def test_get_region(self):
"""test get_region"""
infile = os.path.join(data_dir, "all_reads.bam")
tmp_out = "tmp.bam_read_extract.get_region.bam"
expected_bam = os.path.join(data_dir, "region.1.60-181.bam")
bam_read_extract.get_region(infile, "1", 59, 180, tmp_out)
self.assertTrue(read_names_match(expected_bam, tmp_out))
os.unlink(tmp_out)
expected_bam = os.path.join(data_dir, "region.1.61-180.bam")
bam_read_extract.get_region(infile, "1", 60, 179, tmp_out)
self.assertTrue(read_names_match(expected_bam, tmp_out))
os.unlink(tmp_out)
def test_get_region(self):
'''test get_region'''
infile = os.path.join(data_dir, 'all_reads.bam')
tmp_out = 'tmp.bam_read_extract.get_region.bam'
expected_bam = os.path.join(data_dir, 'region.1.60-181.bam')
bam_read_extract.get_region(infile, '1', 59, 180, tmp_out)
self.assertTrue(read_names_match(expected_bam, tmp_out))
os.unlink(tmp_out)
expected_bam = os.path.join(data_dir, 'region.1.61-180.bam')
bam_read_extract.get_region(infile, '1', 60, 179, tmp_out)
self.assertTrue(read_names_match(expected_bam, tmp_out))
os.unlink(tmp_out)
def _run_quasimap_one_split(self, split_file, unmapped_reads_file=None):
logging.info(f"Start quasimap on split file {split_file.filename}")
split_reads_file = os.path.join(
self.split_output_dir,
f"split.{split_file.file_number}.reads.bam",
)
bam_read_extract.get_region(
self.reads_files[0],
split_file.chrom,
split_file.chrom_start,
split_file.chrom_end,
split_reads_file,
)
quasimap_dir = os.path.join(
self.split_output_dir,
f"split.{split_file.file_number}.gramtools.quasimap",
)
if self.use_unmapped_reads:
reads_files = [unmapped_reads_file, split_reads_file]
else:
reads_files = [split_reads_file]
build_report, quasimap_report = gramtools.run_gramtools(
split_file.gramtools_build_dir,
quasimap_dir,
split_file.filename,
self.ref_fasta,
reads_files,
kmer_size=self.gramtools_kmer_size,
)
read_cov = self._get_read_coverage_one_split(split_file, quasimap_dir)
if self.clean:
os.unlink(split_reads_file)
logging.info(f"Finish quasimap on split file {split_file.filename}")
return read_cov, build_report, quasimap_report
def _run_gramtools_with_split_vcf(self):
logging.info('Splitting VCF files into chunks (if not already done)')
chunker = vcf_chunker.VcfChunker(
self.split_input_dir,
vcf_infile=self.clustered_vcf,
ref_fasta=self.ref_fasta,
variants_per_split=self.variants_per_split,
alleles_per_split=self.alleles_per_split,
max_read_length=self.max_read_length,
total_splits=self.total_splits,
flank_length=self.max_read_length,
gramtools_kmer_size=self.gramtools_kmer_size,
)
chunker.make_split_files()
self.gramtools_kmer_size = chunker.gramtools_kmer_size
logging.info('VCF file split into ' + str(chunker.total_split_files) +
' chunks')
try:
os.mkdir(self.split_output_dir)
except:
raise Error('Error making output split directory ' +
self.split_output_dir)
unmapped_reads_file = os.path.join(self.split_output_dir,
'unmapped_reads.bam')
bam_read_extract.get_unmapped_reads(self.reads_files[0],
unmapped_reads_file)
split_vcf_outfiles = {}
split_vcf_outfiles_unfiltered = {}
mean_depths = []
depth_variances = []
for ref_name, split_file_list in chunker.vcf_split_files.items():
split_vcf_outfiles[ref_name] = []
split_vcf_outfiles_unfiltered[ref_name] = []
for split_file in split_file_list:
logging.info(
