def parse_gff(file, feature):
genes = []
number = 0
for line in file:
m = gff_pattern.match(line)
if m and m.group('feature') == feature:
gene = Gene(seqname=qutils.correct_name(m.group('seqname')),
start=int(m.group('start')),
end=int(m.group('end')))
attributes = m.group('attributes').split(';')
for attr in attributes:
if attr and attr != '' and '=' in attr:
key, val = attr.split('=')
if key.lower() == 'id':
gene.id = val
if key.lower() == 'name':
gene.name = val
gene.number = number
number += 1
genes.append(gene)
return genes
def parse_ncbi(ncbi_file):
annotation_pattern = re.compile(r'Annotation: (?P<seqname>.+) \((?P<start>\d+)\.\.(?P<end>\d+)(, complement)?\)', re.I)
chromosome_pattern = re.compile(r'Chromosome: (?P<chromosome>\S+);', re.I)
id_pattern = re.compile(r'ID: (?P<id>\d+)', re.I)
genes = []
line = ncbi_file.readline()
while line != '':
while line.rstrip() == '' or line.startswith('##'):
if line == '':
break
line = ncbi_file.readline()
m = ncbi_start_pattern.match(line.rstrip())
while not m:
m = ncbi_start_pattern.match(line.rstrip())
gene = Gene(number=int(m.group('number')),
name=qutils.correct_name(m.group('name')))
the_rest_lines = []
line = ncbi_file.readline()
while line != '' and not ncbi_start_pattern.match(line.rstrip()):
the_rest_lines.append(line.rstrip())
line = ncbi_file.readline()
for info_line in the_rest_lines:
if info_line.startswith('Chromosome:'):
m = re.match(chromosome_pattern, info_line)
if m:
gene.chromosome = m.group('chromosome')
if info_line.startswith('Annotation:'):
m = re.match(annotation_pattern, info_line)
if m:
gene.seqname = m.group('seqname')
gene.start = int(m.group('start'))
gene.end = int(m.group('end'))
to_trim = 'Chromosome' + ' ' + str(gene.chromosome)
if gene.chromosome and gene.seqname.startswith(to_trim):
gene.seqname = gene.seqname[len(to_trim):]
gene.seqname.lstrip(' ,')
else:
logger.warning('Wrong NCBI annotation for gene ' + str(gene.number) + '. ' + gene.name + '. Skipping this gene.')
if info_line.startswith('ID:'):
m = re.match(id_pattern, info_line)
if m:
gene.id = m.group('id')
else:
logger.warning('Can\'t parse gene\'s ID in NCBI format. Gene is ' + str(gene.number) + '. ' + gene.name + '. Skipping it.')
if gene.start is not None and gene.end is not None:
genes.append(gene)
# raise ParseException('NCBI format parsing error: provide start and end for gene ' + gene.number + '. ' + gene.name + '.')
return genes
def correct_seq(seq_name, seq, ref_name, ref_fasta_ext, total_references, ref_fpath):
seq_fname = ref_name
seq_fname += ref_fasta_ext
if total_references > 1:
corr_seq_fpath = corrected_ref_fpaths[-1]
else:
corr_seq_fpath = qutils.unique_corrected_fpath(os.path.join(corrected_dirpath, seq_fname))
corrected_ref_fpaths.append(corr_seq_fpath)
corr_seq_name = qutils.name_from_fpath(corr_seq_fpath)
corr_seq_name += '_' + qutils.correct_name(seq_name[:20])
if not qconfig.no_check:
corr_seq = seq.upper()
dic = {'M': 'N', 'K': 'N', 'R': 'N', 'Y': 'N', 'W': 'N', 'S': 'N', 'V': 'N', 'B': 'N', 'H': 'N', 'D': 'N'}
pat = "(%s)" % "|".join(map(re.escape, dic.keys()))
corr_seq = re.sub(pat, lambda m: dic[m.group()], corr_seq)
if re.compile(r'[^ACGTN]').search(corr_seq):
logger.warning('Skipping ' + ref_fpath + ' because it contains non-ACGTN characters.',
indent=' ')
return None, None
fastaparser.write_fasta(corr_seq_fpath, [(corr_seq_name, seq)], 'a')
fastaparser.write_fasta(combined_ref_fpath, [(corr_seq_name, seq)], 'a')
contigs_analyzer.ref_labels_by_chromosomes[corr_seq_name] = qutils.name_from_fpath(corr_seq_fpath)
chromosomes_by_refs[ref_name].append((corr_seq_name, len(seq)))
return corr_seq_name, corr_seq_fpath
def parse_gff(file, feature):
genes = []
number = 0
for line in file:
m = gff_pattern.match(line)
if m and m.group('feature').lower() == feature:
gene = Gene(seqname=qutils.correct_name(m.group('seqname')),
start=int(m.group('start')),
end=int(m.group('end')))
attributes = m.group('attributes').split(';')
for attr in attributes:
if attr and attr != '' and '=' in attr:
key = attr.split('=')[0]
val = attr[len(key) + 1:]
if key.lower() == 'id':
gene.id = val
if key.lower() == 'name':
gene.name = val
gene.number = number
number += 1
genes.append(gene)
return genes
def parse_ncbi(ncbi_file):
annotation_pattern = re.compile(r'Annotation: (?P<seqname>.+) \((?P<start>\d+)\.\.(?P<end>\d+)(, complement)?\)', re.I)
chromosome_pattern = re.compile(r'Chromosome: (?P<chromosome>\S+);', re.I)
id_pattern = re.compile(r'ID: (?P<id>\d+)', re.I)
genes = []
line = ncbi_file.readline()
while line != '':
while line.rstrip() == '' or line.startswith('##'):
if line == '':
break
line = ncbi_file.readline()
m = ncbi_start_pattern.match(line.rstrip())
while not m:
m = ncbi_start_pattern.match(line.rstrip())
gene = Gene(number=int(m.group('number')),
name=qutils.correct_name(m.group('name')))
the_rest_lines = []
line = ncbi_file.readline()
while line != '' and not ncbi_start_pattern.match(line.rstrip()):
the_rest_lines.append(line.rstrip())
line = ncbi_file.readline()
for info_line in the_rest_lines:
if info_line.startswith('Chromosome:'):
m = re.match(chromosome_pattern, info_line)
if m:
gene.chromosome = m.group('chromosome')
if info_line.startswith('Annotation:'):
m = re.match(annotation_pattern, info_line)
if m:
gene.seqname = m.group('seqname')
gene.start = int(m.group('start'))
gene.end = int(m.group('end'))
to_trim = 'Chromosome' + ' ' + str(gene.chromosome)
if gene.chromosome and gene.seqname.startswith(to_trim):
gene.seqname = gene.seqname[len(to_trim):]
gene.seqname.lstrip(' ,')
else:
logger.warning('Wrong NCBI annotation for gene ' + str(gene.number) + '. ' + gene.name + '. Skipping this gene.')
if info_line.startswith('ID:'):
m = re.match(id_pattern, info_line)
if m:
gene.id = m.group('id')
else:
logger.warning('Can\'t parse gene\'s ID in NCBI format. Gene is ' + str(gene.number) + '. ' + gene.name + '. Skipping it.')
if gene.start is not None and gene.end is not None:
genes.append(gene)
# raise ParseException('NCBI format parsing error: provide start and end for gene ' + gene.number + '. ' + gene.name + '.')
return genes
def correct_seq(seq_name, seq, ref_name, ref_fasta_ext, total_references):
seq_fname = ref_name
if total_references > 1:
seq_fname += '_' + qutils.correct_name(seq_name[:20])
seq_fname += ref_fasta_ext
corr_seq_fpath = qutils.unique_corrected_fpath(os.path.join(corrected_dirpath, seq_fname))
corr_seq_name = qutils.name_from_fpath(corr_seq_fpath)
corrected_ref_fpaths.append(corr_seq_fpath)
fastaparser.write_fasta(corr_seq_fpath, [(corr_seq_name, seq)], 'a')
fastaparser.write_fasta(combined_ref_fpath, [(corr_seq_name, seq)], 'a')
return corr_seq_name
def correct_fasta(original_fpath, corrected_fpath, min_contig,
is_reference=False):
modified_fasta_entries = []
for first_line, seq in fastaparser.read_fasta(original_fpath):
if (len(seq) >= min_contig) or is_reference:
corr_name = qutils.correct_name(first_line)
# seq to uppercase, because we later looking only uppercase letters
corr_seq = seq.upper()
# correcting alternatives (gage can't work with alternatives)
# dic = {'M': 'A', 'K': 'G', 'R': 'A', 'Y': 'C', 'W': 'A', 'S': 'C', 'V': 'A', 'B': 'C', 'H': 'A', 'D': 'A'}
dic = {'M': 'N', 'K': 'N', 'R': 'N', 'Y': 'N', 'W': 'N', 'S': 'N', 'V': 'N', 'B': 'N', 'H': 'N', 'D': 'N'}
pat = "(%s)" % "|".join(map(re.escape, dic.keys()))
corr_seq = re.sub(pat, lambda m: dic[m.group()], corr_seq)
# make sure that only A, C, G, T or N are in the sequence
if re.compile(r'[^ACGTN]').search(corr_seq):
logger.warning('Skipping ' + original_fpath + ' because it contains non-ACGTN characters.',
indent=' ')
return False
modified_fasta_entries.append((corr_name, corr_seq))
fastaparser.write_fasta(corrected_fpath, modified_fasta_entries)
if is_reference:
ref_len = sum(len(chr_seq) for (chr_name, chr_seq) in modified_fasta_entries)
if ref_len > qconfig.MAX_REFERENCE_LENGTH:
_, fasta_ext = os.path.splitext(corrected_fpath)
splitted_ref_dirpath = os.path.join(os.path.dirname(corrected_fpath), 'splitted_ref')
os.makedirs(splitted_ref_dirpath)
for i, (chr_name, chr_seq) in enumerate(modified_fasta_entries):
if len(chr_seq) > qconfig.MAX_REFERENCE_LENGTH:
logger.warning("Skipping chromosome " + chr_name + " because it length is greater than " +
str(qconfig.MAX_REFERENCE_LENGTH) + " (Nucmer's constraint).")
continue
splitted_ref_fpath = os.path.join(splitted_ref_dirpath, "chr_" + str(i + 1)) + fasta_ext
qconfig.splitted_ref.append(splitted_ref_fpath)
fastaparser.write_fasta(splitted_ref_fpath, [(chr_name, chr_seq)])
if len(qconfig.splitted_ref) == 0:
logger.warning("Skipping reference because all of its chromosomes exceeded Nucmer's constraint.")
return False
return True
def correct_fasta(original_fpath, corrected_fpath, min_contig,
is_reference=False):
modified_fasta_entries = []
for first_line, seq in fastaparser.read_fasta(original_fpath):
if (len(seq) >= min_contig) or is_reference:
corr_name = qutils.correct_name(first_line)
# seq to uppercase, because we later looking only uppercase letters
corr_seq = seq.upper()
# correcting alternatives (gage can't work with alternatives)
# dic = {'M': 'A', 'K': 'G', 'R': 'A', 'Y': 'C', 'W': 'A', 'S': 'C', 'V': 'A', 'B': 'C', 'H': 'A', 'D': 'A'}
dic = {'M': 'N', 'K': 'N', 'R': 'N', 'Y': 'N', 'W': 'N', 'S': 'N', 'V': 'N', 'B': 'N', 'H': 'N', 'D': 'N'}
pat = "(%s)" % "|".join(map(re.escape, dic.keys()))
corr_seq = re.sub(pat, lambda m: dic[m.group()], corr_seq)
# make sure that only A, C, G, T or N are in the sequence
if re.compile(r'[^ACGTN]').search(corr_seq):
logger.warning('Skipping ' + original_fpath + ' because it contains non-ACGTN characters.',
indent=' ')
return False
modified_fasta_entries.append((corr_name, corr_seq))
fastaparser.write_fasta(corrected_fpath, modified_fasta_entries)
if is_reference:
ref_len = sum(len(chr_seq) for (chr_name, chr_seq) in modified_fasta_entries)
if ref_len > qconfig.MAX_REFERENCE_LENGTH:
_, fasta_ext = os.path.splitext(corrected_fpath)
splitted_ref_dirpath = os.path.join(os.path.dirname(corrected_fpath), 'splitted_ref')
os.makedirs(splitted_ref_dirpath)
for i, (chr_name, chr_seq) in enumerate(modified_fasta_entries):
if len(chr_seq) > qconfig.MAX_REFERENCE_LENGTH:
logger.warning("Skipping chromosome " + chr_name + " because it length is greater than " +
str(qconfig.MAX_REFERENCE_LENGTH) + " (Nucmer's constraint).")
continue
splitted_ref_fpath = os.path.join(splitted_ref_dirpath, "chr_" + str(i + 1)) + fasta_ext
qconfig.splitted_ref.append(splitted_ref_fpath)
fastaparser.write_fasta(splitted_ref_fpath, [(chr_name, chr_seq)])
if len(qconfig.splitted_ref) == 0:
logger.warning("Skipping reference because all of its chromosomes exceeded Nucmer's constraint.")
return False
return True
def correct_seq(seq_name, seq, ref_name, ref_fasta_ext, total_references):
seq_fname = ref_name
if total_references > 1:
seq_fname += '_' + qutils.correct_name(seq_name[:20])
seq_fname += ref_fasta_ext
corr_seq_fpath = qutils.unique_corrected_fpath(
os.path.join(corrected_dirpath, seq_fname))
corr_seq_name = qutils.name_from_fpath(corr_seq_fpath)
corrected_ref_fpaths.append(corr_seq_fpath)
fastaparser.write_fasta(corr_seq_fpath, [(corr_seq_name, seq)], 'a')
fastaparser.write_fasta(combined_ref_fpath, [(corr_seq_name, seq)],
'a')
return corr_seq_name
def parse_txt(file):
genes = []
for line in file:
m = txt_pattern_gi.match(line)
if not m:
m = txt_pattern.match(line)
if m:
gene = Gene(number=int(m.group('number')),
seqname=qutils.correct_name(m.group('seqname')))
s = int(m.group('start'))
e = int(m.group('end'))
gene.start = min(s, e)
gene.end = max(s, e)
gene.id = m.group('number')
genes.append(gene)
return genes
def correct_seq(seq_name, seq, ref_name, ref_fasta_ext, total_references,
ref_fpath):
seq_fname = ref_name
seq_fname += ref_fasta_ext
if total_references > 1:
corr_seq_fpath = corrected_ref_fpaths[-1]
else:
corr_seq_fpath = qutils.unique_corrected_fpath(
os.path.join(corrected_dirpath, seq_fname))
corrected_ref_fpaths.append(corr_seq_fpath)
corr_seq_name = qutils.name_from_fpath(corr_seq_fpath)
corr_seq_name += '_' + qutils.correct_name(seq_name[:20])
if not qconfig.no_check:
corr_seq = seq.upper()
dic = {
'M': 'N',
'K': 'N',
'R': 'N',
'Y': 'N',
'W': 'N',
'S': 'N',
'V': 'N',
'B': 'N',
'H': 'N',
'D': 'N'
}
pat = "(%s)" % "|".join(map(re.escape, dic.keys()))
corr_seq = re.sub(pat, lambda m: dic[m.group()], corr_seq)
if re.compile(r'[^ACGTN]').search(corr_seq):
logger.warning('Skipping ' + ref_fpath +
' because it contains non-ACGTN characters.',
indent=' ')
return None, None
fastaparser.write_fasta(corr_seq_fpath, [(corr_seq_name, seq)], 'a')
fastaparser.write_fasta(combined_ref_fpath, [(corr_seq_name, seq)],
'a')
contigs_analyzer.ref_labels_by_chromosomes[
corr_seq_name] = qutils.name_from_fpath(corr_seq_fpath)
chromosomes_by_refs[ref_name].append((corr_seq_name, len(seq)))
return corr_seq_name, corr_seq_fpath
def js_data_gen(assemblies, contigs_fpaths, chr_names, chromosomes_length, output_dir_path, cov_fpath, ref_fpath, genome_size):
chr_to_aligned_blocks = dict()
for chr in chr_names:
chr_init = []
for fpath in contigs_fpaths:
f = Alignment('FICTIVE', 0, 0, 0, 0, False, 0, 0, None)
f.label = qutils.label_from_fpath(fpath)
f.unshifted_start = 0
f.unshifted_end = 0
chr_init.append(f)
chr_to_aligned_blocks.setdefault(chr, chr_init)
for assembly in assemblies.assemblies:
for align in assembly.alignments:
chr_to_aligned_blocks[align.ref_name].append(align)
summary_fname = 'alignment_summary.html'
summary_path = os.path.join(output_dir_path, summary_fname)
output_all_files_dir_path = os.path.join(output_dir_path, alignment_plots_dirname)
if not os.path.exists(output_all_files_dir_path):
os.mkdir(output_all_files_dir_path)
import contigs_analyzer
if contigs_analyzer.ref_labels_by_chromosomes:
contig_names_by_refs = contigs_analyzer.ref_labels_by_chromosomes
chr_full_names = list(set([contig_names_by_refs[contig] for contig in chr_names]))
elif genome_size < MAX_SIZE_FOR_COMB_PLOT and len(chr_names) >= MIN_CONTIGS_FOR_COMB_PLOT:
chr_full_names = [NAME_FOR_ONE_PLOT]
else:
chr_full_names = chr_names
if cov_fpath:
cov_data = dict()
not_covered = dict()
cur_len = dict()
with open(cov_fpath, 'r') as coverage:
name = chr_names[0]
contig_to_chr = {}
for chr in chr_full_names:
cov_data.setdefault(chr, [])
not_covered.setdefault(chr, [])
cur_len.setdefault(chr, 0)
if contigs_analyzer.ref_labels_by_chromosomes:
contigs = [contig for contig in chr_names if contig_names_by_refs[contig] == chr]
elif chr == NAME_FOR_ONE_PLOT:
contigs = chr_names
else:
contigs = [chr]
for contig in contigs:
contig_to_chr[contig] = chr
for index, line in enumerate(coverage):
c = list(line.split())
name = contig_to_chr[qutils.correct_name(c[0])]
cur_len[name] += int(c[2])
if index % 100 == 0 and index > 0:
cov_data[name].append(cur_len[name]/100)
cur_len[name] = 0
if c[2] == '0':
not_covered[name].append(c[1])
chr_sizes = {}
num_contigs = {}
aligned_bases = genome_analyzer.get_ref_aligned_lengths()
aligned_bases_by_chr = {}
num_misassemblies = {}
aligned_assemblies = {}
for i, chr in enumerate(chr_full_names):
short_chr = chr[:30]
num_misassemblies[chr] = 0
aligned_bases_by_chr[chr] = []
aligned_assemblies[chr] = []
with open(os.path.join(output_all_files_dir_path, 'data_%s.js' % short_chr), 'w') as result:
result.write('"use strict";\n')
if contigs_analyzer.ref_labels_by_chromosomes:
contigs = [contig for contig in chr_names if contig_names_by_refs[contig] == chr]
result.write('var links_to_chromosomes = {};\n')
links_to_chromosomes = []
used_chromosomes = []
elif chr == NAME_FOR_ONE_PLOT:
contigs = chr_names
else:
contigs = [chr]
chr_size = sum([chromosomes_length[contig] for contig in contigs])
chr_sizes[chr] = chr_size
num_contigs[chr] = len(contigs)
for contig in contigs:
aligned_bases_by_chr[chr].extend(aligned_bases[contig])
data_str = 'var chromosomes_len = {};\n'
for contig in contigs:
l = chromosomes_length[contig]
data_str += 'chromosomes_len["{contig}"] = {l};\n'.format(**locals())
result.write(data_str)
# adding assembly data
data_str = 'var contig_data = {};\n'
data_str += 'contig_data["{chr}"] = [ '.format(**locals())
prev_len = 0
chr_lengths = [0] + [chromosomes_length[contig] for contig in contigs]
for num_contig, contig in enumerate(contigs):
if num_contig > 0:
prev_len += chr_lengths[num_contig]
if len(chr_to_aligned_blocks[contig]) > 0:
for alignment in chr_to_aligned_blocks[contig]:
if alignment.misassembled:
num_misassemblies[chr] += 1
corr_start = prev_len + alignment.unshifted_start
corr_end = prev_len + alignment.unshifted_end
data_str += '{{name: "{alignment.name}", corr_start: {corr_start}, corr_end: {corr_end},' \
'start: {alignment.unshifted_start}, end: {alignment.unshifted_end}, assembly: "{alignment.label}", similar: "{alignment.similar}", misassembled: "{alignment.misassembled}" '.format(**locals())
if alignment.name != 'FICTIVE':
if len(aligned_assemblies[chr]) < len(contigs_fpaths) and alignment.label not in aligned_assemblies[chr]:
aligned_assemblies[chr].append(alignment.label)
data_str += ', structure: ['
for el in alignment.misassembled_structure:
if type(el) == list:
if el[5] in contigs:
num_chr = contigs.index(el[5])
corr_len = sum(chr_lengths[:num_chr+1])
else:
corr_len = -int(el[1])
if contigs_analyzer.ref_labels_by_chromosomes and el[5] not in used_chromosomes:
used_chromosomes.append(el[5])
new_chr = contig_names_by_refs[el[5]]
links_to_chromosomes.append('links_to_chromosomes["{el[5]}"] = "{new_chr}";\n'.format(**locals()))
corr_start = corr_len + int(el[0])
corr_end = corr_len + int(el[1])
data_str += '{{type: "A", corr_start: {corr_start}, corr_end: {corr_end}, start: {el[0]}, end: {el[1]}, start_in_contig: {el[2]}, end_in_contig: {el[3]}, IDY: {el[4]}, chr: "{el[5]}"}},'.format(**locals())
elif type(el) == str:
data_str += '{{type: "M", mstype: "{el}"}},'.format(**locals())
if data_str[-1] == '[':
data_str = data_str + ']},'
else:
data_str = data_str[: -1] + ']},'
else: data_str += '},'
data_str = data_str[:-1] + '];\n\n'
result.write(data_str)
if contigs_analyzer.ref_labels_by_chromosomes:
result.write(''.join(links_to_chromosomes))
if cov_fpath:
# adding coverage data
data_str = 'var coverage_data = {};\n'
if cov_data[chr]:
data_str += 'coverage_data["{chr}"] = [ '.format(**locals())
for e in cov_data[chr]:
data_str += '{e},'.format(**locals())
if len(data_str) > 10000 and e != cov_data[chr][-1]:
result.write(data_str)
data_str = ''
data_str = data_str[:-1] + '];\n'
result.write(data_str)
data_str = ''
data_str = 'var not_covered = {};\n'
data_str += 'not_covered["{chr}"] = [ '.format(**locals())
if len(not_covered[chr]) > 0:
for e in not_covered[chr]:
data_str += '{e},'.format(**locals())
if len(data_str) > 10000 and e != cov_data[chr][-1]:
result.write(data_str)
data_str = ''
data_str = data_str[:-1]
data_str += '];\n'
result.write(data_str)
data_str = ''
with open(html_saver.get_real_path('_chr_templ.html'), 'r') as template:
with open(os.path.join(output_all_files_dir_path, '_{short_chr}.html'.format(**locals())), 'w') as result:
for line in template:
if line.find('<script type="text/javascript" src=""></script>') != -1:
result.write('<script type="text/javascript" src="data_{short_chr}.js"></script>\n'.format(**locals()))
else:
result.write(line)
if line.find('<body>') != -1:
chr_size = chr_sizes[chr]
chr_name = chr.replace('_', ' ')
if len(chr_name) > 50:
chr_name = chr_name[:50] + '...'
title = 'CONTIG ALIGNMENT BROWSER: %s (' % chr_name + ('%s fragments, ' % num_contigs[chr] if num_contigs[chr] > 1 else '') + '%s bp)' % format_long_numbers(chr_size)
result.write('<div class = "block title"><a href="../{summary_fname}"><button class="back_button">↵</button></a>{title}</div>\n'.format(**locals()))
if line.find('<script type="text/javascript">') != -1:
chromosome = '","'.join(contigs)
result.write('var CHROMOSOME = "{chr}";\n'.format(**locals()))
result.write('var chrContigs = ["{chromosome}"];\n'.format(**locals()))
with open(html_saver.get_real_path('alignment_summary_templ.html'), 'r') as template:
with open(summary_path, 'w') as result:
num_aligned_assemblies = [len(aligned_assemblies[chr]) for chr in chr_full_names]
is_unaligned_asm_exists = len(set(num_aligned_assemblies)) > 1
for line in template:
result.write(line)
if line.find('<!--- assemblies: ---->') != -1:
if not is_unaligned_asm_exists:
result.write('<div class="subtitle"># assemblies: %s</div>' % len(contigs_fpaths))
if line.find('<!--- th_assemblies: ---->') != -1:
if is_unaligned_asm_exists:
result.write('<th># assemblies</th>')
if line.find('<!--- references: ---->') != -1:
for chr in sorted(chr_full_names):
result.write('<tr>')
short_chr = chr[:30]
chr_link = os.path.join(alignment_plots_dirname, '_{short_chr}.html'.format(**locals()))
chr_name = chr.replace('_', ' ')
aligned_lengths = [aligned_len for aligned_len in aligned_bases_by_chr[chr] if aligned_len is not None]
chr_genome = sum(aligned_lengths) * 100.0 / (chr_sizes[chr] * len(contigs_fpaths))
chr_size = chr_sizes[chr]
result.write('<td><a href="%s">%s</a></td>' % (chr_link, chr_name))
result.write('<td>%s</td>' % num_contigs[chr])
result.write('<td>%s</td>' % format_long_numbers(chr_size))
if is_unaligned_asm_exists:
result.write('<td>%s</td>' % len(aligned_assemblies[chr]))
result.write('<td>%.3f</td>' % chr_genome)
result.write('<td>%s</td>' % num_misassemblies[chr])
result.write('</tr>')
copyfile(html_saver.get_real_path(os.path.join('static', 'contig_alignment_plot.css')),
os.path.join(output_all_files_dir_path, 'contig_alignment_plot.css'))
copyfile(html_saver.get_real_path(os.path.join('static', 'd3.js')),
os.path.join(output_all_files_dir_path, 'd3.js'))
copyfile(html_saver.get_real_path(os.path.join('static', 'scripts', 'contig_alignment_plot_script.js')),
os.path.join(output_all_files_dir_path, 'contig_alignment_plot_script.js'))
def get_corr_name(name):
return qutils.correct_name(name)
def parse_nucmer_contig_report(report_fpath, sorted_ref_names, cumulative_ref_lengths):
aligned_blocks = []
with open(report_fpath) as report_file:
misassembled_contigs_ids = []
for line in report_file:
if line.startswith('Analyzing contigs...'):
break
cur_contig_id = ''
last_contig_id = ''
misassembled_id_to_structure = dict()
for line in report_file:
if line.startswith('CONTIG:'):
cur_contig_id = line.split('CONTIG:')[1].strip()
last_contig_id = cur_contig_id.split(' ')[0]
if last_contig_id not in misassembled_id_to_structure:
misassembled_id_to_structure[last_contig_id] = [False]
if (line.find('Alignment') != -1 or line.find('most ') != -1) and line.find('Excluding') == -1:
l = line.split(':')[1].split(' ')
misassembled_id_to_structure[last_contig_id].append([l[1], l[2], l[4], l[5], l[10], qutils.correct_name(l[12])])
if line.find('misassembly') != -1 and line.find('Fake') == -1:
misassembled_id_to_structure[last_contig_id].append(line.split('(')[1].split(')')[0])
if line.find('Extensive misassembly') != -1 and cur_contig_id != '':
misassembled_contigs_ids.append(cur_contig_id.split()[0])
cur_contig_id = ''
if line.startswith('Analyzing coverage...'):
break
cur_shift = 0
ref_blocks = []
for line in report_file:
split_line = line.strip().split(' ')
if split_line and split_line[0] == 'Reference':
ref_name = split_line[1][:-1]
if ref_name in sorted_ref_names:
cur_shift = cumulative_ref_lengths[sorted_ref_names.index(ref_name)]
else:
logger.warning('reference name ' + ref_name + ' not found in file with reference!\nCannot draw contig alignment plot!')
return None
elif split_line and split_line[0] == 'Align' and 'Excluding' not in split_line and 'Fake' not in split_line:
unshifted_start = int(split_line[2])
unshifted_end = int(split_line[3])
start = unshifted_start + cur_shift
end = unshifted_end + cur_shift
contig_id = split_line[4]
start_in_contig = int(split_line[5])
end_in_contig = int(split_line[6])
is_rc = ((start - end) * (start_in_contig - end_in_contig)) < 0
position_in_contig = min(start_in_contig, end_in_contig)
position_in_ref = max(int(split_line[2]), int(split_line[3]))
block = Alignment(
contig_id, start, end, unshifted_start, unshifted_end, is_rc,
position_in_contig, position_in_ref, ref_name)
if contig_id in misassembled_contigs_ids:
block.misassembled = True
block.misassembled_structure = misassembled_id_to_structure[contig_id]
if contig_id in misassembled_contigs_ids:
block.misassembled = True
aligned_blocks.append(block)
if ref_blocks:
aligned_blocks.extend(ref_blocks)
return aligned_blocks
def get_corr_name(name):
return qutils.correct_name(name)
def correct_fasta(original_fpath,
corrected_fpath,
min_contig,
is_reference=False):
modified_fasta_entries = []
for first_line, seq in fastaparser.read_fasta(original_fpath):
if (len(seq) >= min_contig) or is_reference:
corr_name = qutils.correct_name(first_line)
if not qconfig.no_check:
# seq to uppercase, because we later looking only uppercase letters
corr_seq = seq.upper()
# correcting alternatives (gage can't work with alternatives)
# dic = {'M': 'A', 'K': 'G', 'R': 'A', 'Y': 'C', 'W': 'A', 'S': 'C', 'V': 'A', 'B': 'C', 'H': 'A', 'D': 'A'}
dic = {
'M': 'N',
'K': 'N',
'R': 'N',
'Y': 'N',
'W': 'N',
'S': 'N',
'V': 'N',
'B': 'N',
'H': 'N',
'D': 'N'
}
pat = "(%s)" % "|".join(map(re.escape, dic.keys()))
corr_seq = re.sub(pat, lambda m: dic[m.group()], corr_seq)
# make sure that only A, C, G, T or N are in the sequence
if re.compile(r'[^ACGTN]').search(corr_seq):
logger.warning(
'Skipping ' + original_fpath +
' because it contains non-ACGTN characters.',
indent=' ')
return False
else:
corr_seq = seq
modified_fasta_entries.append((corr_name, corr_seq))
fastaparser.write_fasta(corrected_fpath, modified_fasta_entries)
if is_reference:
ref_len = sum(
len(chr_seq) for (chr_name, chr_seq) in modified_fasta_entries)
if ref_len > qconfig.MAX_REFERENCE_FILE_LENGTH:
qconfig.splitted_ref = [
] # important for MetaQUAST which runs QUAST multiple times
_, fasta_ext = os.path.splitext(corrected_fpath)
split_ref_dirpath = os.path.join(os.path.dirname(corrected_fpath),
'split_ref')
if os.path.exists(split_ref_dirpath):
shutil.rmtree(split_ref_dirpath, ignore_errors=True)
os.makedirs(split_ref_dirpath)
max_len = min(ref_len / qconfig.max_threads,
qconfig.MAX_REFERENCE_LENGTH)
cur_part_len = 0
cur_part_num = 1
cur_part_fpath = os.path.join(split_ref_dirpath,
"part_%d" % cur_part_num) + fasta_ext
for (chr_name, chr_seq) in modified_fasta_entries:
cur_chr_len = len(chr_seq)
if cur_chr_len > qconfig.MAX_REFERENCE_LENGTH:
logger.warning("Skipping chromosome " + chr_name +
" because its length is greater than " +
str(qconfig.MAX_REFERENCE_LENGTH) +
" (Nucmer's constraint).")
continue
cur_part_len += cur_chr_len
if cur_part_len > max_len and cur_part_len != cur_chr_len:
qconfig.splitted_ref.append(cur_part_fpath)
cur_part_len = cur_chr_len
cur_part_num += 1
cur_part_fpath = os.path.join(
split_ref_dirpath,
"part_%d" % cur_part_num) + fasta_ext
fastaparser.write_fasta(cur_part_fpath, [(chr_name, chr_seq)],
mode='a')
if cur_part_len > 0:
qconfig.splitted_ref.append(cur_part_fpath)
if len(qconfig.splitted_ref) == 0:
logger.warning(
"Skipping reference because all of its chromosomes exceeded Nucmer's constraint."
)
return False
return True
def parse_nucmer_contig_report(report_fpath, sorted_ref_names,
cumulative_ref_lengths):
aligned_blocks = []
with open(report_fpath) as report_file:
misassembled_contigs_ids = []
for line in report_file:
if line.startswith('Analyzing contigs...'):
break
cur_contig_id = ''
last_contig_id = ''
misassembled_id_to_structure = dict()
for line in report_file:
if line.startswith('CONTIG:'):
cur_contig_id = line.split('CONTIG:')[1].strip()
last_contig_id = cur_contig_id.split(' ')[0]
if last_contig_id not in misassembled_id_to_structure:
misassembled_id_to_structure[last_contig_id] = [False]
if (line.find('Alignment') != -1 or
line.find('most ') != -1) and line.find('Excluding') == -1:
l = line.split(':')[1].split(' ')
misassembled_id_to_structure[last_contig_id].append([
l[1], l[2], l[4], l[5], l[10],
qutils.correct_name(l[12])
])
if line.find('misassembly') != -1 and line.find('Fake') == -1:
misassembled_id_to_structure[last_contig_id].append(
line.split('(')[1].split(')')[0])
if line.find(
'Extensive misassembly') != -1 and cur_contig_id != '':
misassembled_contigs_ids.append(cur_contig_id.split()[0])
cur_contig_id = ''
if line.startswith('Analyzing coverage...'):
break
cur_shift = 0
ref_blocks = []
for line in report_file:
split_line = line.strip().split(' ')
if split_line and split_line[0] == 'Reference':
ref_name = split_line[1][:-1]
if ref_name in sorted_ref_names:
cur_shift = cumulative_ref_lengths[sorted_ref_names.index(
ref_name)]
else:
logger.warning(
'reference name ' + ref_name +
' not found in file with reference!\nCannot draw contig alignment plot!'
)
return None
elif split_line and split_line[
0] == 'Align' and 'Excluding' not in split_line and 'Fake' not in split_line:
unshifted_start = int(split_line[2])
unshifted_end = int(split_line[3])
start = unshifted_start + cur_shift
end = unshifted_end + cur_shift
contig_id = split_line[4]
start_in_contig = int(split_line[5])
end_in_contig = int(split_line[6])
is_rc = ((start - end) * (start_in_contig - end_in_contig)) < 0
position_in_contig = min(start_in_contig, end_in_contig)
position_in_ref = max(int(split_line[2]), int(split_line[3]))
block = Alignment(contig_id, start, end, unshifted_start,
unshifted_end, is_rc, position_in_contig,
position_in_ref, ref_name)
if contig_id in misassembled_contigs_ids:
block.misassembled = True
block.misassembled_structure = misassembled_id_to_structure[
contig_id]
if contig_id in misassembled_contigs_ids:
block.misassembled = True
aligned_blocks.append(block)
if ref_blocks:
aligned_blocks.extend(ref_blocks)
return aligned_blocks
def correct_fasta(original_fpath, corrected_fpath, min_contig,
is_reference=False):
modified_fasta_entries = []
for first_line, seq in fastaparser.read_fasta(original_fpath):
if (len(seq) >= min_contig) or is_reference:
corr_name = qutils.correct_name(first_line)
if not qconfig.no_check:
# seq to uppercase, because we later looking only uppercase letters
corr_seq = seq.upper()
# correcting alternatives (gage can't work with alternatives)
# dic = {'M': 'A', 'K': 'G', 'R': 'A', 'Y': 'C', 'W': 'A', 'S': 'C', 'V': 'A', 'B': 'C', 'H': 'A', 'D': 'A'}
dic = {'M': 'N', 'K': 'N', 'R': 'N', 'Y': 'N', 'W': 'N', 'S': 'N', 'V': 'N', 'B': 'N', 'H': 'N', 'D': 'N'}
pat = "(%s)" % "|".join(map(re.escape, dic.keys()))
corr_seq = re.sub(pat, lambda m: dic[m.group()], corr_seq)
# make sure that only A, C, G, T or N are in the sequence
if re.compile(r'[^ACGTN]').search(corr_seq):
logger.warning('Skipping ' + original_fpath + ' because it contains non-ACGTN characters.',
indent=' ')
return False
else:
corr_seq = seq
modified_fasta_entries.append((corr_name, corr_seq))
fastaparser.write_fasta(corrected_fpath, modified_fasta_entries)
if is_reference:
ref_len = sum(len(chr_seq) for (chr_name, chr_seq) in modified_fasta_entries)
if ref_len > qconfig.MAX_REFERENCE_FILE_LENGTH:
qconfig.splitted_ref = [] # important for MetaQUAST which runs QUAST multiple times
_, fasta_ext = os.path.splitext(corrected_fpath)
split_ref_dirpath = os.path.join(os.path.dirname(corrected_fpath), 'split_ref')
if os.path.exists(split_ref_dirpath):
shutil.rmtree(split_ref_dirpath, ignore_errors=True)
os.makedirs(split_ref_dirpath)
max_len = min(ref_len/qconfig.max_threads, qconfig.MAX_REFERENCE_LENGTH)
cur_part_len = 0
cur_part_num = 1
cur_part_fpath = os.path.join(split_ref_dirpath, "part_%d" % cur_part_num) + fasta_ext
for (chr_name, chr_seq) in modified_fasta_entries:
cur_chr_len = len(chr_seq)
if cur_chr_len > qconfig.MAX_REFERENCE_LENGTH:
logger.warning("Skipping chromosome " + chr_name + " because its length is greater than " +
str(qconfig.MAX_REFERENCE_LENGTH) + " (Nucmer's constraint).")
continue
cur_part_len += cur_chr_len
if cur_part_len > max_len and cur_part_len != cur_chr_len:
qconfig.splitted_ref.append(cur_part_fpath)
cur_part_len = cur_chr_len
cur_part_num += 1
cur_part_fpath = os.path.join(split_ref_dirpath, "part_%d" % cur_part_num) + fasta_ext
fastaparser.write_fasta(cur_part_fpath, [(chr_name, chr_seq)], mode='a')
if cur_part_len > 0:
qconfig.splitted_ref.append(cur_part_fpath)
if len(qconfig.splitted_ref) == 0:
logger.warning("Skipping reference because all of its chromosomes exceeded Nucmer's constraint.")
return False
return True
def js_data_gen(assemblies, contigs_fpaths, chr_names, chromosomes_length,
output_dir_path, cov_fpath, ref_fpath, genome_size):
chr_to_aligned_blocks = dict()
for chr in chr_names:
chr_init = []
for fpath in contigs_fpaths:
f = Alignment('FICTIVE', 0, 0, 0, 0, False, 0, 0, None)
f.label = qutils.label_from_fpath(fpath)
f.unshifted_start = 0
f.unshifted_end = 0
chr_init.append(f)
chr_to_aligned_blocks.setdefault(chr, chr_init)
for assembly in assemblies.assemblies:
for align in assembly.alignments:
chr_to_aligned_blocks[align.ref_name].append(align)
summary_fname = 'alignment_summary.html'
summary_path = os.path.join(output_dir_path, summary_fname)
output_all_files_dir_path = os.path.join(output_dir_path,
alignment_plots_dirname)
if not os.path.exists(output_all_files_dir_path):
os.mkdir(output_all_files_dir_path)
import contigs_analyzer
if contigs_analyzer.ref_labels_by_chromosomes:
contig_names_by_refs = contigs_analyzer.ref_labels_by_chromosomes
chr_full_names = list(
set([contig_names_by_refs[contig] for contig in chr_names]))
elif genome_size < MAX_SIZE_FOR_COMB_PLOT and len(
chr_names) >= MIN_CONTIGS_FOR_COMB_PLOT:
chr_full_names = [NAME_FOR_ONE_PLOT]
else:
chr_full_names = chr_names
if cov_fpath:
cov_data = dict()
not_covered = dict()
cur_len = dict()
with open(cov_fpath, 'r') as coverage:
name = chr_names[0]
contig_to_chr = {}
for chr in chr_full_names:
cov_data.setdefault(chr, [])
not_covered.setdefault(chr, [])
cur_len.setdefault(chr, 0)
if contigs_analyzer.ref_labels_by_chromosomes:
contigs = [
contig for contig in chr_names
if contig_names_by_refs[contig] == chr
]
elif chr == NAME_FOR_ONE_PLOT:
contigs = chr_names
else:
contigs = [chr]
for contig in contigs:
contig_to_chr[contig] = chr
for index, line in enumerate(coverage):
c = list(line.split())
name = contig_to_chr[qutils.correct_name(c[0])]
cur_len[name] += int(c[2])
if index % 100 == 0 and index > 0:
cov_data[name].append(cur_len[name] / 100)
cur_len[name] = 0
if c[2] == '0':
not_covered[name].append(c[1])
chr_sizes = {}
num_contigs = {}
aligned_bases = genome_analyzer.get_ref_aligned_lengths()
aligned_bases_by_chr = {}
num_misassemblies = {}
aligned_assemblies = {}
for i, chr in enumerate(chr_full_names):
short_chr = chr[:30]
num_misassemblies[chr] = 0
aligned_bases_by_chr[chr] = []
aligned_assemblies[chr] = []
with open(
os.path.join(output_all_files_dir_path,
'data_%s.js' % short_chr), 'w') as result:
result.write('"use strict";\n')
if contigs_analyzer.ref_labels_by_chromosomes:
contigs = [
contig for contig in chr_names
if contig_names_by_refs[contig] == chr
]
result.write('var links_to_chromosomes = {};\n')
links_to_chromosomes = []
used_chromosomes = []
elif chr == NAME_FOR_ONE_PLOT:
contigs = chr_names
else:
contigs = [chr]
chr_size = sum([chromosomes_length[contig] for contig in contigs])
chr_sizes[chr] = chr_size
num_contigs[chr] = len(contigs)
for contig in contigs:
aligned_bases_by_chr[chr].extend(aligned_bases[contig])
data_str = 'var chromosomes_len = {};\n'
for contig in contigs:
l = chromosomes_length[contig]
data_str += 'chromosomes_len["{contig}"] = {l};\n'.format(
**locals())
result.write(data_str)
# adding assembly data
data_str = 'var contig_data = {};\n'
data_str += 'contig_data["{chr}"] = [ '.format(**locals())
prev_len = 0
chr_lengths = [0] + [
chromosomes_length[contig] for contig in contigs
]
for num_contig, contig in enumerate(contigs):
if num_contig > 0:
prev_len += chr_lengths[num_contig]
if len(chr_to_aligned_blocks[contig]) > 0:
for alignment in chr_to_aligned_blocks[contig]:
if alignment.misassembled:
num_misassemblies[chr] += 1
corr_start = prev_len + alignment.unshifted_start
corr_end = prev_len + alignment.unshifted_end
data_str += '{{name: "{alignment.name}", corr_start: {corr_start}, corr_end: {corr_end},' \
'start: {alignment.unshifted_start}, end: {alignment.unshifted_end}, assembly: "{alignment.label}", similar: "{alignment.similar}", misassembled: "{alignment.misassembled}" '.format(**locals())
if alignment.name != 'FICTIVE':
if len(aligned_assemblies[chr]) < len(
contigs_fpaths
) and alignment.label not in aligned_assemblies[
chr]:
aligned_assemblies[chr].append(alignment.label)
data_str += ', structure: ['
for el in alignment.misassembled_structure:
if type(el) == list:
if el[5] in contigs:
num_chr = contigs.index(el[5])
corr_len = sum(chr_lengths[:num_chr +
1])
else:
corr_len = -int(el[1])
if contigs_analyzer.ref_labels_by_chromosomes and el[
5] not in used_chromosomes:
used_chromosomes.append(el[5])
new_chr = contig_names_by_refs[
el[5]]
links_to_chromosomes.append(
'links_to_chromosomes["{el[5]}"] = "{new_chr}";\n'
.format(**locals()))
corr_start = corr_len + int(el[0])
corr_end = corr_len + int(el[1])
data_str += '{{type: "A", corr_start: {corr_start}, corr_end: {corr_end}, start: {el[0]}, end: {el[1]}, start_in_contig: {el[2]}, end_in_contig: {el[3]}, IDY: {el[4]}, chr: "{el[5]}"}},'.format(
**locals())
elif type(el) == str:
data_str += '{{type: "M", mstype: "{el}"}},'.format(
**locals())
if data_str[-1] == '[':
data_str = data_str + ']},'
else:
data_str = data_str[:-1] + ']},'
else:
data_str += '},'
data_str = data_str[:-1] + '];\n\n'
result.write(data_str)
if contigs_analyzer.ref_labels_by_chromosomes:
result.write(''.join(links_to_chromosomes))
if cov_fpath:
# adding coverage data
data_str = 'var coverage_data = {};\n'
if cov_data[chr]:
data_str += 'coverage_data["{chr}"] = [ '.format(
**locals())
for e in cov_data[chr]:
data_str += '{e},'.format(**locals())
if len(data_str) > 10000 and e != cov_data[chr][-1]:
result.write(data_str)
data_str = ''
data_str = data_str[:-1] + '];\n'
result.write(data_str)
data_str = ''
data_str = 'var not_covered = {};\n'
data_str += 'not_covered["{chr}"] = [ '.format(**locals())
if len(not_covered[chr]) > 0:
for e in not_covered[chr]:
data_str += '{e},'.format(**locals())
if len(data_str) > 10000 and e != cov_data[chr][-1]:
result.write(data_str)
data_str = ''
data_str = data_str[:-1]
data_str += '];\n'
result.write(data_str)
data_str = ''
with open(html_saver.get_real_path('_chr_templ.html'),
'r') as template:
with open(
os.path.join(output_all_files_dir_path,
'_{short_chr}.html'.format(**locals())),
'w') as result:
for line in template:
if line.find(
'<script type="text/javascript" src=""></script>'
) != -1:
result.write(
'<script type="text/javascript" src="data_{short_chr}.js"></script>\n'
.format(**locals()))
else:
result.write(line)
if line.find('<body>') != -1:
chr_size = chr_sizes[chr]
chr_name = chr.replace('_', ' ')
if len(chr_name) > 50:
chr_name = chr_name[:50] + '...'
title = 'CONTIG ALIGNMENT BROWSER: %s (' % chr_name + (
'%s fragments, ' % num_contigs[chr]
if num_contigs[chr] > 1 else ''
) + '%s bp)' % format_long_numbers(chr_size)
result.write(
'<div class = "block title"><a href="../{summary_fname}"><button class="back_button">↵</button></a>{title}</div>\n'
.format(**locals()))
if line.find(
'<script type="text/javascript">') != -1:
chromosome = '","'.join(contigs)
result.write(
'var CHROMOSOME = "{chr}";\n'.format(
**locals()))
result.write(
'var chrContigs = ["{chromosome}"];\n'.
format(**locals()))
with open(html_saver.get_real_path('alignment_summary_templ.html'),
'r') as template:
with open(summary_path, 'w') as result:
num_aligned_assemblies = [
len(aligned_assemblies[chr]) for chr in chr_full_names
]
is_unaligned_asm_exists = len(set(num_aligned_assemblies)) > 1
for line in template:
result.write(line)
if line.find('<!--- assemblies: ---->') != -1:
if not is_unaligned_asm_exists:
result.write(
'<div class="subtitle"># assemblies: %s</div>' %
len(contigs_fpaths))
if line.find('<!--- th_assemblies: ---->') != -1:
if is_unaligned_asm_exists:
result.write('<th># assemblies</th>')
if line.find('<!--- references: ---->') != -1:
for chr in sorted(chr_full_names):
result.write('<tr>')
short_chr = chr[:30]
chr_link = os.path.join(
alignment_plots_dirname,
'_{short_chr}.html'.format(**locals()))
chr_name = chr.replace('_', ' ')
aligned_lengths = [
aligned_len
for aligned_len in aligned_bases_by_chr[chr]
if aligned_len is not None
]
chr_genome = sum(aligned_lengths) * 100.0 / (
chr_sizes[chr] * len(contigs_fpaths))
chr_size = chr_sizes[chr]
result.write('<td><a href="%s">%s</a></td>' %
(chr_link, chr_name))
result.write('<td>%s</td>' % num_contigs[chr])
result.write('<td>%s</td>' %
format_long_numbers(chr_size))
if is_unaligned_asm_exists:
result.write('<td>%s</td>' %
len(aligned_assemblies[chr]))
result.write('<td>%.3f</td>' % chr_genome)
result.write('<td>%s</td>' % num_misassemblies[chr])
result.write('</tr>')
copyfile(
html_saver.get_real_path(
os.path.join('static', 'contig_alignment_plot.css')),
os.path.join(output_all_files_dir_path, 'contig_alignment_plot.css'))
copyfile(html_saver.get_real_path(os.path.join('static', 'd3.js')),
os.path.join(output_all_files_dir_path, 'd3.js'))
copyfile(
html_saver.get_real_path(
os.path.join('static', 'scripts',
'contig_alignment_plot_script.js')),
os.path.join(output_all_files_dir_path,
'contig_alignment_plot_script.js'))