein), 60): gff.write('##' + gene.protein[i:i + 60] + '\n') gff.write('\n') gff.close()
def align_and_analyze(is_cyclic, index, contigs_fpath, output_dirpath, ref_fpath, old_contigs_fpath, bed_fpath, parallel_by_chr=False, threads=1): nucmer_output_dirpath = create_nucmer_output_dir(output_dirpath) assembly_label = qutils.label_from_fpath(contigs_fpath) corr_assembly_label = qutils.label_from_fpath_for_fname(contigs_fpath) nucmer_fpath = join(nucmer_output_dirpath, corr_assembly_label) logger.info(' ' + qutils.index_to_str(index) + assembly_label) if not qconfig.space_efficient: log_out_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.stdout') log_err_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.stderr') icarus_out_fpath = join(output_dirpath, qconfig.icarus_report_fname_pattern % corr_assembly_label) misassembly_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.mis_contigs.info') unaligned_info_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.unaligned.info') else: log_out_fpath = '/dev/null' log_err_fpath = '/dev/null' icarus_out_fpath = '/dev/null' misassembly_fpath = '/dev/null' unaligned_info_fpath = '/dev/null' icarus_out_f = open(icarus_out_fpath, 'w') icarus_header_cols = ['S1', 'E1', 'S2', 'E2', 'Reference', 'Contig', 'IDY', 'Ambiguous', 'Best_group'] icarus_out_f.write('\t'.join(icarus_header_cols) + '\n') misassembly_f = open(misassembly_fpath, 'w') if not qconfig.space_efficient: logger.info(' ' + qutils.index_to_str(index) + 'Logging to files ' + log_out_fpath + ' and ' + os.path.basename(log_err_fpath) + '...') else: logger.info(' ' + qutils.index_to_str(index) + 'Logging is disabled.') coords_fpath, coords_filtered_fpath, unaligned_fpath, show_snps_fpath, used_snps_fpath = \ get_nucmer_aux_out_fpaths(nucmer_fpath) nucmer_status = align_contigs(nucmer_fpath, ref_fpath, contigs_fpath, old_contigs_fpath, index, parallel_by_chr, threads, log_out_fpath, log_err_fpath) if nucmer_status != NucmerStatus.OK: with open(log_err_fpath, 'a') as log_err_f: if nucmer_status == NucmerStatus.ERROR: logger.error(' ' + qutils.index_to_str(index) + 'Failed aligning contigs ' + qutils.label_from_fpath(contigs_fpath) + ' to the reference (non-zero exit code). ' + ('Run with the --debug flag to see additional information.' if not qconfig.debug else '')) elif nucmer_status == NucmerStatus.FAILED: log_err_f.write(qutils.index_to_str(index) + 'Alignment failed for ' + contigs_fpath + ':' + coords_fpath + 'doesn\'t exist.\n') logger.info(' ' + qutils.index_to_str(index) + 'Alignment failed for ' + '\'' + assembly_label + '\'.') elif nucmer_status == NucmerStatus.NOT_ALIGNED: log_err_f.write(qutils.index_to_str(index) + 'Nothing aligned for ' + contigs_fpath + '\n') logger.info(' ' + qutils.index_to_str(index) + 'Nothing aligned for ' + '\'' + assembly_label + '\'.') clean_tmp_files(nucmer_fpath) return nucmer_status, {}, [], [], [] log_out_f = open(log_out_fpath, 'a') # Loading the alignment files log_out_f.write('Parsing coords...\n') aligns = {} coords_file = open(coords_fpath) coords_filtered_file = open(coords_filtered_fpath, 'w') coords_filtered_file.write(coords_file.readline()) coords_filtered_file.write(coords_file.readline()) for line in coords_file: if line.strip() == '': break assert line[0] != '=' #Clear leading spaces from nucmer output #Store nucmer lines in an array mapping = Mapping.from_line(line) aligns.setdefault(mapping.contig, []).append(mapping) # Loading the reference sequences log_out_f.write('Loading reference...