def run_minimap_agb(out_fpath, ref_fpath, contigs_fpath, log_err_fpath, index, max_threads): # run minimap2 for AGB
mask_level = '1' if qconfig.min_IDY < 95 else '0.9'
cmdline = [minimap_fpath(), '-cx', 'asm20', '--mask-level', mask_level, '-N', '100',
'--score-N', '0', '-E', '1,0', '-f', '200', '--cs', '-t', str(max_threads), ref_fpath, contigs_fpath]
return_code = qutils.call_subprocess(cmdline, stdout=open(out_fpath, 'w'), stderr=open(log_err_fpath, 'a'),
indent=' ' + qutils.index_to_str(index))
return return_code
def run_minimap(out_fpath, ref_fpath, contigs_fpath, log_err_fpath, index,
max_threads):
if qconfig.is_agv_mode:
return run_minimap_agv(out_fpath, ref_fpath, contigs_fpath,
log_err_fpath, index, max_threads)
preset = 'asm5' if qconfig.min_IDY >= 95 and not qconfig.is_combined_ref else 'asm10'
# -s -- min CIGAR score, -z -- affects how often to stop alignment extension, -B -- mismatch penalty
# -O -- gap penalty, -r -- max gap size
mask_level = '1' if qconfig.is_combined_ref else '0.9'
num_alignments = '100' if qconfig.is_combined_ref else '50'
additional_options = [
'-B5', '-O4,16', '--no-long-join', '-r',
str(qconfig.MAX_INDEL_LENGTH), '-N', num_alignments, '-s',
str(qconfig.min_alignment), '-z', '200'
]
cmdline = [minimap_fpath(), '-c', '-x', preset] + (additional_options if not qconfig.large_genome else []) + \
['--mask-level', mask_level, '--min-occ', '200', '-g', '2500', '--score-N', '2', '--cs', '-t', str(max_threads), ref_fpath, contigs_fpath]
return_code = qutils.call_subprocess(cmdline,
stdout=open(out_fpath, 'w'),
stderr=open(log_err_fpath, 'a'),
indent=' ' +
qutils.index_to_str(index))
return return_code
def run_minimap_agb(out_fpath, ref_fpath, contigs_fpath, log_err_fpath, index, max_threads): # run minimap2 for AGB
mask_level = '1' if qconfig.min_IDY < 95 else '0.9'
cmdline = [minimap_fpath(), '-cx', 'asm20', '--mask-level', mask_level, '-N', '100',
'--score-N', '0', '-E', '1,0', '-f', '200', '--cs', '-t', str(max_threads), ref_fpath, contigs_fpath]
return_code = qutils.call_subprocess(cmdline, stdout=open(out_fpath, 'w'), stderr=open(log_err_fpath, 'a'),
indent=' ' + qutils.index_to_str(index))
return return_code
def run_minimap(out_fpath, ref_fpath, contigs_fpath, log_err_fpath, index, max_threads):
if qconfig.is_agb_mode:
return run_minimap_agb(out_fpath, ref_fpath, contigs_fpath, log_err_fpath, index, max_threads)
if qconfig.min_IDY < 90:
preset = 'asm20'
elif qconfig.min_IDY < 95:
preset = 'asm10'
else:
preset = 'asm5'
# -s -- min CIGAR score, -z -- affects how often to stop alignment extension, -B -- mismatch penalty
# -O -- gap penalty, -r -- max gap size
mask_level = '1' if qconfig.is_combined_ref else '0.9'
num_alignments = '100' if qconfig.is_combined_ref else '50'
additional_options = ['-B5', '-O4,16', '--no-long-join', '-r', str(qconfig.MAX_INDEL_LENGTH),
'-N', num_alignments, '-s', str(qconfig.min_alignment), '-z', '200']
cmdline = [minimap_fpath(), '-c', '-x', preset] + (additional_options if not qconfig.large_genome else []) + \
['--mask-level', mask_level, '--min-occ', '200', '-g', '2500', '--score-N', '2', '--cs', '-t', str(max_threads), ref_fpath, contigs_fpath]
