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bcbio/bcbio-nextgen | bcbio/bam/coverage.py | plot_multiple_regions_coverage | def plot_multiple_regions_coverage(samples, out_file, data, region_bed=None, stem_bed=None):
"""
given a list of bcbio samples and a bed file or BedTool of regions,
makes a plot of the coverage in the regions for the set of samples
if given a bed file or BedTool of locations in stem_bed with a label,
... | python | def plot_multiple_regions_coverage(samples, out_file, data, region_bed=None, stem_bed=None):
"""
given a list of bcbio samples and a bed file or BedTool of regions,
makes a plot of the coverage in the regions for the set of samples
if given a bed file or BedTool of locations in stem_bed with a label,
... | [
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bcbio/bcbio-nextgen | bcbio/variation/mutect.py | _config_params | def _config_params(base_config, assoc_files, region, out_file, items):
"""Add parameters based on configuration variables, associated files and genomic regions.
"""
params = []
dbsnp = assoc_files.get("dbsnp")
if dbsnp:
params += ["--dbsnp", dbsnp]
cosmic = assoc_files.get("cosmic")
... | python | def _config_params(base_config, assoc_files, region, out_file, items):
"""Add parameters based on configuration variables, associated files and genomic regions.
"""
params = []
dbsnp = assoc_files.get("dbsnp")
if dbsnp:
params += ["--dbsnp", dbsnp]
cosmic = assoc_files.get("cosmic")
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bcbio/bcbio-nextgen | bcbio/variation/mutect.py | _mutect_call_prep | def _mutect_call_prep(align_bams, items, ref_file, assoc_files,
region=None, out_file=None):
"""Preparation work for MuTect.
"""
base_config = items[0]["config"]
broad_runner = broad.runner_from_path("picard", base_config)
broad_runner.run_fn("picard_index_ref", ref_file)
... | python | def _mutect_call_prep(align_bams, items, ref_file, assoc_files,
region=None, out_file=None):
"""Preparation work for MuTect.
"""
base_config = items[0]["config"]
broad_runner = broad.runner_from_path("picard", base_config)
broad_runner.run_fn("picard_index_ref", ref_file)
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bcbio/bcbio-nextgen | bcbio/variation/mutect.py | _SID_call_prep | def _SID_call_prep(align_bams, items, ref_file, assoc_files, region=None, out_file=None):
"""Preparation work for SomaticIndelDetector.
"""
base_config = items[0]["config"]
for x in align_bams:
bam.index(x, base_config)
params = ["-R", ref_file, "-T", "SomaticIndelDetector", "-U", "ALLOW_N_... | python | def _SID_call_prep(align_bams, items, ref_file, assoc_files, region=None, out_file=None):
"""Preparation work for SomaticIndelDetector.
"""
base_config = items[0]["config"]
for x in align_bams:
bam.index(x, base_config)
params = ["-R", ref_file, "-T", "SomaticIndelDetector", "-U", "ALLOW_N_... | [
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bcbio/bcbio-nextgen | bcbio/variation/mutect.py | _fix_mutect_output | def _fix_mutect_output(orig_file, config, out_file, is_paired):
"""Adjust MuTect output to match other callers.
- Rename allelic fraction field in mutect output from FA to FREQ to standarize with other tools
- Remove extra 'none' samples introduced when calling tumor-only samples
"""
out_file_noc =... | python | def _fix_mutect_output(orig_file, config, out_file, is_paired):
"""Adjust MuTect output to match other callers.
- Rename allelic fraction field in mutect output from FA to FREQ to standarize with other tools
- Remove extra 'none' samples introduced when calling tumor-only samples
"""
out_file_noc =... | [
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bcbio/bcbio-nextgen | bcbio/variation/population.py | prep_gemini_db | def prep_gemini_db(fnames, call_info, samples, extras):
"""Prepare a gemini database from VCF inputs prepared with snpEff.
"""
data = samples[0]
name, caller, is_batch = call_info
build_type = _get_build_type(fnames, samples, caller)
out_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"]... | python | def prep_gemini_db(fnames, call_info, samples, extras):
"""Prepare a gemini database from VCF inputs prepared with snpEff.
"""
data = samples[0]
name, caller, is_batch = call_info
build_type = _get_build_type(fnames, samples, caller)
out_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"]... | [
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bcbio/bcbio-nextgen | bcbio/variation/population.py | _back_compatible_gemini | def _back_compatible_gemini(conf_files, data):
"""Provide old install directory for configuration with GEMINI supplied tidy VCFs.
Handles new style (bcbio installed) and old style (GEMINI installed)
configuration and data locations.
"""
if vcfanno.is_human(data, builds=["37"]):
for f in con... | python | def _back_compatible_gemini(conf_files, data):
"""Provide old install directory for configuration with GEMINI supplied tidy VCFs.
Handles new style (bcbio installed) and old style (GEMINI installed)
configuration and data locations.
"""
if vcfanno.is_human(data, builds=["37"]):
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bcbio/bcbio-nextgen | bcbio/variation/population.py | run_vcfanno | def run_vcfanno(vcf_file, data, decomposed=False):
"""Run vcfanno, providing annotations from external databases if needed.
Puts together lua and conf files from multiple inputs by file names.
"""
conf_files = dd.get_vcfanno(data)
if conf_files:
with_basepaths = collections.defaultdict(list... | python | def run_vcfanno(vcf_file, data, decomposed=False):
"""Run vcfanno, providing annotations from external databases if needed.
Puts together lua and conf files from multiple inputs by file names.
"""
conf_files = dd.get_vcfanno(data)
if conf_files:
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bcbio/bcbio-nextgen | bcbio/variation/population.py | get_ped_info | def get_ped_info(data, samples):
"""Retrieve all PED info from metadata
"""
family_id = tz.get_in(["metadata", "family_id"], data, None)
if not family_id:
family_id = _find_shared_batch(samples)
return {
"gender": {"male": 1, "female": 2, "unknown": 0}.get(get_gender(data)),
... | python | def get_ped_info(data, samples):
"""Retrieve all PED info from metadata
"""
family_id = tz.get_in(["metadata", "family_id"], data, None)
if not family_id:
family_id = _find_shared_batch(samples)
return {
"gender": {"male": 1, "female": 2, "unknown": 0}.get(get_gender(data)),
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bcbio/bcbio-nextgen | bcbio/variation/population.py | create_ped_file | def create_ped_file(samples, base_vcf, out_dir=None):
"""Create a GEMINI-compatible PED file, including gender, family and phenotype information.
Checks for a specified `ped` file in metadata, and will use sample information from this file
before reconstituting from metadata information.
"""
out_fi... | python | def create_ped_file(samples, base_vcf, out_dir=None):
"""Create a GEMINI-compatible PED file, including gender, family and phenotype information.
Checks for a specified `ped` file in metadata, and will use sample information from this file
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bcbio/bcbio-nextgen | bcbio/variation/population.py | _is_small_vcf | def _is_small_vcf(vcf_file):
"""Check for small VCFs which we want to analyze quicker.
"""
count = 0
small_thresh = 250
with utils.open_gzipsafe(vcf_file) as in_handle:
for line in in_handle:
if not line.startswith("#"):
count += 1
if count > small_thr... | python | def _is_small_vcf(vcf_file):
"""Check for small VCFs which we want to analyze quicker.
"""
count = 0
small_thresh = 250
with utils.open_gzipsafe(vcf_file) as in_handle:
for line in in_handle:
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bcbio/bcbio-nextgen | bcbio/variation/population.py | get_multisample_vcf | def get_multisample_vcf(fnames, name, caller, data):
"""Retrieve a multiple sample VCF file in a standard location.
Handles inputs with multiple repeated input files from batches.
"""
unique_fnames = []
for f in fnames:
if f not in unique_fnames:
unique_fnames.append(f)
out_... | python | def get_multisample_vcf(fnames, name, caller, data):
"""Retrieve a multiple sample VCF file in a standard location.
Handles inputs with multiple repeated input files from batches.
"""
unique_fnames = []
for f in fnames:
if f not in unique_fnames:
unique_fnames.append(f)
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bcbio/bcbio-nextgen | bcbio/variation/population.py | get_gemini_files | def get_gemini_files(data):
"""Enumerate available gemini data files in a standard installation.
"""
try:
from gemini import annotations, config
except ImportError:
return {}
return {"base": config.read_gemini_config()["annotation_dir"],
"files": annotations.get_anno_file... | python | def get_gemini_files(data):
"""Enumerate available gemini data files in a standard installation.
"""
try:
from gemini import annotations, config
except ImportError:
return {}
return {"base": config.read_gemini_config()["annotation_dir"],
"files": annotations.get_anno_file... | [
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bcbio/bcbio-nextgen | bcbio/variation/population.py | _group_by_batches | def _group_by_batches(samples, check_fn):
"""Group data items into batches, providing details to retrieve results.
"""
batch_groups = collections.defaultdict(list)
singles = []
out_retrieve = []
extras = []
for data in [x[0] for x in samples]:
if check_fn(data):
batch = t... | python | def _group_by_batches(samples, check_fn):
"""Group data items into batches, providing details to retrieve results.
"""
batch_groups = collections.defaultdict(list)
singles = []
out_retrieve = []
extras = []
for data in [x[0] for x in samples]:
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bcbio/bcbio-nextgen | bcbio/variation/population.py | prep_db_parallel | def prep_db_parallel(samples, parallel_fn):
"""Prepares gemini databases in parallel, handling jointly called populations.
"""
batch_groups, singles, out_retrieve, extras = _group_by_batches(samples, _has_variant_calls)
to_process = []
has_batches = False
for (name, caller), info in batch_groups... | python | def prep_db_parallel(samples, parallel_fn):
"""Prepares gemini databases in parallel, handling jointly called populations.
"""
batch_groups, singles, out_retrieve, extras = _group_by_batches(samples, _has_variant_calls)
to_process = []
has_batches = False
for (name, caller), info in batch_groups... | [
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bcbio/bcbio-nextgen | bcbio/workflow/stormseq.py | _get_s3_files | def _get_s3_files(local_dir, file_info, params):
"""Retrieve s3 files to local directory, handling STORMSeq inputs.
"""
assert len(file_info) == 1
files = file_info.values()[0]
fnames = []
for k in ["1", "2"]:
if files[k] not in fnames:
fnames.append(files[k])
out = []
... | python | def _get_s3_files(local_dir, file_info, params):
"""Retrieve s3 files to local directory, handling STORMSeq inputs.
"""
assert len(file_info) == 1
files = file_info.values()[0]
fnames = []
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out = []
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bcbio/bcbio-nextgen | bcbio/pipeline/fastq.py | _gzip_fastq | def _gzip_fastq(in_file, out_dir=None):
"""
gzip a fastq file if it is not already gzipped, handling conversion
from bzip to gzipped files
"""
if fastq.is_fastq(in_file) and not objectstore.is_remote(in_file):
if utils.is_bzipped(in_file):
return _bzip_gzip(in_file, out_dir)
... | python | def _gzip_fastq(in_file, out_dir=None):
"""
gzip a fastq file if it is not already gzipped, handling conversion
from bzip to gzipped files
"""
if fastq.is_fastq(in_file) and not objectstore.is_remote(in_file):
if utils.is_bzipped(in_file):
return _bzip_gzip(in_file, out_dir)
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bcbio/bcbio-nextgen | bcbio/pipeline/fastq.py | _pipeline_needs_fastq | def _pipeline_needs_fastq(config, data):
"""Determine if the pipeline can proceed with a BAM file, or needs fastq conversion.
"""
aligner = config["algorithm"].get("aligner")
support_bam = aligner in alignment.metadata.get("support_bam", [])
return aligner and not support_bam | python | def _pipeline_needs_fastq(config, data):
"""Determine if the pipeline can proceed with a BAM file, or needs fastq conversion.
"""
aligner = config["algorithm"].get("aligner")
support_bam = aligner in alignment.metadata.get("support_bam", [])
return aligner and not support_bam | [
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bcbio/bcbio-nextgen | bcbio/pipeline/fastq.py | convert_bam_to_fastq | def convert_bam_to_fastq(in_file, work_dir, data, dirs, config):
"""Convert BAM input file into FASTQ files.
"""
return alignprep.prep_fastq_inputs([in_file], data) | python | def convert_bam_to_fastq(in_file, work_dir, data, dirs, config):
"""Convert BAM input file into FASTQ files.
"""
return alignprep.prep_fastq_inputs([in_file], data) | [
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bcbio/bcbio-nextgen | bcbio/pipeline/fastq.py | merge | def merge(files, out_file, config):
"""merge smartly fastq files. It recognizes paired fastq files."""
pair1 = [fastq_file[0] for fastq_file in files]
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path = splitext_plus(out_file)
pair1_out_file = path[0] + "_R1" + path[1]
pair2 = [fastq_file[1] for fastq_file... | python | def merge(files, out_file, config):
"""merge smartly fastq files. It recognizes paired fastq files."""
pair1 = [fastq_file[0] for fastq_file in files]
if len(files[0]) > 1:
path = splitext_plus(out_file)
pair1_out_file = path[0] + "_R1" + path[1]
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bcbio/bcbio-nextgen | bcbio/pipeline/fastq.py | _merge_list_fastqs | def _merge_list_fastqs(files, out_file, config):
"""merge list of fastq files into one"""
if not all(map(fastq.is_fastq, files)):
raise ValueError("Not all of the files to merge are fastq files: %s " % (files))
assert all(map(utils.file_exists, files)), ("Not all of the files to merge "
... | python | def _merge_list_fastqs(files, out_file, config):
"""merge list of fastq files into one"""
if not all(map(fastq.is_fastq, files)):
raise ValueError("Not all of the files to merge are fastq files: %s " % (files))
assert all(map(utils.file_exists, files)), ("Not all of the files to merge "
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bcbio/bcbio-nextgen | bcbio/bed/__init__.py | decomment | def decomment(bed_file, out_file):
"""
clean a BED file
"""
if file_exists(out_file):
return out_file
with utils.open_gzipsafe(bed_file) as in_handle, open(out_file, "w") as out_handle:
for line in in_handle:
if line.startswith("#") or line.startswith("browser") or line.... | python | def decomment(bed_file, out_file):
"""
clean a BED file
"""
if file_exists(out_file):
return out_file
with utils.open_gzipsafe(bed_file) as in_handle, open(out_file, "w") as out_handle:
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bcbio/bcbio-nextgen | bcbio/bed/__init__.py | concat | def concat(bed_files, catted=None):
"""
recursively concat a set of BED files, returning a
sorted bedtools object of the result
"""
bed_files = [x for x in bed_files if x]
if len(bed_files) == 0:
if catted:
# move to a .bed extension for downstream tools if not already
... | python | def concat(bed_files, catted=None):
"""
recursively concat a set of BED files, returning a
sorted bedtools object of the result
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bed_files = [x for x in bed_files if x]
if len(bed_files) == 0:
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# move to a .bed extension for downstream tools if not already
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bcbio/bcbio-nextgen | bcbio/bed/__init__.py | merge | def merge(bedfiles):
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given a BED file or list of BED files merge them an return a bedtools object
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if isinstance(bedfiles, list):
catted = concat(bedfiles)
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catted = concat([bedfiles])
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else:
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"""
given a BED file or list of BED files merge them an return a bedtools object
"""
if isinstance(bedfiles, list):
catted = concat(bedfiles)
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catted = concat([bedfiles])
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bcbio/bcbio-nextgen | bcbio/structural/hydra.py | select_unaligned_read_pairs | def select_unaligned_read_pairs(in_bam, extra, out_dir, config):
"""Retrieve unaligned read pairs from input alignment BAM, as two fastq files.
"""
runner = broad.runner_from_config(config)
base, ext = os.path.splitext(os.path.basename(in_bam))
nomap_bam = os.path.join(out_dir, "{}-{}{}".format(base... | python | def select_unaligned_read_pairs(in_bam, extra, out_dir, config):
"""Retrieve unaligned read pairs from input alignment BAM, as two fastq files.
"""
runner = broad.runner_from_config(config)
base, ext = os.path.splitext(os.path.basename(in_bam))
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bcbio/bcbio-nextgen | bcbio/structural/hydra.py | remove_nopairs | def remove_nopairs(in_bam, out_dir, config):
"""Remove any reads without both pairs present in the file.
"""
runner = broad.runner_from_config(config)
out_bam = os.path.join(out_dir, "{}-safepair{}".format(*os.path.splitext(os.path.basename(in_bam))))
if not utils.file_exists(out_bam):
read_... | python | def remove_nopairs(in_bam, out_dir, config):
"""Remove any reads without both pairs present in the file.
"""
runner = broad.runner_from_config(config)
out_bam = os.path.join(out_dir, "{}-safepair{}".format(*os.path.splitext(os.path.basename(in_bam))))
if not utils.file_exists(out_bam):
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bcbio/bcbio-nextgen | bcbio/structural/hydra.py | tiered_alignment | def tiered_alignment(in_bam, tier_num, multi_mappers, extra_args,
genome_build, pair_stats,
work_dir, dirs, config):
"""Perform the alignment of non-mapped reads from previous tier.
"""
nomap_fq1, nomap_fq2 = select_unaligned_read_pairs(in_bam, "tier{}".format(tier_... | python | def tiered_alignment(in_bam, tier_num, multi_mappers, extra_args,
genome_build, pair_stats,
work_dir, dirs, config):
"""Perform the alignment of non-mapped reads from previous tier.
"""
nomap_fq1, nomap_fq2 = select_unaligned_read_pairs(in_bam, "tier{}".format(tier_... | [
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bcbio/bcbio-nextgen | bcbio/structural/hydra.py | convert_bam_to_bed | def convert_bam_to_bed(in_bam, out_file):
"""Convert BAM to bed file using BEDTools.
"""
with file_transaction(out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
subprocess.check_call(["bamToBed", "-i", in_bam, "-tag", "NM"],
stdout=out... | python | def convert_bam_to_bed(in_bam, out_file):
"""Convert BAM to bed file using BEDTools.
"""
with file_transaction(out_file) as tx_out_file:
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bcbio/bcbio-nextgen | bcbio/structural/hydra.py | hydra_breakpoints | def hydra_breakpoints(in_bam, pair_stats):
"""Detect structural variation breakpoints with hydra.
"""
in_bed = convert_bam_to_bed(in_bam)
if os.path.getsize(in_bed) > 0:
pair_bed = pair_discordants(in_bed, pair_stats)
dedup_bed = dedup_discordants(pair_bed)
return run_hydra(dedup... | python | def hydra_breakpoints(in_bam, pair_stats):
"""Detect structural variation breakpoints with hydra.
"""
in_bed = convert_bam_to_bed(in_bam)
if os.path.getsize(in_bed) > 0:
pair_bed = pair_discordants(in_bed, pair_stats)
dedup_bed = dedup_discordants(pair_bed)
return run_hydra(dedup... | [
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bcbio/bcbio-nextgen | bcbio/structural/hydra.py | detect_sv | def detect_sv(align_bam, genome_build, dirs, config):
"""Detect structural variation from discordant aligned pairs.
"""
work_dir = utils.safe_makedir(os.path.join(dirs["work"], "structural"))
pair_stats = shared.calc_paired_insert_stats(align_bam)
fix_bam = remove_nopairs(align_bam, work_dir, config... | python | def detect_sv(align_bam, genome_build, dirs, config):
"""Detect structural variation from discordant aligned pairs.
"""
work_dir = utils.safe_makedir(os.path.join(dirs["work"], "structural"))
pair_stats = shared.calc_paired_insert_stats(align_bam)
fix_bam = remove_nopairs(align_bam, work_dir, config... | [
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bcbio/bcbio-nextgen | bcbio/log/logbook_zmqpush.py | inject | def inject(**params):
"""
A Logbook processor to inject arbitrary information into log records.
Simply pass in keyword arguments and use as a context manager:
>>> with inject(identifier=str(uuid.uuid4())).applicationbound():
... logger.debug('Something happened')
"""
def call... | python | def inject(**params):
"""
A Logbook processor to inject arbitrary information into log records.
Simply pass in keyword arguments and use as a context manager:
>>> with inject(identifier=str(uuid.uuid4())).applicationbound():
... logger.debug('Something happened')
"""
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bcbio/bcbio-nextgen | bcbio/log/logbook_zmqpush.py | ZeroMQPullSubscriber.recv | def recv(self, timeout=None):
"""Overwrite standard recv for timeout calls to catch interrupt errors.
"""
if timeout:
try:
testsock = self._zmq.select([self.socket], [], [], timeout)[0]
except zmq.ZMQError as e:
if e.errno == errno.EINTR:
... | python | def recv(self, timeout=None):
"""Overwrite standard recv for timeout calls to catch interrupt errors.
"""
if timeout:
try:
testsock = self._zmq.select([self.socket], [], [], timeout)[0]
except zmq.ZMQError as e:
if e.errno == errno.EINTR:
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bcbio/bcbio-nextgen | bcbio/variation/pisces.py | run | def run(align_bams, items, ref_file, assoc_files, region=None, out_file=None):
"""Run tumor only pisces calling
Handles bgzipping output file and fixing VCF sample naming to match BAM sample.
"""
paired = vcfutils.get_paired_bams(align_bams, items)
assert paired and not paired.normal_bam, ("Pisces ... | python | def run(align_bams, items, ref_file, assoc_files, region=None, out_file=None):
"""Run tumor only pisces calling
Handles bgzipping output file and fixing VCF sample naming to match BAM sample.
"""
paired = vcfutils.get_paired_bams(align_bams, items)
assert paired and not paired.normal_bam, ("Pisces ... | [
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bcbio/bcbio-nextgen | bcbio/variation/pisces.py | _prep_genome | def _prep_genome(out_dir, data):
"""Create prepped reference directory for pisces.
Requires a custom GenomeSize.xml file present.
"""
genome_name = utils.splitext_plus(os.path.basename(dd.get_ref_file(data)))[0]
out_dir = utils.safe_makedir(os.path.join(out_dir, genome_name))
ref_file = dd.get_... | python | def _prep_genome(out_dir, data):
"""Create prepped reference directory for pisces.
Requires a custom GenomeSize.xml file present.
"""
genome_name = utils.splitext_plus(os.path.basename(dd.get_ref_file(data)))[0]
out_dir = utils.safe_makedir(os.path.join(out_dir, genome_name))
ref_file = dd.get_... | [
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bcbio/bcbio-nextgen | bcbio/variation/deepvariant.py | run | def run(align_bams, items, ref_file, assoc_files, region, out_file):
"""Return DeepVariant calling on germline samples.
region can be a single region or list of multiple regions for multicore calling.
"""
assert not vcfutils.is_paired_analysis(align_bams, items), \
("DeepVariant currently only ... | python | def run(align_bams, items, ref_file, assoc_files, region, out_file):
"""Return DeepVariant calling on germline samples.
region can be a single region or list of multiple regions for multicore calling.
"""
assert not vcfutils.is_paired_analysis(align_bams, items), \
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bcbio/bcbio-nextgen | bcbio/variation/deepvariant.py | _run_germline | def _run_germline(bam_file, data, ref_file, region, out_file):
"""Single sample germline variant calling.
"""
work_dir = utils.safe_makedir("%s-work" % utils.splitext_plus(out_file)[0])
region_bed = strelka2.get_region_bed(region, [data], out_file, want_gzip=False)
example_dir = _make_examples(bam_f... | python | def _run_germline(bam_file, data, ref_file, region, out_file):
"""Single sample germline variant calling.
"""
work_dir = utils.safe_makedir("%s-work" % utils.splitext_plus(out_file)[0])
region_bed = strelka2.get_region_bed(region, [data], out_file, want_gzip=False)
example_dir = _make_examples(bam_f... | [
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bcbio/bcbio-nextgen | bcbio/variation/deepvariant.py | _make_examples | def _make_examples(bam_file, data, ref_file, region_bed, out_file, work_dir):
"""Create example pileup images to feed into variant calling.
"""
log_dir = utils.safe_makedir(os.path.join(work_dir, "log"))
example_dir = utils.safe_makedir(os.path.join(work_dir, "examples"))
if len(glob.glob(os.path.jo... | python | def _make_examples(bam_file, data, ref_file, region_bed, out_file, work_dir):
"""Create example pileup images to feed into variant calling.
"""
log_dir = utils.safe_makedir(os.path.join(work_dir, "log"))
example_dir = utils.safe_makedir(os.path.join(work_dir, "examples"))
if len(glob.glob(os.path.jo... | [
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bcbio/bcbio-nextgen | bcbio/variation/deepvariant.py | _call_variants | def _call_variants(example_dir, region_bed, data, out_file):
"""Call variants from prepared pileup examples, creating tensorflow record file.
"""
tf_out_file = "%s-tfrecord.gz" % utils.splitext_plus(out_file)[0]
if not utils.file_exists(tf_out_file):
with file_transaction(data, tf_out_file) as t... | python | def _call_variants(example_dir, region_bed, data, out_file):
"""Call variants from prepared pileup examples, creating tensorflow record file.
"""
tf_out_file = "%s-tfrecord.gz" % utils.splitext_plus(out_file)[0]
if not utils.file_exists(tf_out_file):
with file_transaction(data, tf_out_file) as t... | [
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bcbio/bcbio-nextgen | bcbio/variation/deepvariant.py | _postprocess_variants | def _postprocess_variants(record_file, data, ref_file, out_file):
"""Post-process variants, converting into standard VCF file.
"""
if not utils.file_uptodate(out_file, record_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = ["dv_postprocess_variants.py", "--ref", ref_fi... | python | def _postprocess_variants(record_file, data, ref_file, out_file):
"""Post-process variants, converting into standard VCF file.
"""
if not utils.file_uptodate(out_file, record_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = ["dv_postprocess_variants.py", "--ref", ref_fi... | [
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bcbio/bcbio-nextgen | bcbio/qc/qsignature.py | run | def run(bam_file, data, out_dir):
""" Run SignatureGenerator to create normalize vcf that later will be input of qsignature_summary
:param bam_file: (str) path of the bam_file
:param data: (list) list containing the all the dictionary
for this sample
:param out_dir: (str) path of t... | python | def run(bam_file, data, out_dir):
""" Run SignatureGenerator to create normalize vcf that later will be input of qsignature_summary
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:param data: (list) list containing the all the dictionary
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bcbio/bcbio-nextgen | bcbio/qc/qsignature.py | summary | def summary(*samples):
"""Run SignatureCompareRelatedSimple module from qsignature tool.
Creates a matrix of pairwise comparison among samples. The
function will not run if the output exists
:param samples: list with only one element containing all samples information
:returns: (dict) with the pat... | python | def summary(*samples):
"""Run SignatureCompareRelatedSimple module from qsignature tool.
Creates a matrix of pairwise comparison among samples. The
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bcbio/bcbio-nextgen | bcbio/qc/qsignature.py | _parse_qsignature_output | def _parse_qsignature_output(in_file, out_file, warning_file, data):
""" Parse xml file produced by qsignature
:param in_file: (str) with the path to the xml file
:param out_file: (str) with the path to output file
:param warning_file: (str) with the path to warning file
:returns: (list) with samp... | python | def _parse_qsignature_output(in_file, out_file, warning_file, data):
""" Parse xml file produced by qsignature
:param in_file: (str) with the path to the xml file
:param out_file: (str) with the path to output file
:param warning_file: (str) with the path to warning file
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bcbio/bcbio-nextgen | bcbio/qc/qsignature.py | _slice_bam_chr21 | def _slice_bam_chr21(in_bam, data):
"""
return only one BAM file with only chromosome 21
"""
sambamba = config_utils.get_program("sambamba", data["config"])
out_file = "%s-chr%s" % os.path.splitext(in_bam)
if not utils.file_exists(out_file):
bam.index(in_bam, data['config'])
with... | python | def _slice_bam_chr21(in_bam, data):
"""
return only one BAM file with only chromosome 21
"""
sambamba = config_utils.get_program("sambamba", data["config"])
out_file = "%s-chr%s" % os.path.splitext(in_bam)
if not utils.file_exists(out_file):
bam.index(in_bam, data['config'])
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bcbio/bcbio-nextgen | bcbio/qc/qsignature.py | _slice_vcf_chr21 | def _slice_vcf_chr21(vcf_file, out_dir):
"""
Slice chr21 of qsignature SNPs to reduce computation time
"""
tmp_file = os.path.join(out_dir, "chr21_qsignature.vcf")
if not utils.file_exists(tmp_file):
cmd = ("grep chr21 {vcf_file} > {tmp_file}").format(**locals())
out = subprocess.che... | python | def _slice_vcf_chr21(vcf_file, out_dir):
"""
Slice chr21 of qsignature SNPs to reduce computation time
"""
tmp_file = os.path.join(out_dir, "chr21_qsignature.vcf")
if not utils.file_exists(tmp_file):
cmd = ("grep chr21 {vcf_file} > {tmp_file}").format(**locals())
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bcbio/bcbio-nextgen | bcbio/variation/vcfanno.py | _combine_files | def _combine_files(orig_files, base_out_file, data, fill_paths=True):
"""Combine multiple input files, fixing file paths if needed.
We fill in full paths from files in the data dictionary if we're
not using basepath (old style GEMINI).
"""
orig_files = [x for x in orig_files if x and utils.file_exi... | python | def _combine_files(orig_files, base_out_file, data, fill_paths=True):
"""Combine multiple input files, fixing file paths if needed.
We fill in full paths from files in the data dictionary if we're
not using basepath (old style GEMINI).
"""
orig_files = [x for x in orig_files if x and utils.file_exi... | [
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bcbio/bcbio-nextgen | bcbio/variation/vcfanno.py | _fill_file_path | def _fill_file_path(line, data):
"""Fill in a full file path in the configuration file from data dictionary.
"""
def _find_file(xs, target):
if isinstance(xs, dict):
for v in xs.values():
f = _find_file(v, target)
if f:
return f
... | python | def _fill_file_path(line, data):
"""Fill in a full file path in the configuration file from data dictionary.
"""
def _find_file(xs, target):
if isinstance(xs, dict):
for v in xs.values():
f = _find_file(v, target)
if f:
return f
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bcbio/bcbio-nextgen | bcbio/variation/vcfanno.py | find_annotations | def find_annotations(data, retriever=None):
"""Find annotation configuration files for vcfanno, using pre-installed inputs.
Creates absolute paths for user specified inputs and finds locally
installed defaults.
Default annotations:
- gemini for variant pipelines
- somatic for variant tumor... | python | def find_annotations(data, retriever=None):
"""Find annotation configuration files for vcfanno, using pre-installed inputs.
Creates absolute paths for user specified inputs and finds locally
installed defaults.
Default annotations:
- gemini for variant pipelines
- somatic for variant tumor... | [
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bcbio/bcbio-nextgen | bcbio/variation/vcfanno.py | annotate_gemini | def annotate_gemini(data, retriever=None):
"""Annotate with population calls if have data installed.
"""
r = dd.get_variation_resources(data)
return all([r.get(k) and objectstore.file_exists_or_remote(r[k]) for k in ["exac", "gnomad_exome"]]) | python | def annotate_gemini(data, retriever=None):
"""Annotate with population calls if have data installed.
"""
r = dd.get_variation_resources(data)
return all([r.get(k) and objectstore.file_exists_or_remote(r[k]) for k in ["exac", "gnomad_exome"]]) | [
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bcbio/bcbio-nextgen | bcbio/variation/vcfanno.py | _annotate_somatic | def _annotate_somatic(data, retriever=None):
"""Annotate somatic calls if we have cosmic data installed.
"""
if is_human(data):
paired = vcfutils.get_paired([data])
if paired:
r = dd.get_variation_resources(data)
if r.get("cosmic") and objectstore.file_exists_or_remot... | python | def _annotate_somatic(data, retriever=None):
"""Annotate somatic calls if we have cosmic data installed.
"""
if is_human(data):
paired = vcfutils.get_paired([data])
if paired:
r = dd.get_variation_resources(data)
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bcbio/bcbio-nextgen | bcbio/variation/vcfanno.py | is_human | def is_human(data, builds=None):
"""Check if human, optionally with build number, search by name or extra GL contigs.
"""
def has_build37_contigs(data):
for contig in ref.file_contigs(dd.get_ref_file(data)):
if contig.name.startswith("GL") or contig.name.find("_gl") >= 0:
... | python | def is_human(data, builds=None):
"""Check if human, optionally with build number, search by name or extra GL contigs.
"""
def has_build37_contigs(data):
for contig in ref.file_contigs(dd.get_ref_file(data)):
if contig.name.startswith("GL") or contig.name.find("_gl") >= 0:
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bcbio/bcbio-nextgen | bcbio/distributed/resources.py | _get_resource_programs | def _get_resource_programs(progs, algs):
"""Retrieve programs used in analysis based on algorithm configurations.
Handles special cases like aligners and variant callers.
"""
checks = {"gatk-vqsr": config_utils.use_vqsr,
"snpeff": config_utils.use_snpeff,
"bcbio-variation-rec... | python | def _get_resource_programs(progs, algs):
"""Retrieve programs used in analysis based on algorithm configurations.
Handles special cases like aligners and variant callers.
"""
checks = {"gatk-vqsr": config_utils.use_vqsr,
"snpeff": config_utils.use_snpeff,
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bcbio/bcbio-nextgen | bcbio/distributed/resources.py | _parent_prefix | def _parent_prefix(prefix):
"""Identify a parent prefix we should add to resources if present in a caller name.
"""
def run(algs):
for alg in algs:
vcs = alg.get("variantcaller")
if vcs:
if isinstance(vcs, dict):
vcs = reduce(operator.add, ... | python | def _parent_prefix(prefix):
"""Identify a parent prefix we should add to resources if present in a caller name.
"""
def run(algs):
for alg in algs:
vcs = alg.get("variantcaller")
if vcs:
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vcs = reduce(operator.add, ... | [
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bcbio/bcbio-nextgen | bcbio/distributed/resources.py | _ensure_min_resources | def _ensure_min_resources(progs, cores, memory, min_memory):
"""Ensure setting match minimum resources required for used programs.
"""
for p in progs:
if p in min_memory:
if not memory or cores * memory < min_memory[p]:
memory = float(min_memory[p]) / cores
return cor... | python | def _ensure_min_resources(progs, cores, memory, min_memory):
"""Ensure setting match minimum resources required for used programs.
"""
for p in progs:
if p in min_memory:
if not memory or cores * memory < min_memory[p]:
memory = float(min_memory[p]) / cores
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bcbio/bcbio-nextgen | bcbio/distributed/resources.py | _get_prog_memory | def _get_prog_memory(resources, cores_per_job):
"""Get expected memory usage, in Gb per core, for a program from resource specification.
"""
out = None
for jvm_opt in resources.get("jvm_opts", []):
if jvm_opt.startswith("-Xmx"):
out = _str_memory_to_gb(jvm_opt[4:])
memory = resou... | python | def _get_prog_memory(resources, cores_per_job):
"""Get expected memory usage, in Gb per core, for a program from resource specification.
"""
out = None
for jvm_opt in resources.get("jvm_opts", []):
if jvm_opt.startswith("-Xmx"):
out = _str_memory_to_gb(jvm_opt[4:])
memory = resou... | [
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bcbio/bcbio-nextgen | bcbio/distributed/resources.py | _scale_cores_to_memory | def _scale_cores_to_memory(cores, mem_per_core, sysinfo, system_memory):
"""Scale multicore usage to avoid excessive memory usage based on system information.
"""
total_mem = "%.2f" % (cores * mem_per_core + system_memory)
if "cores" not in sysinfo:
return cores, total_mem, 1.0
total_mem = ... | python | def _scale_cores_to_memory(cores, mem_per_core, sysinfo, system_memory):
"""Scale multicore usage to avoid excessive memory usage based on system information.
"""
total_mem = "%.2f" % (cores * mem_per_core + system_memory)
if "cores" not in sysinfo:
return cores, total_mem, 1.0
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bcbio/bcbio-nextgen | bcbio/distributed/resources.py | _scale_jobs_to_memory | def _scale_jobs_to_memory(jobs, mem_per_core, sysinfo):
"""When scheduling jobs with single cores, avoid overscheduling due to memory.
"""
if "cores" not in sysinfo:
return jobs, 1.0
sys_mem_per_core = float(sysinfo["memory"]) / float(sysinfo["cores"])
if sys_mem_per_core < mem_per_core:
... | python | def _scale_jobs_to_memory(jobs, mem_per_core, sysinfo):
"""When scheduling jobs with single cores, avoid overscheduling due to memory.
"""
if "cores" not in sysinfo:
return jobs, 1.0
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bcbio/bcbio-nextgen | bcbio/distributed/resources.py | calculate | def calculate(parallel, items, sysinfo, config, multiplier=1,
max_multicore=None):
"""Determine cores and workers to use for this stage based on used programs.
multiplier specifies the number of regions items will be split into during
processing.
max_multicore specifies an optional limit o... | python | def calculate(parallel, items, sysinfo, config, multiplier=1,
max_multicore=None):
"""Determine cores and workers to use for this stage based on used programs.
multiplier specifies the number of regions items will be split into during
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bcbio/bcbio-nextgen | bcbio/ngsalign/hisat2.py | create_splicesites_file | def create_splicesites_file(gtf_file, align_dir, data):
"""
if not pre-created, make a splicesites file to use with hisat2
"""
out_file = os.path.join(align_dir, "ref-transcripts-splicesites.txt")
if file_exists(out_file):
return out_file
safe_makedir(align_dir)
hisat2_ss = config_ut... | python | def create_splicesites_file(gtf_file, align_dir, data):
"""
if not pre-created, make a splicesites file to use with hisat2
"""
out_file = os.path.join(align_dir, "ref-transcripts-splicesites.txt")
if file_exists(out_file):
return out_file
safe_makedir(align_dir)
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bcbio/bcbio-nextgen | bcbio/ngsalign/hisat2.py | get_splicejunction_file | def get_splicejunction_file(align_dir, data):
"""
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splicesites file to go along with the provided file, if available.
this combines the two together and outputs a combined file of all
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"""
locate the splice junction file from hisat2. hisat2 outputs a novel
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | write_info | def write_info(dirs, parallel, config):
"""Write cluster or local filesystem resources, spinning up cluster if not present.
"""
if parallel["type"] in ["ipython"] and not parallel.get("run_local"):
out_file = _get_cache_file(dirs, parallel)
if not utils.file_exists(out_file):
sys... | python | def write_info(dirs, parallel, config):
"""Write cluster or local filesystem resources, spinning up cluster if not present.
"""
if parallel["type"] in ["ipython"] and not parallel.get("run_local"):
out_file = _get_cache_file(dirs, parallel)
if not utils.file_exists(out_file):
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | _get_machine_info | def _get_machine_info(parallel, sys_config, dirs, config):
"""Get machine resource information from the job scheduler via either the command line or the queue.
"""
if parallel.get("queue") and parallel.get("scheduler"):
# dictionary as switch statement; can add new scheduler implementation functions... | python | def _get_machine_info(parallel, sys_config, dirs, config):
"""Get machine resource information from the job scheduler via either the command line or the queue.
"""
if parallel.get("queue") and parallel.get("scheduler"):
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | _slurm_info | def _slurm_info(queue):
"""Returns machine information for a slurm job scheduler.
"""
cl = "sinfo -h -p {} --format '%c %m %D'".format(queue)
num_cpus, mem, num_nodes = subprocess.check_output(shlex.split(cl)).decode().split()
# if the queue contains multiple memory configurations, the minimum value... | python | def _slurm_info(queue):
"""Returns machine information for a slurm job scheduler.
"""
cl = "sinfo -h -p {} --format '%c %m %D'".format(queue)
num_cpus, mem, num_nodes = subprocess.check_output(shlex.split(cl)).decode().split()
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | _torque_info | def _torque_info(queue):
"""Return machine information for a torque job scheduler using pbsnodes.
To identify which host to use it tries to parse available hosts
from qstat -Qf `acl_hosts`. If found, it uses these and gets the
first node from pbsnodes matching to the list. If no attached
hosts are ... | python | def _torque_info(queue):
"""Return machine information for a torque job scheduler using pbsnodes.
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | _torque_queue_nodes | def _torque_queue_nodes(queue):
"""Retrieve the nodes available for a queue.
Parses out nodes from `acl_hosts` in qstat -Qf and extracts the
initial names of nodes used in pbsnodes.
"""
qstat_out = subprocess.check_output(["qstat", "-Qf", queue]).decode()
hosts = []
in_hosts = False
for... | python | def _torque_queue_nodes(queue):
"""Retrieve the nodes available for a queue.
Parses out nodes from `acl_hosts` in qstat -Qf and extracts the
initial names of nodes used in pbsnodes.
"""
qstat_out = subprocess.check_output(["qstat", "-Qf", queue]).decode()
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | _sge_info | def _sge_info(queue):
"""Returns machine information for an sge job scheduler.
"""
qhost_out = subprocess.check_output(["qhost", "-q", "-xml"]).decode()
qstat_queue = ["-q", queue] if queue and "," not in queue else []
qstat_out = subprocess.check_output(["qstat", "-f", "-xml"] + qstat_queue).decode... | python | def _sge_info(queue):
"""Returns machine information for an sge job scheduler.
"""
qhost_out = subprocess.check_output(["qhost", "-q", "-xml"]).decode()
qstat_queue = ["-q", queue] if queue and "," not in queue else []
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | _sge_get_slots | def _sge_get_slots(xmlstring):
""" Get slot information from qstat
"""
rootxml = ET.fromstring(xmlstring)
my_machine_dict = {}
for queue_list in rootxml.iter("Queue-List"):
# find all hosts supporting queues
my_hostname = queue_list.find("name").text.rsplit("@")[-1]
my_slots ... | python | def _sge_get_slots(xmlstring):
""" Get slot information from qstat
"""
rootxml = ET.fromstring(xmlstring)
my_machine_dict = {}
for queue_list in rootxml.iter("Queue-List"):
# find all hosts supporting queues
my_hostname = queue_list.find("name").text.rsplit("@")[-1]
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | _sge_get_mem | def _sge_get_mem(xmlstring, queue_name):
""" Get memory information from qhost
"""
rootxml = ET.fromstring(xmlstring)
my_machine_dict = {}
# on some machines rootxml.tag looks like "{...}qhost" where the "{...}" gets prepended to all attributes
rootTag = rootxml.tag.rstrip("qhost")
for host ... | python | def _sge_get_mem(xmlstring, queue_name):
""" Get memory information from qhost
"""
rootxml = ET.fromstring(xmlstring)
my_machine_dict = {}
# on some machines rootxml.tag looks like "{...}qhost" where the "{...}" gets prepended to all attributes
rootTag = rootxml.tag.rstrip("qhost")
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | get_info | def get_info(dirs, parallel, resources=None):
"""Retrieve cluster or local filesystem resources from pre-retrieved information.
"""
# Allow custom specification of cores/memory in resources
if resources and isinstance(resources, dict) and "machine" in resources:
minfo = resources["machine"]
... | python | def get_info(dirs, parallel, resources=None):
"""Retrieve cluster or local filesystem resources from pre-retrieved information.
"""
# Allow custom specification of cores/memory in resources
if resources and isinstance(resources, dict) and "machine" in resources:
minfo = resources["machine"]
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bcbio/bcbio-nextgen | bcbio/provenance/system.py | machine_info | def machine_info():
"""Retrieve core and memory information for the current machine.
"""
import psutil
BYTES_IN_GIG = 1073741824.0
free_bytes = psutil.virtual_memory().total
return [{"memory": float("%.1f" % (free_bytes / BYTES_IN_GIG)), "cores": multiprocessing.cpu_count(),
"name":... | python | def machine_info():
"""Retrieve core and memory information for the current machine.
"""
import psutil
BYTES_IN_GIG = 1073741824.0
free_bytes = psutil.virtual_memory().total
return [{"memory": float("%.1f" % (free_bytes / BYTES_IN_GIG)), "cores": multiprocessing.cpu_count(),
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bcbio/bcbio-nextgen | bcbio/rnaseq/dexseq.py | run_count | def run_count(bam_file, dexseq_gff, stranded, out_file, data):
"""
run dexseq_count on a BAM file
"""
assert file_exists(bam_file), "%s does not exist." % bam_file
sort_order = bam._get_sort_order(bam_file, {})
assert sort_order, "Cannot determine sort order of %s." % bam_file
strand_flag = ... | python | def run_count(bam_file, dexseq_gff, stranded, out_file, data):
"""
run dexseq_count on a BAM file
"""
assert file_exists(bam_file), "%s does not exist." % bam_file
sort_order = bam._get_sort_order(bam_file, {})
assert sort_order, "Cannot determine sort order of %s." % bam_file
strand_flag = ... | [
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bcbio/bcbio-nextgen | bcbio/bam/trim.py | _trim_adapters | def _trim_adapters(fastq_files, out_dir, data):
"""
for small insert sizes, the read length can be longer than the insert
resulting in the reverse complement of the 3' adapter being sequenced.
this takes adapter sequences and trims the only the reverse complement
of the adapter
MYSEQUENCEAAAARE... | python | def _trim_adapters(fastq_files, out_dir, data):
"""
for small insert sizes, the read length can be longer than the insert
resulting in the reverse complement of the 3' adapter being sequenced.
this takes adapter sequences and trims the only the reverse complement
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bcbio/bcbio-nextgen | bcbio/bam/trim.py | _cutadapt_trim | def _cutadapt_trim(fastq_files, quality_format, adapters, out_files, log_file, data):
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"""
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... | python | def _cutadapt_trim(fastq_files, quality_format, adapters, out_files, log_file, data):
"""Trimming with cutadapt.
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if all([utils.file_exists(x) for x in out_files]):
return out_files
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bcbio/bcbio-nextgen | bcbio/bam/trim.py | _cutadapt_trim_cmd | def _cutadapt_trim_cmd(fastq_files, quality_format, adapters, out_files, data):
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bcbio/bcbio-nextgen | bcbio/bam/trim.py | _cutadapt_se_cmd | def _cutadapt_se_cmd(fastq_files, out_files, base_cmd, data):
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"""
this has to use the -o option, not redirect to stdout in order for
gzipping to be supported
"""
min_length = dd.get_min_read_length(data)
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bcbio/bcbio-nextgen | bcbio/bam/trim.py | _cutadapt_pe_cmd | def _cutadapt_pe_cmd(fastq_files, out_files, quality_format, base_cmd, data):
"""
run cutadapt in paired end mode
"""
fq1, fq2 = [objectstore.cl_input(x) for x in fastq_files]
of1, of2 = out_files
base_cmd += " --minimum-length={min_length} ".format(min_length=dd.get_min_read_length(data))
f... | python | def _cutadapt_pe_cmd(fastq_files, out_files, quality_format, base_cmd, data):
"""
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fq1, fq2 = [objectstore.cl_input(x) for x in fastq_files]
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bcbio/bcbio-nextgen | bcbio/variation/realign.py | gatk_realigner_targets | def gatk_realigner_targets(runner, align_bam, ref_file, config, dbsnp=None,
region=None, out_file=None, deep_coverage=False,
variant_regions=None, known_vrns=None):
"""Generate a list of interval regions for realignment around indels.
"""
if not known_vr... | python | def gatk_realigner_targets(runner, align_bam, ref_file, config, dbsnp=None,
region=None, out_file=None, deep_coverage=False,
variant_regions=None, known_vrns=None):
"""Generate a list of interval regions for realignment around indels.
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bcbio/bcbio-nextgen | bcbio/variation/realign.py | gatk_indel_realignment_cl | def gatk_indel_realignment_cl(runner, align_bam, ref_file, intervals,
tmp_dir, region=None, deep_coverage=False,
known_vrns=None):
"""Prepare input arguments for GATK indel realignment.
"""
if not known_vrns:
known_vrns = {}
params = ["... | python | def gatk_indel_realignment_cl(runner, align_bam, ref_file, intervals,
tmp_dir, region=None, deep_coverage=False,
known_vrns=None):
"""Prepare input arguments for GATK indel realignment.
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bcbio/bcbio-nextgen | bcbio/variation/realign.py | has_aligned_reads | def has_aligned_reads(align_bam, region=None):
"""Check if the aligned BAM file has any reads in the region.
region can be a chromosome string ("chr22"),
a tuple region (("chr22", 1, 100)) or a file of regions.
"""
import pybedtools
if region is not None:
if isinstance(region, six.strin... | python | def has_aligned_reads(align_bam, region=None):
"""Check if the aligned BAM file has any reads in the region.
region can be a chromosome string ("chr22"),
a tuple region (("chr22", 1, 100)) or a file of regions.
"""
import pybedtools
if region is not None:
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bcbio/bcbio-nextgen | bcbio/cwl/defs.py | s | def s(name, parallel, inputs, outputs, image, programs=None, disk=None, cores=None, unlist=None,
no_files=False):
"""Represent a step in a workflow.
name -- The run function name, which must match a definition in distributed/multitasks
inputs -- List of input keys required for the function. Each key ... | python | def s(name, parallel, inputs, outputs, image, programs=None, disk=None, cores=None, unlist=None,
no_files=False):
"""Represent a step in a workflow.
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bcbio/bcbio-nextgen | bcbio/cwl/defs.py | w | def w(name, parallel, workflow, internal):
"""A workflow, allowing specification of sub-workflows for nested parallelization.
name and parallel are documented under the Step (s) function.
workflow -- a list of Step tuples defining the sub-workflow
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bcbio/bcbio-nextgen | bcbio/cwl/defs.py | et | def et(name, parallel, inputs, outputs, expression):
"""Represent an ExpressionTool that reorders inputs using javascript.
"""
ExpressionTool = collections.namedtuple("ExpressionTool", "name inputs outputs expression parallel")
return ExpressionTool(name, inputs, outputs, expression, parallel) | python | def et(name, parallel, inputs, outputs, expression):
"""Represent an ExpressionTool that reorders inputs using javascript.
"""
ExpressionTool = collections.namedtuple("ExpressionTool", "name inputs outputs expression parallel")
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bcbio/bcbio-nextgen | bcbio/cwl/defs.py | cwlout | def cwlout(key, valtype=None, extensions=None, fields=None, exclude=None):
"""Definition of an output variable, defining the type and associated secondary files.
"""
out = {"id": key}
if valtype:
out["type"] = valtype
if fields:
out["fields"] = fields
if extensions:
out["... | python | def cwlout(key, valtype=None, extensions=None, fields=None, exclude=None):
"""Definition of an output variable, defining the type and associated secondary files.
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out = {"id": key}
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bcbio/bcbio-nextgen | bcbio/cwl/defs.py | _variant_hla | def _variant_hla(checkpoints):
"""Add hla analysis to workflow, if configured.
"""
if not checkpoints.get("hla"):
return [], []
hla = [s("hla_to_rec", "multi-batch",
[["hla", "fastq"],
["config", "algorithm", "hlacaller"]],
[cwlout("hla_rec", "record")],... | python | def _variant_hla(checkpoints):
"""Add hla analysis to workflow, if configured.
"""
if not checkpoints.get("hla"):
return [], []
hla = [s("hla_to_rec", "multi-batch",
[["hla", "fastq"],
["config", "algorithm", "hlacaller"]],
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bcbio/bcbio-nextgen | bcbio/cwl/defs.py | variant | def variant(samples):
"""Variant calling workflow definition for CWL generation.
"""
checkpoints = _variant_checkpoints(samples)
if checkpoints["align"]:
align_wf = _alignment(checkpoints)
alignin = [["files"], ["analysis"],
["config", "algorithm", "align_split_size"],... | python | def variant(samples):
"""Variant calling workflow definition for CWL generation.
"""
checkpoints = _variant_checkpoints(samples)
if checkpoints["align"]:
align_wf = _alignment(checkpoints)
alignin = [["files"], ["analysis"],
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bcbio/bcbio-nextgen | bcbio/structural/plot.py | breakpoints_by_caller | def breakpoints_by_caller(bed_files):
"""
given a list of BED files of the form
chrom start end caller
return a BedTool of breakpoints as each line with
the fourth column the caller with evidence for the breakpoint
chr1 1 10 caller1 -> chr1 1 1 caller1
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bcbio/bcbio-nextgen | bcbio/structural/plot.py | _get_sv_callers | def _get_sv_callers(items):
"""
return a sorted list of all of the structural variant callers run
"""
callers = []
for data in items:
for sv in data.get("sv", []):
callers.append(sv["variantcaller"])
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"""
return a sorted list of all of the structural variant callers run
"""
callers = []
for data in items:
for sv in data.get("sv", []):
callers.append(sv["variantcaller"])
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bcbio/bcbio-nextgen | bcbio/structural/plot.py | _prioritize_plot_regions | def _prioritize_plot_regions(region_bt, data, out_dir=None):
"""Avoid plotting large numbers of regions due to speed issues. Prioritize most interesting.
XXX For now, just removes larger regions and avoid plotting thousands of regions.
Longer term we'll insert biology-based prioritization.
"""
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"""Avoid plotting large numbers of regions due to speed issues. Prioritize most interesting.
XXX For now, just removes larger regions and avoid plotting thousands of regions.
Longer term we'll insert biology-based prioritization.
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bcbio/bcbio-nextgen | bcbio/structural/plot.py | by_regions | def by_regions(items):
"""Plot for a union set of combined ensemble regions across all of the data
items.
"""
work_dir = os.path.join(dd.get_work_dir(items[0]), "structural", "coverage")
safe_makedir(work_dir)
out_file = os.path.join(work_dir, "%s-coverage.pdf" % (dd.get_sample_name(items[0])... | python | def by_regions(items):
"""Plot for a union set of combined ensemble regions across all of the data
items.
"""
work_dir = os.path.join(dd.get_work_dir(items[0]), "structural", "coverage")
safe_makedir(work_dir)
out_file = os.path.join(work_dir, "%s-coverage.pdf" % (dd.get_sample_name(items[0])... | [
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | finalize_sv | def finalize_sv(orig_vcf, data, items):
"""Finalize structural variants, adding effects and splitting if needed.
"""
paired = vcfutils.get_paired(items)
# For paired/somatic, attach combined calls to tumor sample
if paired:
sample_vcf = orig_vcf if paired.tumor_name == dd.get_sample_name(dat... | python | def finalize_sv(orig_vcf, data, items):
"""Finalize structural variants, adding effects and splitting if needed.
"""
paired = vcfutils.get_paired(items)
# For paired/somatic, attach combined calls to tumor sample
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | _get_sv_exclude_file | def _get_sv_exclude_file(items):
"""Retrieve SV file of regions to exclude.
"""
sv_bed = utils.get_in(items[0], ("genome_resources", "variation", "sv_repeat"))
if sv_bed and os.path.exists(sv_bed):
return sv_bed | python | def _get_sv_exclude_file(items):
"""Retrieve SV file of regions to exclude.
"""
sv_bed = utils.get_in(items[0], ("genome_resources", "variation", "sv_repeat"))
if sv_bed and os.path.exists(sv_bed):
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | _get_variant_regions | def _get_variant_regions(items):
"""Retrieve variant regions defined in any of the input items.
"""
return list(filter(lambda x: x is not None,
[tz.get_in(("config", "algorithm", "variant_regions"), data)
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"""Retrieve variant regions defined in any of the input items.
"""
return list(filter(lambda x: x is not None,
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | prepare_exclude_file | def prepare_exclude_file(items, base_file, chrom=None):
"""Prepare a BED file for exclusion.
Excludes high depth and centromere regions which contribute to long run times and
false positive structural variant calls.
"""
items = shared.add_highdepth_genome_exclusion(items)
out_file = "%s-exclude... | python | def prepare_exclude_file(items, base_file, chrom=None):
"""Prepare a BED file for exclusion.
Excludes high depth and centromere regions which contribute to long run times and
false positive structural variant calls.
"""
items = shared.add_highdepth_genome_exclusion(items)
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | exclude_by_ends | def exclude_by_ends(in_file, exclude_file, data, in_params=None):
"""Exclude calls based on overlap of the ends with exclusion regions.
Removes structural variants with either end being in a repeat: a large
source of false positives.
Parameters tuned based on removal of LCR overlapping false positives... | python | def exclude_by_ends(in_file, exclude_file, data, in_params=None):
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | _find_to_filter | def _find_to_filter(in_file, exclude_file, params, to_exclude):
"""Identify regions in the end file that overlap the exclusion file.
We look for ends with a large percentage in a repeat or where the end contains
an entire repeat.
"""
for feat in pybedtools.BedTool(in_file).intersect(pybedtools.BedT... | python | def _find_to_filter(in_file, exclude_file, params, to_exclude):
"""Identify regions in the end file that overlap the exclusion file.
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | get_sv_chroms | def get_sv_chroms(items, exclude_file):
"""Retrieve chromosomes to process on, avoiding extra skipped chromosomes.
"""
exclude_regions = {}
for region in pybedtools.BedTool(exclude_file):
if int(region.start) == 0:
exclude_regions[region.chrom] = int(region.end)
out = []
with... | python | def get_sv_chroms(items, exclude_file):
"""Retrieve chromosomes to process on, avoiding extra skipped chromosomes.
"""
exclude_regions = {}
for region in pybedtools.BedTool(exclude_file):
if int(region.start) == 0:
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | _extract_split_and_discordants | def _extract_split_and_discordants(in_bam, work_dir, data):
"""Retrieve split-read alignments from input BAM file.
"""
sr_file = os.path.join(work_dir, "%s-sr.bam" % os.path.splitext(os.path.basename(in_bam))[0])
disc_file = os.path.join(work_dir, "%s-disc.bam" % os.path.splitext(os.path.basename(in_bam... | python | def _extract_split_and_discordants(in_bam, work_dir, data):
"""Retrieve split-read alignments from input BAM file.
"""
sr_file = os.path.join(work_dir, "%s-sr.bam" % os.path.splitext(os.path.basename(in_bam))[0])
disc_file = os.path.join(work_dir, "%s-disc.bam" % os.path.splitext(os.path.basename(in_bam... | [
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | find_existing_split_discordants | def find_existing_split_discordants(data):
"""Check for pre-calculated split reads and discordants done as part of alignment streaming.
"""
in_bam = dd.get_align_bam(data)
sr_file = "%s-sr.bam" % os.path.splitext(in_bam)[0]
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if utils.file_ex... | python | def find_existing_split_discordants(data):
"""Check for pre-calculated split reads and discordants done as part of alignment streaming.
"""
in_bam = dd.get_align_bam(data)
sr_file = "%s-sr.bam" % os.path.splitext(in_bam)[0]
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | get_split_discordants | def get_split_discordants(data, work_dir):
"""Retrieve split and discordant reads, potentially calculating with extract_sv_reads as needed.
"""
align_bam = dd.get_align_bam(data)
sr_bam, disc_bam = find_existing_split_discordants(data)
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work_dir = (work_dir if not os.access(os.... | python | def get_split_discordants(data, work_dir):
"""Retrieve split and discordant reads, potentially calculating with extract_sv_reads as needed.
"""
align_bam = dd.get_align_bam(data)
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bcbio/bcbio-nextgen | bcbio/structural/shared.py | get_cur_batch | def get_cur_batch(items):
"""Retrieve name of the batch shared between all items in a group.
"""
batches = []
for data in items:
batch = tz.get_in(["metadata", "batch"], data, [])
batches.append(set(batch) if isinstance(batch, (list, tuple)) else set([batch]))
combo_batches = reduce(... | python | def get_cur_batch(items):
"""Retrieve name of the batch shared between all items in a group.
"""
batches = []
for data in items:
batch = tz.get_in(["metadata", "batch"], data, [])
batches.append(set(batch) if isinstance(batch, (list, tuple)) else set([batch]))
combo_batches = reduce(... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/shared.py#L270-L283 | train |
bcbio/bcbio-nextgen | bcbio/structural/shared.py | calc_paired_insert_stats | def calc_paired_insert_stats(in_bam, nsample=1000000):
"""Retrieve statistics for paired end read insert distances.
"""
dists = []
n = 0
with pysam.Samfile(in_bam, "rb") as in_pysam:
for read in in_pysam:
if read.is_proper_pair and read.is_read1:
n += 1
... | python | def calc_paired_insert_stats(in_bam, nsample=1000000):
"""Retrieve statistics for paired end read insert distances.
"""
dists = []
n = 0
with pysam.Samfile(in_bam, "rb") as in_pysam:
for read in in_pysam:
if read.is_proper_pair and read.is_read1:
n += 1
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/shared.py#L307-L319 | train |
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