def process_sample_coverage(job, addresses, keyspace, auth, sample, program, samples):
connection.setup(addresses, keyspace, auth_provider=auth)
with open("{}.sambamba_coverage.bed".format(samples[sample]['library_name']), 'rb') as coverage:
reader = csv.reader(coverage, delimiter='\t')
header = reader.next()
threshold_indices = list()
thresholds = list()
index = 0
for element in header:
if element.startswith("percentage"):
threshold = element.replace('percentage', '')
threshold_indices.append(index)
thresholds.append(int(threshold))
index += 1
for row in reader:
threshold_data = defaultdict(float)
index = 0
for threshold in thresholds:
threshold_data[threshold] = row[threshold_indices[index]]
index += 1
sample_data = SampleCoverage.create(sample=samples[sample]['sample_name'],
library_name=samples[sample]['library_name'],
run_id=samples[sample]['run_id'],
num_libraries_in_run=samples[sample]['num_libraries_in_run'],
sequencer_id=samples[sample]['sequencer'],
program_name=program,
extraction=samples[sample]['extraction'],
panel=samples[sample]['panel'],
target_pool=samples[sample]['target_pool'],
amplicon=row[3],
num_reads=row[4],
mean_coverage=row[5],
thresholds=thresholds,
perc_bp_cov_at_thresholds=threshold_data)
amplicon_data = AmpliconCoverage.create(amplicon=row[3],
sample=samples[sample]['sample_name'],
library_name=samples[sample]['library_name'],
run_id=samples[sample]['run_id'],
num_libraries_in_run=samples[sample]['num_libraries_in_run'],
sequencer_id=samples[sample]['sequencer'],
program_name=program,
extraction=samples[sample]['extraction'],
panel=samples[sample]['panel'],
target_pool=samples[sample]['target_pool'],
num_reads=row[4],
mean_coverage=row[5],
thresholds=thresholds,
perc_bp_cov_at_thresholds=threshold_data)
def process_sample_coverage(job, addresses, keyspace, auth, sample, program, samples):
connection.setup(addresses, keyspace, auth_provider=auth)
with open("{}.sambamba_coverage.bed".format(samples[sample]['library_name']), 'rb') as coverage:
reader = csv.reader(coverage, delimiter='\t')
header = reader.next()
threshold_indices = list()
thresholds = list()
index = 0
for element in header:
if element.startswith("percentage"):
threshold = element.replace('percentage', '')
threshold_indices.append(index)
thresholds.append(int(threshold))
index += 1
for row in reader:
threshold_data = defaultdict(float)
index = 0
for threshold in thresholds:
threshold_data[threshold] = row[threshold_indices[index]]
index += 1
sample_data = SampleCoverage.create(sample=samples[sample]['sample_name'],
library_name=samples[sample]['library_name'],
run_id=samples[sample]['run_id'],
num_libraries_in_run=samples[sample]['num_libraries_in_run'],
sequencer_id=samples[sample]['sequencer'],
program_name=program,
extraction=samples[sample]['extraction'],
panel=samples[sample]['panel'],
target_pool=samples[sample]['target_pool'],
amplicon=row[3],
num_reads=row[4],
mean_coverage=row[5],
thresholds=thresholds,
perc_bp_cov_at_thresholds=threshold_data)
amplicon_data = AmpliconCoverage.create(amplicon=row[3],
sample=samples[sample]['sample_name'],
library_name=samples[sample]['library_name'],
run_id=samples[sample]['run_id'],
num_libraries_in_run=samples[sample]['num_libraries_in_run'],
sequencer_id=samples[sample]['sequencer'],
program_name=program,
extraction=samples[sample]['extraction'],
panel=samples[sample]['panel'],
target_pool=samples[sample]['target_pool'],
num_reads=row[4],
mean_coverage=row[5],
thresholds=thresholds,
perc_bp_cov_at_thresholds=threshold_data)
def subsample_bam(job, addresses, keyspace, auth, name, samples, config, seed, fraction, iteration):
"""Use samtools view to subsample an input file to the specified fraction"""
library_name = "subsample-{}-{}-{}".format(samples[name]['library_name'], fraction, iteration)
sublog = "subsample-{}-{}-{}.log".format(name, fraction, iteration)
input_bam = "{}.recalibrated.sorted.bam".format(samples[name]['library_name'])
subsampled_bam = "subsample-{}-{}-{}.bam".format(samples[name]['library_name'], fraction, iteration)
samcommand = "samtools view -s {seed}.{fraction} -b {input} > {output}".format(seed=seed,
fraction=fraction,
input=input_bam,
output=subsampled_bam)
index_command = "samtools index {}".format(subsampled_bam)
index_log = "{}.index.log".format(subsampled_bam)
output = "{}.sambamba_coverage.bed".format(subsampled_bam)
logfile = "{}.sambamba_coverage.log".format(subsampled_bam)
command = ("{}".format(config['sambamba']['bin']),
"depth region",
"-L",
"{}".format(samples[name]['regions']),
"-t",
"{}".format(config['sambamba']['num_cores']),
"-T",
"{}".format(config['coverage_threshold']),
"-T",
"{}".format(config['coverage_threshold2']),
"{}".format(subsampled_bam),
">",
"{}".format(output))
job.fileStore.logToMaster("Samtools ViewCommand: {}\n".format(samcommand))
pipeline.run_and_log_command(samcommand, sublog)
job.fileStore.logToMaster("Samtools Index Command: {}\n".format(index_command))
pipeline.run_and_log_command(index_command, index_log)
job.fileStore.logToMaster("SamBamba Coverage Command: {}\n".format(command))
pipeline.run_and_log_command(" ".join(command), logfile)
connection.setup(addresses, keyspace, auth_provider=auth)
job.fileStore.logToMaster("Adding coverage data: {}\n".format(samcommand))
num_libs = (float(samples[name]['num_libraries_in_run']) * (1 / (float(fraction) / 100.00)))
with open(output, 'rb') as coverage:
reader = csv.reader(coverage, delimiter='\t')
header = reader.next()
threshold_indices = list()
thresholds = list()
index = 0
for element in header:
if element.startswith("percentage"):
threshold = element.replace('percentage', '')
threshold_indices.append(index)
thresholds.append(int(threshold))
index += 1
for row in reader:
threshold_data = defaultdict(float)
index = 0
for threshold in thresholds:
threshold_data[threshold] = row[threshold_indices[index]]
index += 1
sample_data = SampleCoverage.create(sample=samples[name]['sample_name'],
library_name=library_name,
run_id="subsample-{}".format(fraction),
num_libraries_in_run=num_libs,
sequencer_id=samples[name]['sequencer'],
program_name="sambamba",
extraction=samples[name]['extraction'],
panel=samples[name]['panel'],
target_pool=samples[name]['target_pool'],
amplicon=row[3],
num_reads=row[4],
mean_coverage=row[5],
thresholds=thresholds,
perc_bp_cov_at_thresholds=threshold_data)
amplicon_data = AmpliconCoverage.create(amplicon=row[3],
sample=samples[name]['sample_name'],
library_name=library_name,
run_id="subsample-{}".format(fraction),
num_libraries_in_run=num_libs,
sequencer_id=samples[name]['sequencer'],
program_name="sambamba",
extraction=samples[name]['extraction'],
panel=samples[name]['panel'],
target_pool=samples[name]['target_pool'],
num_reads=row[4],
mean_coverage=row[5],
thresholds=thresholds,
perc_bp_cov_at_thresholds=threshold_data)
def subsample_bam(job, addresses, keyspace, auth, name, samples, config, seed,
fraction, iteration):
"""Use samtools view to subsample an input file to the specified fraction"""
library_name = "subsample-{}-{}-{}".format(samples[name]['library_name'],
fraction, iteration)
sublog = "subsample-{}-{}-{}.log".format(name, fraction, iteration)
input_bam = "{}.recalibrated.sorted.bam".format(
samples[name]['library_name'])
subsampled_bam = "subsample-{}-{}-{}.bam".format(
samples[name]['library_name'], fraction, iteration)
samcommand = "samtools view -s {seed}.{fraction} -b {input} > {output}".format(
seed=seed, fraction=fraction, input=input_bam, output=subsampled_bam)
index_command = "samtools index {}".format(subsampled_bam)
index_log = "{}.index.log".format(subsampled_bam)
output = "{}.sambamba_coverage.bed".format(subsampled_bam)
logfile = "{}.sambamba_coverage.log".format(subsampled_bam)
command = ("{}".format(config['sambamba']['bin']), "depth region", "-L",
"{}".format(samples[name]['regions']), "-t",
"{}".format(config['sambamba']['num_cores']), "-T",
"{}".format(config['coverage_threshold']), "-T",
"{}".format(config['coverage_threshold2']),
"{}".format(subsampled_bam), ">", "{}".format(output))
job.fileStore.logToMaster("Samtools ViewCommand: {}\n".format(samcommand))
pipeline.run_and_log_command(samcommand, sublog)
job.fileStore.logToMaster(
"Samtools Index Command: {}\n".format(index_command))
pipeline.run_and_log_command(index_command, index_log)
job.fileStore.logToMaster(
"SamBamba Coverage Command: {}\n".format(command))
pipeline.run_and_log_command(" ".join(command), logfile)
connection.setup(addresses, keyspace, auth_provider=auth)
job.fileStore.logToMaster("Adding coverage data: {}\n".format(samcommand))
num_libs = (float(samples[name]['num_libraries_in_run']) *
(1 / (float(fraction) / 100.00)))
with open(output, 'rb') as coverage:
reader = csv.reader(coverage, delimiter='\t')
header = reader.next()
threshold_indices = list()
thresholds = list()
index = 0
for element in header:
if element.startswith("percentage"):
threshold = element.replace('percentage', '')
threshold_indices.append(index)
thresholds.append(int(threshold))
index += 1
for row in reader:
threshold_data = defaultdict(float)
index = 0
for threshold in thresholds:
threshold_data[threshold] = row[threshold_indices[index]]
index += 1
sample_data = SampleCoverage.create(
sample=samples[name]['sample_name'],
library_name=library_name,
run_id="subsample-{}".format(fraction),
num_libraries_in_run=num_libs,
sequencer_id=samples[name]['sequencer'],
program_name="sambamba",
extraction=samples[name]['extraction'],
panel=samples[name]['panel'],
target_pool=samples[name]['target_pool'],
amplicon=row[3],
num_reads=row[4],
mean_coverage=row[5],
thresholds=thresholds,
perc_bp_cov_at_thresholds=threshold_data)
amplicon_data = AmpliconCoverage.create(
amplicon=row[3],
sample=samples[name]['sample_name'],
library_name=library_name,
run_id="subsample-{}".format(fraction),
num_libraries_in_run=num_libs,
sequencer_id=samples[name]['sequencer'],
program_name="sambamba",
extraction=samples[name]['extraction'],
panel=samples[name]['panel'],
target_pool=samples[name]['target_pool'],
num_reads=row[4],
mean_coverage=row[5],
thresholds=thresholds,
perc_bp_cov_at_thresholds=threshold_data)