\n') # TODO: move up ref_lens = {} ref_features = {} for name, seq in fastaparser.read_fasta(ref_fpath): name = name.split()[0] # no spaces in reference header ref_lens[name] = len(seq) log_out_f.write('\tLoaded [%s]\n' % name) #Loading the SNP calls if qconfig.show_snps: log_out_f.write('Loading SNPs...\n') used_snps_file = None snps = {} if qconfig.show_snps: prev_line = None for line in open_gzipsafe(show_snps_fpath): #print "$line"; line = line.split() if not line[0].isdigit(): continue if prev_line and line == prev_line: continue ref = line[10] ctg = line[11] pos = int(line[0]) # Kolya: python don't convert int<->str types automatically loc = int(line[3]) # Kolya: same as above # if (! exists $line[11]) { die "Malformed line in SNP file. Please check that show-snps has completed succesfully.\n$line\n[$line[9]][$line[10]][$line[11]]\n"; } if pos in snps.setdefault(ref, {}).setdefault(ctg, {}): snps.setdefault(ref, {}).setdefault(ctg, {})[pos].append(SNP(ref_pos=pos, ctg_pos=loc, ref_nucl=line[1], ctg_nucl=line[2])) else: snps.setdefault(ref, {}).setdefault(ctg, {})[pos] = [SNP(ref_pos=pos, ctg_pos=loc, ref_nucl=line[1], ctg_nucl=line[2])] prev_line = line used_snps_file = open_gzipsafe(used_snps_fpath, 'w') # Loading the regions (if any) regions = {} total_reg_len = 0 total_regions = 0 # # TODO: gff # log_out_f.write('Loading regions...\n') # log_out_f.write('\tNo regions given, using whole reference.\n') for name, seq_len in ref_lens.items(): regions.setdefault(name, []).append([1, seq_len]) total_regions += 1 total_reg_len += seq_len log_out_f.write('\tTotal Regions: %d\n' % total_regions) log_out_f.write('\tTotal Region Length: %d\n' % total_reg_len) ca_output = CAOutput(stdout_f=log_out_f, misassembly_f=misassembly_f, coords_filtered_f=coords_filtered_file, used_snps_f=used_snps_file, icarus_out_f=icarus_out_f) log_out_f.write('Analyzing contigs...\n') result, ref_aligns, total_indels_info, aligned_lengths, misassembled_contigs, misassemblies_in_contigs, aligned_lengths_by_contigs =\ analyze_contigs(ca_output, contigs_fpath, unaligned_fpath, unaligned_info_fpath, aligns, ref_features, ref_lens, is_cyclic) # if qconfig.large_genome: # log_out_f.write('Analyzing large blocks...\n') # large_misassembly_fpath = add_suffix(misassembly_fpath, 'large_blocks') if not qconfig.space_efficient else '/dev/null' # ca_large_output = CAOutput(stdout_f=log_out_f, misassembly_f=open(large_misassembly_fpath, 'w'), # coords_filtered_f=coords_filtered_file, used_snps_f=open('/dev/null', 'w'), icarus_out_f=open('/dev/null', 'w')) # min_alignment, extensive_mis_threshold = qconfig.min_alignment, qconfig.extensive_misassembly_threshold # qconfig.min_alignment, qconfig.extensive_misassembly_threshold = qconfig.LARGE_MIN_ALIGNMENT, qconfig.LARGE_EXTENSIVE_MIS_THRESHOLD # result.update(analyze_contigs(ca_large_output, contigs_fpath, '/dev/null', '/dev/null', # aligns, ref_features, ref_lens, is_cyclic, large_misassemblies_search=True)[0]) # qconfig.min_alignment, qconfig.extensive_misassembly_threshold = min_alignment, extensive_mis_threshold log_out_f.write('Analyzing coverage...