return_code = qutils.call_subprocess(cmdline, stdout=open(out_fpath, 'w'), stderr=open(log_err_fpath, 'a'),
indent=' ' + qutils.index_to_str(index))
return return_code
def align_kmers(output_dir, ref_fpath, kmers_fpath, log_err_fpath,
max_threads):
out_fpath = join(output_dir, 'kmers.coords')
cmdline = [
minimap_fpath(), '-cx', 'sr', '-s' + str(qconfig.unique_kmer_len * 2),
'--frag=no', '-t',
str(max_threads), ref_fpath, kmers_fpath
]
qutils.call_subprocess(cmdline,
stdout=open(out_fpath, 'w'),
stderr=open(log_err_fpath, 'a'),
indent=' ')
kmers_pos_by_chrom = defaultdict(list)
kmers_by_chrom = defaultdict(list)
with open(out_fpath) as f:
for line in f:
fs = line.split('\t')
if len(fs) < 10:
continue
contig, chrom, pos = fs[0], fs[5], fs[7]
kmers_pos_by_chrom[chrom].append(int(pos))
kmers_by_chrom[chrom].append(int(contig))
return kmers_by_chrom, kmers_pos_by_chrom
def get_unique_covered_regions(ref_fpath,
tmp_dir,
log_fpath,
binary_fpath,
insert_size,
uncovered_fpath,
use_long_reads=False):
red_genome_dir = os.path.join(tmp_dir, 'tmp_red')
if isdir(red_genome_dir):
shutil.rmtree(red_genome_dir)
os.makedirs(red_genome_dir)
ref_name = qutils.name_from_fpath(ref_fpath)
ref_symlink = os.path.join(red_genome_dir, ref_name +
'.fa') ## Red recognizes only *.fa files
if os.path.islink(ref_symlink):
os.remove(ref_symlink)
os.symlink(ref_fpath, ref_symlink)
logger.info(' ' + 'Running repeat masking tool...')
repeats_fpath = os.path.join(tmp_dir, ref_name + '.rpt')
if is_non_empty_file(repeats_fpath):
return_code = 0
logger.info(' ' + 'Using existing file ' + repeats_fpath + '...')
else:
return_code = qutils.call_subprocess([
binary_fpath, '-gnm', red_genome_dir, '-rpt', tmp_dir, '-frm', '2',
'-min', '5'
],
stdout=open(log_fpath, 'w'),
stderr=open(log_fpath, 'w'),
indent=' ')
if return_code == 0 and repeats_fpath and exists(repeats_fpath):
long_repeats_fpath = os.path.join(
tmp_dir,
qutils.name_from_fpath(ref_fpath) + '.long.rpt')
with open(long_repeats_fpath, 'w') as out:
with open(repeats_fpath) as in_f:
for line in in_f:
l = line.split('\t')
repeat_len = int(l[2]) - int(l[1])
if repeat_len >= insert_size:
out.write(line[1:])
repeats_fasta_fpath = os.path.join(
tmp_dir,
qutils.name_from_fpath(ref_fpath) + '.fasta')
coords_fpath = os.path.join(
tmp_dir,
qutils.name_from_fpath(ref_fpath) + '.rpt.coords.txt')
if not is_non_empty_file(coords_fpath):
fasta_index_fpath = ref_fpath + '.fai'
if exists(fasta_index_fpath):
os.remove(fasta_index_fpath)
qutils.call_subprocess([
bedtools_fpath('bedtools'), 'getfasta', '-fi', ref_fpath,
'-bed', long_repeats_fpath, '-fo', repeats_fasta_fpath
],
stderr=open(log_fpath, 'w'),
indent=' ')
cmdline = [
minimap_fpath(), '-c', '-x', 'asm10', '-N', '50',
'--mask-level', '1', '--no-long-join', '-r', '100', '-t',
str(qconfig.max_threads), '-z', '200', ref_fpath,
repeats_fasta_fpath
]
qutils.call_subprocess(cmdline,
stdout=open(coords_fpath, 'w'),
stderr=open(log_fpath, 'a'))
filtered_repeats_fpath, repeats_regions = check_repeats_instances(
coords_fpath, long_repeats_fpath, use_long_reads)
unique_covered_regions = remove_repeat_regions(ref_fpath,
filtered_repeats_fpath,
uncovered_fpath)
return unique_covered_regions, repeats_regions
return None, None