'===== Start analysing variants in VCF split file ' +
split_file.filename + ' =====')
split_reads_file = os.path.join(
self.split_output_dir,
'split.' + str(split_file.file_number) + '.reads.bam')
bam_read_extract.get_region(
self.reads_files[0],
split_file.chrom,
split_file.chrom_start,
split_file.chrom_end,
split_reads_file,
)
gramtools_quasimap_dir = os.path.join(
self.split_output_dir, 'split.' +
str(split_file.file_number) + '.gramtools.quasimap')
build_report, quasimap_report = gramtools.run_gramtools(
split_file.gramtools_build_dir,
gramtools_quasimap_dir,
split_file.filename,
self.ref_fasta,
[unmapped_reads_file, split_reads_file],
self.max_read_length,
kmer_size=self.gramtools_kmer_size,
)
logging.info('Loading split gramtools quasimap output files ' +
gramtools_quasimap_dir)
perl_generated_vcf = os.path.join(
split_file.gramtools_build_dir, 'perl_generated_vcf')
mean_depth, depth_variance, vcf_header, vcf_records, allele_coverage, allele_groups = gramtools.load_gramtools_vcf_and_allele_coverage_files(
perl_generated_vcf, gramtools_quasimap_dir)
mean_depths.append(mean_depth)
depth_variances.append(depth_variance)
logging.info('Finished loading gramtools files')
if self.sample_name is None:
sample_name = vcf_file_read.get_sample_name_from_vcf_header_lines(
vcf_header)
else:
sample_name = self.sample_name
assert sample_name is not None
split_vcf_out = os.path.join(
self.split_output_dir,
'split.' + str(split_file.file_number) + '.out.vcf')
unfiltered_vcf_out = os.path.join(
self.split_output_dir,
'split.' + str(split_file.file_number) +
'.out.debug.calls_with_zero_cov_alleles.vcf')
logging.info('Writing VCf output file ' + split_vcf_out +
' for split VCF file ' + split_file.filename)
gramtools.write_vcf_annotated_using_coverage_from_gramtools(
mean_depth,
vcf_records,
allele_coverage,
allele_groups,
self.read_error_rate,
unfiltered_vcf_out,
self.gramtools_kmer_size,
sample_name=sample_name,
max_read_length=self.max_read_length,
filtered_outfile=split_vcf_out,
)
split_vcf_outfiles[ref_name].append(split_vcf_out)
split_vcf_outfiles_unfiltered[ref_name].append(
unfiltered_vcf_out)
if self.clean:
logging.info(
'Cleaning gramtools files from split VCF file ' +
split_file.filename)
if not self.user_supplied_gramtools_build_dir:
os.rename(
os.path.join(split_file.gramtools_build_dir,
'build_report.json'),
split_file.gramtools_build_dir + '.report.json')
shutil.rmtree(split_file.gramtools_build_dir)
os.unlink(split_file.filename)
os.rename(
os.path.join(gramtools_quasimap_dir, 'report.json'),
gramtools_quasimap_dir + '.report.json')
shutil.rmtree(gramtools_quasimap_dir)
os.unlink(split_reads_file)
logging.info(
'===== Finish analysing variants in VCF split file ' +
split_file.filename + ' =====')
logging.info('Merging VCF files into one output file ' +
self.final_vcf)
chunker.merge_files(split_vcf_outfiles, self.final_vcf)
chunker.merge_files(split_vcf_outfiles_unfiltered,
self.unfiltered_vcf_file)
mean_depth = statistics.mean(mean_depths)
depth_variance = statistics.mean(depth_variances)
logging.info(
f'Adding GT_CONF_PERCENTLE to final VCF file {self.final_vcf}, using mean depth {mean_depth}, depth variance {depth_variance}, error rate {self.read_error_rate}, and {self.genotype_simulation_iterations} simulation iterations'
)
Adjudicator._add_gt_conf_percentile_to_vcf_file(
self.final_vcf, mean_depth, depth_variance, self.read_error_rate,
self.genotype_simulation_iterations)
if self.clean:
logging.info('Deleting temp split VCF files')
for d in split_vcf_outfiles, split_vcf_outfiles_unfiltered:
for file_list in d.values():
for filename in file_list:
os.unlink(filename)
os.unlink(unmapped_reads_file)
def _run_gramtools_with_split_vcf(self):
logging.info("Splitting VCF files into chunks (if not already done)")
chunker = vcf_chunker.VcfChunker(
self.split_input_dir,
vcf_infile=self.clustered_vcf,
ref_fasta=self.ref_fasta,
variants_per_split=self.variants_per_split,
alleles_per_split=self.alleles_per_split,
max_read_length=self.max_read_length,
total_splits=self.total_splits,
flank_length=self.max_read_length,
gramtools_kmer_size=self.gramtools_kmer_size,
)
chunker.make_split_files()
self.gramtools_kmer_size = chunker.gramtools_kmer_size
logging.info("VCF file split into " + str(chunker.total_split_files) +
" chunks")
try:
os.mkdir(self.split_output_dir)
except:
raise Exception("Error making output split directory " +
self.split_output_dir)
if self.use_unmapped_reads:
unmapped_reads_file = os.path.join(self.split_output_dir,
"unmapped_reads.bam")
bam_read_extract.get_unmapped_reads(self.reads_files[0],
unmapped_reads_file)
split_vcf_outfiles = {}
split_vcf_outfiles_unfiltered = {}
for ref_name, split_file_list in chunker.vcf_split_files.items():
split_vcf_outfiles[ref_name] = []
split_vcf_outfiles_unfiltered[ref_name] = []
for split_file in split_file_list:
logging.info(
"===== Start analysing variants in VCF split file " +
split_file.filename + " =====")
split_reads_file = os.path.join(
self.split_output_dir,
"split." + str(split_file.file_number) + ".reads.bam",
)
bam_read_extract.get_region(
self.reads_files[0],
split_file.chrom,
split_file.chrom_start,
split_file.chrom_end,
split_reads_file,
)
gramtools_quasimap_dir = os.path.join(
self.split_output_dir,
"split." + str(split_file.file_number) +
".gramtools.quasimap",
)
if self.use_unmapped_reads:
reads_files = [unmapped_reads_file, split_reads_file]
else:
reads_files = [split_reads_file]
split_vcf_out = os.path.join(
self.split_output_dir,
"split." + str(split_file.file_number) + ".out.vcf",
)
unfiltered_vcf_out = os.path.join(
self.split_output_dir,
"split." + str(split_file.file_number) +
".out.debug.calls_with_zero_cov_alleles.vcf",
)
self.run_adjudicate(
split_file.gramtools_build_dir,
gramtools_quasimap_dir,
split_file.filename,
reads_files,
split_vcf_out,
unfiltered_vcf_out,
)
if self.clean:
os.unlink(split_reads_file)
if not self.user_supplied_gramtools_build_dir:
os.unlink(split_file.filename)
split_vcf_outfiles[ref_name].append(split_vcf_out)
split_vcf_outfiles_unfiltered[ref_name].append(
unfiltered_vcf_out)
logging.info(
"===== Finish analysing variants in VCF split file " +
split_file.filename + " =====")
logging.info("Merging VCF files into one output file " +
self.final_vcf)
chunker.merge_files(split_vcf_outfiles, self.final_vcf)
chunker.merge_files(split_vcf_outfiles_unfiltered,
self.unfiltered_vcf_file)
self.run_gt_conf()
if self.clean:
logging.info("Deleting temp split VCF files")
for d in split_vcf_outfiles, split_vcf_outfiles_unfiltered:
for file_list in d.values():
for filename in file_list:
os.unlink(filename)
if self.use_unmapped_reads:
os.unlink(unmapped_reads_file)