\n') if qconfig.show_snps: log_out_f.write('Writing SNPs into ' + used_snps_fpath + '\n') result.update(analyze_coverage(ca_output, regions, ref_aligns, ref_features, snps, total_indels_info)) result = print_results(contigs_fpath, log_out_f, used_snps_fpath, total_indels_info, result) if not qconfig.space_efficient: ## outputting misassembled contigs to separate file fasta = [(name, seq) for name, seq in fastaparser.read_fasta(contigs_fpath) if name in misassembled_contigs.keys()] fastaparser.write_fasta(join(output_dirpath, qutils.name_from_fpath(contigs_fpath) + '.mis_contigs.fa'), fasta) if qconfig.is_combined_ref: alignment_tsv_fpath = join(output_dirpath, "alignments_" + corr_assembly_label + '.tsv') unique_contigs_fpath = join(output_dirpath, qconfig.unique_contigs_fname_pattern % corr_assembly_label) logger.debug(' ' + qutils.index_to_str(index) + 'Alignments: ' + qutils.relpath(alignment_tsv_fpath)) used_contigs = set() with open(unique_contigs_fpath, 'w') as unique_contigs_f: with open(alignment_tsv_fpath, 'w') as alignment_tsv_f: for chr_name, aligns in ref_aligns.items(): alignment_tsv_f.write(chr_name) contigs = set([align.contig for align in aligns]) for contig in contigs: alignment_tsv_f.write('\t' + contig) if qconfig.is_combined_ref: ref_name = ref_labels_by_chromosomes[chr_name] align_by_contigs = defaultdict(int) for align in aligns: align_by_contigs[align.contig] += align.len2 for contig, aligned_len in align_by_contigs.items(): if contig in used_contigs: continue used_contigs.add(contig) len_cov_pattern = re.compile(r'_length_([\d\.]+)_cov_([\d\.]+)') if len_cov_pattern.findall(contig): contig_len = len_cov_pattern.findall(contig)[0][0] contig_cov = len_cov_pattern.findall(contig)[0][1] if aligned_len / float(contig_len) > 0.9: unique_contigs_f.write(ref_name + '\t' + str(aligned_len) + '\t' + contig_cov + '\n') alignment_tsv_f.write('\n') close_handlers(ca_output) logger.info(' ' + qutils.index_to_str(index) + 'Analysis is finished.') logger.debug('') clean_tmp_files(nucmer_fpath) if not qconfig.no_gzip: compress_nucmer_output(logger, nucmer_fpath) if not ref_aligns: return NucmerStatus.NOT_ALIGNED, result, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs else: return NucmerStatus.OK, result, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs
def align_and_analyze(is_cyclic, index, contigs_fpath, output_dirpath, ref_fpath, old_contigs_fpath, bed_fpath, parallel_by_chr=False, threads=1): nucmer_output_dirpath = create_nucmer_output_dir(output_dirpath) assembly_label = qutils.label_from_fpath(contigs_fpath) corr_assembly_label = qutils.label_from_fpath_for_fname(contigs_fpath) nucmer_fpath = join(nucmer_output_dirpath, corr_assembly_label) logger.info(' ' + qutils.index_to_str(index) + assembly_label) if not qconfig.space_efficient: log_out_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.stdout') log_err_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.stderr') icarus_out_fpath = join(output_dirpath, qconfig.icarus_report_fname_pattern % corr_assembly_label) misassembly_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.mis_contigs.info') unaligned_info_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.unaligned.info') else: log_out_fpath = '/dev/null' log_err_fpath = '/dev/null' icarus_out_fpath = '/dev/null' misassembly_fpath = '/dev/null' unaligned_info_fpath = '/dev/null' icarus_out_f = open(icarus_out_fpath, 'w') icarus_header_cols = ['S1', 'E1', 'S2', 'E2', 'Reference', 'Contig', 'IDY', 'Ambiguous', 'Best_group'] icarus_out_f.write('\t'.join(icarus_header_cols) + '\n') misassembly_f = open(misassembly_fpath, 'w') if not qconfig.space_efficient: logger.info(' ' + qutils.index_to_str(index) + 'Logging to files ' + log_out_fpath + ' and ' + os.path.basename(log_err_fpath) + '...') else: logger.info(' ' + qutils.index_to_str(index) + 'Logging is disabled.') coords_fpath, coords_filtered_fpath, unaligned_fpath, show_snps_fpath, used_snps_fpath = \ get_nucmer_aux_out_fpaths(nucmer_fpath) nucmer_status = align_contigs(nucmer_fpath, ref_fpath, contigs_fpath, old_contigs_fpath, index, parallel_by_chr, threads, log_out_fpath, log_err_fpath) if nucmer_status != NucmerStatus.OK: with open(log_err_fpath, 'a') as log_err_f: if nucmer_status == NucmerStatus.ERROR: logger.error(' ' + qutils.index_to_str(index) + 'Failed aligning contigs ' + qutils.label_from_fpath(contigs_fpath) + ' to the reference (non-zero exit code). ' + ('Run with the --debug flag to see additional information.' if not qconfig.debug else '')) elif nucmer_status == NucmerStatus.FAILED: log_err_f.write(qutils.index_to_str(index) + 'Alignment failed for ' + contigs_fpath + ':' + coords_fpath + 'doesn\'t exist.\n') logger.info(' ' + qutils.index_to_str(index) + 'Alignment failed for ' + '\'' + assembly_label + '\'.') elif nucmer_status == NucmerStatus.NOT_ALIGNED: log_err_f.write(qutils.index_to_str(index) + 'Nothing aligned for ' + contigs_fpath + '\n') logger.info(' ' + qutils.index_to_str(index) + 'Nothing aligned for ' + '\'' + assembly_label + '\'.') clean_tmp_files(nucmer_fpath) return nucmer_status, {}, [], [], [] log_out_f = open(log_out_fpath, 'a') # Loading the alignment files log_out_f.write('Parsing coords...\n') aligns = {} coords_file = open(coords_fpath) coords_filtered_file = open(coords_filtered_fpath, 'w') coords_filtered_file.write(coords_file.readline()) coords_filtered_file.write(coords_file.readline()) for line in coords_file: if line.strip() == '': break assert line[0] != '=' #Clear leading spaces from nucmer output #Store nucmer lines in an array mapping = Mapping.from_line(line) aligns.setdefault(mapping.contig, []).append(mapping) # Loading the reference sequences log_out_f.write('Loading reference...\n') # TODO: move up references = {} ref_features = {} for name, seq in fastaparser.read_fasta(ref_fpath): name = name.split()[0] # no spaces in reference header references[name] = seq log_out_f.write('\tLoaded [%s]\n' % name) #Loading the SNP calls if qconfig.show_snps: log_out_f.write('Loading SNPs...\n') used_snps_file = None snps = {} if qconfig.show_snps: prev_line = None for line in open_gzipsafe(show_snps_fpath): #print "$line"; line = line.split() if not line[0].isdigit(): continue if prev_line and line == prev_line: continue ref = line[10] ctg = line[11] pos = int(line[0]) # Kolya: python don't convert int<->str types automatically loc = int(line[3]) # Kolya: same as above # if (! exists $line[11]) { die "Malformed line in SNP file. Please check that show-snps has completed succesfully.\n$line\n[$line[9]][$line[10]][$line[11]]\n"; } if pos in snps.setdefault(ref, {}).setdefault(ctg, {}): snps.setdefault(ref, {}).setdefault(ctg, {})[pos].append(SNP(ref_pos=pos, ctg_pos=loc, ref_nucl=line[1], ctg_nucl=line[2])) else: snps.setdefault(ref, {}).setdefault(ctg, {})[pos] = [SNP(ref_pos=pos, ctg_pos=loc, ref_nucl=line[1], ctg_nucl=line[2])] prev_line = line used_snps_file = open_gzipsafe(used_snps_fpath, 'w') # Loading the regions (if any) regions = {} ref_lens = {} total_reg_len = 0 total_regions = 0 # # TODO: gff # log_out_f.write('Loading regions...\n') # log_out_f.write('\tNo regions given, using whole reference.\n') for name, seq in references.items(): regions.setdefault(name, []).append([1, len(seq)]) ref_lens[name] = len(seq) total_regions += 1 total_reg_len += ref_lens[name] log_out_f.write('\tTotal Regions: %d\n' % total_regions) log_out_f.write('\tTotal Region Length: %d\n' % total_reg_len) ca_output = CAOutput(stdout_f=log_out_f, misassembly_f=misassembly_f, coords_filtered_f=coords_filtered_file, used_snps_f=used_snps_file, icarus_out_f=icarus_out_f) log_out_f.write('Analyzing contigs...\n') result, ref_aligns, total_indels_info, aligned_lengths, misassembled_contigs, misassemblies_in_contigs, aligned_lengths_by_contigs =\ analyze_contigs(ca_output, contigs_fpath, unaligned_fpath, unaligned_info_fpath, aligns, ref_features, ref_lens, is_cyclic) log_out_f.write('Analyzing coverage...\n') if qconfig.show_snps: log_out_f.write('Writing SNPs into ' + used_snps_fpath + '\n') result.update(analyze_coverage(ca_output, regions, ref_aligns, ref_features, snps, total_indels_info)) result = print_results(contigs_fpath, log_out_f, used_snps_fpath, total_indels_info, result) if not qconfig.space_efficient: ## outputting misassembled contigs to separate file fasta = [(name, seq) for name, seq in fastaparser.read_fasta(contigs_fpath) if name in misassembled_contigs.keys()] fastaparser.write_fasta(join(output_dirpath, qutils.name_from_fpath(contigs_fpath) + '.mis_contigs.fa'), fasta) if qconfig.is_combined_ref: alignment_tsv_fpath = join(output_dirpath, "alignments_" + corr_assembly_label + '.tsv') unique_contigs_fpath = join(output_dirpath, qconfig.unique_contigs_fname_pattern % corr_assembly_label) logger.debug(' ' + qutils.index_to_str(index) + 'Alignments: ' + qutils.relpath(alignment_tsv_fpath)) used_contigs = set() with open(unique_contigs_fpath, 'w') as unique_contigs_f: with open(alignment_tsv_fpath, 'w') as alignment_tsv_f: for chr_name, aligns in ref_aligns.items(): alignment_tsv_f.write(chr_name) contigs = set([align.contig for align in aligns]) for contig in contigs: alignment_tsv_f.write('\t' + contig) if qconfig.is_combined_ref: ref_name = ref_labels_by_chromosomes[chr_name] align_by_contigs = defaultdict(int) for align in aligns: align_by_contigs[align.contig] += align.len2 for contig, aligned_len in align_by_contigs.items(): if contig in used_contigs: continue used_contigs.add(contig) len_cov_pattern = re.compile(r'_length_([\d\.]+)_cov_([\d\.]+)') if len_cov_pattern.findall(contig): contig_len = len_cov_pattern.findall(contig)[0][0] contig_cov = len_cov_pattern.findall(contig)[0][1] if aligned_len / float(contig_len) > 0.9: unique_contigs_f.write(ref_name + '\t' + str(aligned_len) + '\t' + contig_cov + '\n') alignment_tsv_f.write('\n') close_handlers(ca_output) logger.info(' ' + qutils.index_to_str(index) + 'Analysis is finished.') logger.debug('') clean_tmp_files(nucmer_fpath) if not qconfig.no_gzip: compress_nucmer_output(logger, nucmer_fpath) if not ref_aligns: return NucmerStatus.NOT_ALIGNED, result, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs else: return NucmerStatus.OK, result, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs