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bcbio/bcbio-nextgen | bcbio/pipeline/genome.py | get_resources | def get_resources(genome, ref_file, data):
"""Retrieve genome information from a genome-references.yaml file.
"""
base_dir = os.path.normpath(os.path.dirname(ref_file))
resource_file = os.path.join(base_dir, "%s-resources.yaml" % genome.replace("-test", ""))
if not os.path.exists(resource_file):
... | python | def get_resources(genome, ref_file, data):
"""Retrieve genome information from a genome-references.yaml file.
"""
base_dir = os.path.normpath(os.path.dirname(ref_file))
resource_file = os.path.join(base_dir, "%s-resources.yaml" % genome.replace("-test", ""))
if not os.path.exists(resource_file):
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bcbio/bcbio-nextgen | bcbio/pipeline/genome.py | add_required_resources | def add_required_resources(resources):
"""Add default or empty values for required resources referenced in CWL
"""
required = [["variation", "cosmic"], ["variation", "clinvar"], ["variation", "dbsnp"],
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"""Add default or empty values for required resources referenced in CWL
"""
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bcbio/bcbio-nextgen | bcbio/pipeline/genome.py | ensure_annotations | def ensure_annotations(resources, data):
"""Prepare any potentially missing annotations for downstream processing in a local directory.
"""
transcript_gff = tz.get_in(["rnaseq", "transcripts"], resources)
if transcript_gff and utils.file_exists(transcript_gff):
out_dir = os.path.join(tz.get_in([... | python | def ensure_annotations(resources, data):
"""Prepare any potentially missing annotations for downstream processing in a local directory.
"""
transcript_gff = tz.get_in(["rnaseq", "transcripts"], resources)
if transcript_gff and utils.file_exists(transcript_gff):
out_dir = os.path.join(tz.get_in([... | [
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bcbio/bcbio-nextgen | bcbio/pipeline/genome.py | abs_file_paths | def abs_file_paths(xs, base_dir=None, ignore_keys=None, fileonly_keys=None, cur_key=None,
do_download=True):
"""Normalize any file paths found in a subdirectory of configuration input.
base_dir -- directory to normalize relative paths to
ignore_keys -- algorithm key names to ignore norma... | python | def abs_file_paths(xs, base_dir=None, ignore_keys=None, fileonly_keys=None, cur_key=None,
do_download=True):
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bcbio/bcbio-nextgen | bcbio/pipeline/genome.py | _get_galaxy_tool_info | def _get_galaxy_tool_info(galaxy_base):
"""Retrieve Galaxy tool-data information from defaults or galaxy config file.
"""
ini_file = os.path.join(galaxy_base, "universe_wsgi.ini")
info = {"tool_data_table_config_path": os.path.join(galaxy_base, "tool_data_table_conf.xml"),
"tool_data_path": ... | python | def _get_galaxy_tool_info(galaxy_base):
"""Retrieve Galaxy tool-data information from defaults or galaxy config file.
"""
ini_file = os.path.join(galaxy_base, "universe_wsgi.ini")
info = {"tool_data_table_config_path": os.path.join(galaxy_base, "tool_data_table_conf.xml"),
"tool_data_path": ... | [
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bcbio/bcbio-nextgen | bcbio/pipeline/genome.py | get_builds | def get_builds(galaxy_base):
"""Retrieve configured genome builds and reference files, using Galaxy configuration files.
Allows multiple dbkey specifications in the same file, using the most recently added.
"""
name = "samtools"
galaxy_config = _get_galaxy_tool_info(galaxy_base)
galaxy_dt = _ge... | python | def get_builds(galaxy_base):
"""Retrieve configured genome builds and reference files, using Galaxy configuration files.
Allows multiple dbkey specifications in the same file, using the most recently added.
"""
name = "samtools"
galaxy_config = _get_galaxy_tool_info(galaxy_base)
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bcbio/bcbio-nextgen | bcbio/variation/varscan.py | _get_jvm_opts | def _get_jvm_opts(config, tmp_dir):
"""Retrieve common options for running VarScan.
Handles jvm_opts, setting user and country to English to avoid issues
with different locales producing non-compliant VCF.
"""
resources = config_utils.get_resources("varscan", config)
jvm_opts = resources.get("jv... | python | def _get_jvm_opts(config, tmp_dir):
"""Retrieve common options for running VarScan.
Handles jvm_opts, setting user and country to English to avoid issues
with different locales producing non-compliant VCF.
"""
resources = config_utils.get_resources("varscan", config)
jvm_opts = resources.get("jv... | [
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bcbio/bcbio-nextgen | bcbio/variation/varscan.py | _varscan_options_from_config | def _varscan_options_from_config(config):
"""Retrieve additional options for VarScan from the configuration.
"""
opts = ["--min-coverage 5", "--p-value 0.98", "--strand-filter 1"]
resources = config_utils.get_resources("varscan", config)
if resources.get("options"):
opts += [str(x) for x in ... | python | def _varscan_options_from_config(config):
"""Retrieve additional options for VarScan from the configuration.
"""
opts = ["--min-coverage 5", "--p-value 0.98", "--strand-filter 1"]
resources = config_utils.get_resources("varscan", config)
if resources.get("options"):
opts += [str(x) for x in ... | [
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bcbio/bcbio-nextgen | bcbio/variation/varscan.py | spv_freq_filter | def spv_freq_filter(line, tumor_index):
"""Filter VarScan calls based on the SPV value and frequency.
Removes calls with SPV < 0.05 and a tumor FREQ > 0.35.
False positives dominate these higher frequency, low SPV calls. They appear
to be primarily non-somatic/germline variants not removed by other fi... | python | def spv_freq_filter(line, tumor_index):
"""Filter VarScan calls based on the SPV value and frequency.
Removes calls with SPV < 0.05 and a tumor FREQ > 0.35.
False positives dominate these higher frequency, low SPV calls. They appear
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bcbio/bcbio-nextgen | bcbio/variation/varscan.py | _create_sample_list | def _create_sample_list(in_bams, vcf_file):
"""Pull sample names from input BAMs and create input sample list.
"""
out_file = "%s-sample_list.txt" % os.path.splitext(vcf_file)[0]
with open(out_file, "w") as out_handle:
for in_bam in in_bams:
with pysam.Samfile(in_bam, "rb") as work_b... | python | def _create_sample_list(in_bams, vcf_file):
"""Pull sample names from input BAMs and create input sample list.
"""
out_file = "%s-sample_list.txt" % os.path.splitext(vcf_file)[0]
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bcbio/bcbio-nextgen | bcbio/variation/varscan.py | _varscan_work | def _varscan_work(align_bams, ref_file, items, target_regions, out_file):
"""Perform SNP and indel genotyping with VarScan.
"""
config = items[0]["config"]
orig_out_file = out_file
out_file = orig_out_file.replace(".vcf.gz", ".vcf")
max_read_depth = "1000"
sample_list = _create_sample_list... | python | def _varscan_work(align_bams, ref_file, items, target_regions, out_file):
"""Perform SNP and indel genotyping with VarScan.
"""
config = items[0]["config"]
orig_out_file = out_file
out_file = orig_out_file.replace(".vcf.gz", ".vcf")
max_read_depth = "1000"
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bcbio/bcbio-nextgen | bcbio/distributed/ipythontasks.py | apply | def apply(object, args=None, kwargs=None):
"""Python3 apply replacement for double unpacking of inputs during apply.
Thanks to: https://github.com/stefanholek/apply
"""
if args is None:
args = ()
if kwargs is None:
kwargs = {}
return object(*args, **kwargs) | python | def apply(object, args=None, kwargs=None):
"""Python3 apply replacement for double unpacking of inputs during apply.
Thanks to: https://github.com/stefanholek/apply
"""
if args is None:
args = ()
if kwargs is None:
kwargs = {}
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bcbio/bcbio-nextgen | bcbio/structural/annotate.py | add_genes | def add_genes(in_file, data, max_distance=10000, work_dir=None):
"""Add gene annotations to a BED file from pre-prepared RNA-seq data.
max_distance -- only keep annotations within this distance of event
"""
gene_file = regions.get_sv_bed(data, "exons", out_dir=os.path.dirname(in_file))
if gene_file... | python | def add_genes(in_file, data, max_distance=10000, work_dir=None):
"""Add gene annotations to a BED file from pre-prepared RNA-seq data.
max_distance -- only keep annotations within this distance of event
"""
gene_file = regions.get_sv_bed(data, "exons", out_dir=os.path.dirname(in_file))
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bcbio/bcbio-nextgen | bcbio/structural/annotate.py | _add_genes_to_bed | def _add_genes_to_bed(in_file, gene_file, fai_file, out_file, data, max_distance=10000):
"""Re-usable subcomponent that annotates BED file genes from another BED
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try:
input_rec = next(iter(pybedtools.BedTool(in_file)))
except StopIteration: # empty file
utils.copy_plus(in_file, out_... | python | def _add_genes_to_bed(in_file, gene_file, fai_file, out_file, data, max_distance=10000):
"""Re-usable subcomponent that annotates BED file genes from another BED
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try:
input_rec = next(iter(pybedtools.BedTool(in_file)))
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bcbio/bcbio-nextgen | bcbio/distributed/clusterk.py | create | def create(parallel):
"""Create a queue based on the provided parallel arguments.
TODO Startup/tear-down. Currently using default queue for testing
"""
queue = {k: v for k, v in parallel.items() if k in ["queue", "cores_per_job", "mem"]}
yield queue | python | def create(parallel):
"""Create a queue based on the provided parallel arguments.
TODO Startup/tear-down. Currently using default queue for testing
"""
queue = {k: v for k, v in parallel.items() if k in ["queue", "cores_per_job", "mem"]}
yield queue | [
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bcbio/bcbio-nextgen | bcbio/distributed/clusterk.py | runner | def runner(queue, parallel):
"""Run individual jobs on an existing queue.
"""
def run(fn_name, items):
logger.info("clusterk: %s" % fn_name)
assert "wrapper" in parallel, "Clusterk requires bcbio-nextgen-vm wrapper"
fn = getattr(__import__("{base}.clusterktasks".format(base=parallel[... | python | def runner(queue, parallel):
"""Run individual jobs on an existing queue.
"""
def run(fn_name, items):
logger.info("clusterk: %s" % fn_name)
assert "wrapper" in parallel, "Clusterk requires bcbio-nextgen-vm wrapper"
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bcbio/bcbio-nextgen | bcbio/structural/prioritize.py | is_gene_list | def is_gene_list(bed_file):
"""Check if the file is only a list of genes, not a BED
"""
with utils.open_gzipsafe(bed_file) as in_handle:
for line in in_handle:
if not line.startswith("#"):
if len(line.split()) == 1:
return True
else:
... | python | def is_gene_list(bed_file):
"""Check if the file is only a list of genes, not a BED
"""
with utils.open_gzipsafe(bed_file) as in_handle:
for line in in_handle:
if not line.startswith("#"):
if len(line.split()) == 1:
return True
else:
... | [
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bcbio/bcbio-nextgen | bcbio/structural/prioritize.py | _find_gene_list_from_bed | def _find_gene_list_from_bed(bed_file, base_file, data):
"""Retrieve list of gene names from input BED file.
"""
# Check for a gene list, we can just return that.
if is_gene_list(bed_file):
return bed_file
out_file = "%s-genes.txt" % utils.splitext_plus(base_file)[0]
if not os.path.exist... | python | def _find_gene_list_from_bed(bed_file, base_file, data):
"""Retrieve list of gene names from input BED file.
"""
# Check for a gene list, we can just return that.
if is_gene_list(bed_file):
return bed_file
out_file = "%s-genes.txt" % utils.splitext_plus(base_file)[0]
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bcbio/bcbio-nextgen | bcbio/structural/prioritize.py | _combine_files | def _combine_files(tsv_files, work_dir, data):
"""Combine multiple priority tsv files into a final sorted output.
"""
header = "\t".join(["caller", "sample", "chrom", "start", "end", "svtype",
"lof", "annotation", "split_read_support", "paired_support_PE", "paired_support_PR"])
s... | python | def _combine_files(tsv_files, work_dir, data):
"""Combine multiple priority tsv files into a final sorted output.
"""
header = "\t".join(["caller", "sample", "chrom", "start", "end", "svtype",
"lof", "annotation", "split_read_support", "paired_support_PE", "paired_support_PR"])
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bcbio/bcbio-nextgen | bcbio/structural/prioritize.py | _cnvkit_prioritize | def _cnvkit_prioritize(sample, genes, allele_file, metrics_file):
"""Summarize non-diploid calls with copy numbers and confidence intervals.
"""
mdf = pd.read_table(metrics_file)
mdf.columns = [x.lower() for x in mdf.columns]
if len(genes) > 0:
mdf = mdf[mdf["gene"].str.contains("|".join(gen... | python | def _cnvkit_prioritize(sample, genes, allele_file, metrics_file):
"""Summarize non-diploid calls with copy numbers and confidence intervals.
"""
mdf = pd.read_table(metrics_file)
mdf.columns = [x.lower() for x in mdf.columns]
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bcbio/bcbio-nextgen | bcbio/structural/prioritize.py | _cnv_prioritize | def _cnv_prioritize(data):
"""Perform confidence interval based prioritization for CNVs.
"""
supported = {"cnvkit": {"inputs": ["call_file", "segmetrics"], "fn": _cnvkit_prioritize}}
pcall = None
priority_files = None
for call in data.get("sv", []):
if call["variantcaller"] in supported:... | python | def _cnv_prioritize(data):
"""Perform confidence interval based prioritization for CNVs.
"""
supported = {"cnvkit": {"inputs": ["call_file", "segmetrics"], "fn": _cnvkit_prioritize}}
pcall = None
priority_files = None
for call in data.get("sv", []):
if call["variantcaller"] in supported:... | [
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | get_default_jvm_opts | def get_default_jvm_opts(tmp_dir=None, parallel_gc=False):
"""Retrieve default JVM tuning options
Avoids issues with multiple spun up Java processes running into out of memory errors.
Parallel GC can use a lot of cores on big machines and primarily helps reduce task latency
and responsiveness which are... | python | def get_default_jvm_opts(tmp_dir=None, parallel_gc=False):
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Avoids issues with multiple spun up Java processes running into out of memory errors.
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | _get_gatk_opts | def _get_gatk_opts(config, names, tmp_dir=None, memscale=None, include_gatk=True, parallel_gc=False):
"""Retrieve GATK memory specifications, moving down a list of potential specifications.
"""
if include_gatk and "gatk4" in dd.get_tools_off({"config": config}):
opts = ["-U", "LENIENT_VCF_PROCESSING... | python | def _get_gatk_opts(config, names, tmp_dir=None, memscale=None, include_gatk=True, parallel_gc=False):
"""Retrieve GATK memory specifications, moving down a list of potential specifications.
"""
if include_gatk and "gatk4" in dd.get_tools_off({"config": config}):
opts = ["-U", "LENIENT_VCF_PROCESSING... | [
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | _clean_java_out | def _clean_java_out(version_str):
"""Remove extra environmental information reported in java when querying for versions.
Java will report information like _JAVA_OPTIONS environmental variables in the output.
"""
out = []
for line in version_str.decode().split("\n"):
if line.startswith("Pick... | python | def _clean_java_out(version_str):
"""Remove extra environmental information reported in java when querying for versions.
Java will report information like _JAVA_OPTIONS environmental variables in the output.
"""
out = []
for line in version_str.decode().split("\n"):
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | get_mutect_version | def get_mutect_version(mutect_jar):
"""Retrieves version from input jar name since there is not an easy way to get MuTect version.
Check mutect jar for SomaticIndelDetector, which is an Appistry feature
"""
cl = ["java", "-Xms128m", "-Xmx256m"] + get_default_jvm_opts() + ["-jar", mutect_jar, "-h"]
w... | python | def get_mutect_version(mutect_jar):
"""Retrieves version from input jar name since there is not an easy way to get MuTect version.
Check mutect jar for SomaticIndelDetector, which is an Appistry feature
"""
cl = ["java", "-Xms128m", "-Xmx256m"] + get_default_jvm_opts() + ["-jar", mutect_jar, "-h"]
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | gatk_cmd | def gatk_cmd(name, jvm_opts, params, config=None):
"""Retrieve PATH to gatk using locally installed java.
"""
if name == "gatk":
if isinstance(config, dict) and "config" not in config:
data = {"config": config}
else:
data = config
if not data or "gatk4" not in... | python | def gatk_cmd(name, jvm_opts, params, config=None):
"""Retrieve PATH to gatk using locally installed java.
"""
if name == "gatk":
if isinstance(config, dict) and "config" not in config:
data = {"config": config}
else:
data = config
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | _gatk4_cmd | def _gatk4_cmd(jvm_opts, params, data):
"""Retrieve unified command for GATK4, using 'gatk'. GATK3 is 'gatk3'.
"""
gatk_cmd = utils.which(os.path.join(os.path.dirname(os.path.realpath(sys.executable)), "gatk"))
return "%s && export PATH=%s:\"$PATH\" && gatk --java-options '%s' %s" % \
(utils.cle... | python | def _gatk4_cmd(jvm_opts, params, data):
"""Retrieve unified command for GATK4, using 'gatk'. GATK3 is 'gatk3'.
"""
gatk_cmd = utils.which(os.path.join(os.path.dirname(os.path.realpath(sys.executable)), "gatk"))
return "%s && export PATH=%s:\"$PATH\" && gatk --java-options '%s' %s" % \
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | runner_from_path | def runner_from_path(cmd, config):
"""Simple command line runner that expects a bash cmd in the PATH.
This makes Picard tools back compatible with new approach of a single
jar + bash script.
"""
if cmd.endswith("picard"):
return PicardCmdRunner(cmd, config)
else:
raise ValueErro... | python | def runner_from_path(cmd, config):
"""Simple command line runner that expects a bash cmd in the PATH.
This makes Picard tools back compatible with new approach of a single
jar + bash script.
"""
if cmd.endswith("picard"):
return PicardCmdRunner(cmd, config)
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner._set_default_versions | def _set_default_versions(self, config):
"""Retrieve pre-computed version information for expensive to retrieve versions.
Starting up GATK takes a lot of resources so we do it once at start of analysis.
"""
out = []
for name in ["gatk", "gatk4", "picard", "mutect"]:
v... | python | def _set_default_versions(self, config):
"""Retrieve pre-computed version information for expensive to retrieve versions.
Starting up GATK takes a lot of resources so we do it once at start of analysis.
"""
out = []
for name in ["gatk", "gatk4", "picard", "mutect"]:
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner.new_resources | def new_resources(self, program):
"""Set new resource usage for the given program.
This allows customization of memory usage for particular sub-programs
of GATK like HaplotypeCaller.
"""
resources = config_utils.get_resources(program, self._config)
if resources.get("jvm_o... | python | def new_resources(self, program):
"""Set new resource usage for the given program.
This allows customization of memory usage for particular sub-programs
of GATK like HaplotypeCaller.
"""
resources = config_utils.get_resources(program, self._config)
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner.run_fn | def run_fn(self, name, *args, **kwds):
"""Run pre-built functionality that used Broad tools by name.
See the gatkrun, picardrun module for available functions.
"""
fn = None
to_check = [picardrun]
for ns in to_check:
try:
fn = getattr(ns, name... | python | def run_fn(self, name, *args, **kwds):
"""Run pre-built functionality that used Broad tools by name.
See the gatkrun, picardrun module for available functions.
"""
fn = None
to_check = [picardrun]
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner.cl_picard | def cl_picard(self, command, options, memscale=None):
"""Prepare a Picard commandline.
"""
options = ["%s=%s" % (x, y) for x, y in options]
options.append("VALIDATION_STRINGENCY=SILENT")
return self._get_picard_cmd(command, memscale=memscale) + options | python | def cl_picard(self, command, options, memscale=None):
"""Prepare a Picard commandline.
"""
options = ["%s=%s" % (x, y) for x, y in options]
options.append("VALIDATION_STRINGENCY=SILENT")
return self._get_picard_cmd(command, memscale=memscale) + options | [
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner.run | def run(self, command, options, pipe=False, get_stdout=False, memscale=None):
"""Run a Picard command with the provided option pairs.
"""
cl = self.cl_picard(command, options, memscale=memscale)
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"""Run a Picard command with the provided option pairs.
"""
cl = self.cl_picard(command, options, memscale=memscale)
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner.cl_mutect | def cl_mutect(self, params, tmp_dir):
"""Define parameters to run the mutect paired algorithm.
"""
gatk_jar = self._get_jar("muTect", ["mutect"])
# Decrease memory slightly from configuration to avoid memory allocation errors
jvm_opts = config_utils.adjust_opts(self._jvm_opts,
... | python | def cl_mutect(self, params, tmp_dir):
"""Define parameters to run the mutect paired algorithm.
"""
gatk_jar = self._get_jar("muTect", ["mutect"])
# Decrease memory slightly from configuration to avoid memory allocation errors
jvm_opts = config_utils.adjust_opts(self._jvm_opts,
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner.run_gatk | def run_gatk(self, params, tmp_dir=None, log_error=True,
data=None, region=None, memscale=None, parallel_gc=False, ld_preload=False):
"""Top level interface to running a GATK command.
ld_preload injects required libraries for Java JNI calls:
https://gatkforums.broadinstitute.or... | python | def run_gatk(self, params, tmp_dir=None, log_error=True,
data=None, region=None, memscale=None, parallel_gc=False, ld_preload=False):
"""Top level interface to running a GATK command.
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner.get_gatk_version | def get_gatk_version(self):
"""Retrieve GATK version, handling locally and config cached versions.
Calling version can be expensive due to all the startup and shutdown
of JVMs, so we prefer cached version information.
"""
if self._gatk_version is None:
self._set_defau... | python | def get_gatk_version(self):
"""Retrieve GATK version, handling locally and config cached versions.
Calling version can be expensive due to all the startup and shutdown
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"""
if self._gatk_version is None:
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner.get_mutect_version | def get_mutect_version(self):
"""Retrieve the Mutect version.
"""
if self._mutect_version is None:
mutect_jar = self._get_jar("muTect", ["mutect"])
self._mutect_version = get_mutect_version(mutect_jar)
return self._mutect_version | python | def get_mutect_version(self):
"""Retrieve the Mutect version.
"""
if self._mutect_version is None:
mutect_jar = self._get_jar("muTect", ["mutect"])
self._mutect_version = get_mutect_version(mutect_jar)
return self._mutect_version | [
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner.gatk_major_version | def gatk_major_version(self):
"""Retrieve the GATK major version, handling multiple GATK distributions.
Has special cases for GATK nightly builds, Appistry releases and
GATK prior to 2.3.
"""
full_version = self.get_gatk_version()
# Working with a recent version if using... | python | def gatk_major_version(self):
"""Retrieve the GATK major version, handling multiple GATK distributions.
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"""
full_version = self.get_gatk_version()
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner._get_picard_cmd | def _get_picard_cmd(self, command, memscale=None):
"""Retrieve the base Picard command, handling both shell scripts and directory of jars.
"""
resources = config_utils.get_resources("picard", self._config)
if memscale:
jvm_opts = get_picard_opts(self._config, memscale=memscal... | python | def _get_picard_cmd(self, command, memscale=None):
"""Retrieve the base Picard command, handling both shell scripts and directory of jars.
"""
resources = config_utils.get_resources("picard", self._config)
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bcbio/bcbio-nextgen | bcbio/broad/__init__.py | BroadRunner._get_jar | def _get_jar(self, command, alts=None, allow_missing=False):
"""Retrieve the jar for running the specified command.
"""
dirs = []
for bdir in [self._gatk_dir, self._picard_ref]:
dirs.extend([bdir,
os.path.join(bdir, os.pardir, "gatk")])
if alt... | python | def _get_jar(self, command, alts=None, allow_missing=False):
"""Retrieve the jar for running the specified command.
"""
dirs = []
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bcbio/bcbio-nextgen | bcbio/utils.py | cpmap | def cpmap(cores=1):
"""Configurable parallel map context manager.
Returns appropriate map compatible function based on configuration:
- Local single core (the default)
- Multiple local cores
"""
if int(cores) == 1:
yield itertools.imap
else:
if futures is None:
r... | python | def cpmap(cores=1):
"""Configurable parallel map context manager.
Returns appropriate map compatible function based on configuration:
- Local single core (the default)
- Multiple local cores
"""
if int(cores) == 1:
yield itertools.imap
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bcbio/bcbio-nextgen | bcbio/utils.py | map_wrap | def map_wrap(f):
"""Wrap standard function to easily pass into 'map' processing.
"""
@functools.wraps(f)
def wrapper(*args, **kwargs):
return f(*args, **kwargs)
return wrapper | python | def map_wrap(f):
"""Wrap standard function to easily pass into 'map' processing.
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@functools.wraps(f)
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bcbio/bcbio-nextgen | bcbio/utils.py | unpack_worlds | def unpack_worlds(items):
"""Handle all the ways we can pass multiple samples for back-compatibility.
"""
# Unpack nested lists of samples grouped together (old IPython style)
if isinstance(items[0], (list, tuple)) and len(items[0]) == 1:
out = []
for d in items:
assert len(d... | python | def unpack_worlds(items):
"""Handle all the ways we can pass multiple samples for back-compatibility.
"""
# Unpack nested lists of samples grouped together (old IPython style)
if isinstance(items[0], (list, tuple)) and len(items[0]) == 1:
out = []
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bcbio/bcbio-nextgen | bcbio/utils.py | safe_makedir | def safe_makedir(dname):
"""Make a directory if it doesn't exist, handling concurrent race conditions.
"""
if not dname:
return dname
num_tries = 0
max_tries = 5
while not os.path.exists(dname):
# we could get an error here if multiple processes are creating
# the directo... | python | def safe_makedir(dname):
"""Make a directory if it doesn't exist, handling concurrent race conditions.
"""
if not dname:
return dname
num_tries = 0
max_tries = 5
while not os.path.exists(dname):
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bcbio/bcbio-nextgen | bcbio/utils.py | tmpfile | def tmpfile(*args, **kwargs):
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finally:
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"""Make a tempfile, safely cleaning up file descriptors on completion.
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try:
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bcbio/bcbio-nextgen | bcbio/utils.py | file_exists | def file_exists(fname):
"""Check if a file exists and is non-empty.
"""
try:
return fname and os.path.exists(fname) and os.path.getsize(fname) > 0
except OSError:
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"""Check if a file exists and is non-empty.
"""
try:
return fname and os.path.exists(fname) and os.path.getsize(fname) > 0
except OSError:
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bcbio/bcbio-nextgen | bcbio/utils.py | get_size | def get_size(path):
""" Returns the size in bytes if `path` is a file,
or the size of all files in `path` if it's a directory.
Analogous to `du -s`.
"""
if os.path.isfile(path):
return os.path.getsize(path)
return sum(get_size(os.path.join(path, f)) for f in os.listdir(path)) | python | def get_size(path):
""" Returns the size in bytes if `path` is a file,
or the size of all files in `path` if it's a directory.
Analogous to `du -s`.
"""
if os.path.isfile(path):
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bcbio/bcbio-nextgen | bcbio/utils.py | read_galaxy_amqp_config | def read_galaxy_amqp_config(galaxy_config, base_dir):
"""Read connection information on the RabbitMQ server from Galaxy config.
"""
galaxy_config = add_full_path(galaxy_config, base_dir)
config = six.moves.configparser.ConfigParser()
config.read(galaxy_config)
amqp_config = {}
for option in ... | python | def read_galaxy_amqp_config(galaxy_config, base_dir):
"""Read connection information on the RabbitMQ server from Galaxy config.
"""
galaxy_config = add_full_path(galaxy_config, base_dir)
config = six.moves.configparser.ConfigParser()
config.read(galaxy_config)
amqp_config = {}
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bcbio/bcbio-nextgen | bcbio/utils.py | move_safe | def move_safe(origin, target):
"""
Move file, skip if exists
"""
if origin == target:
return origin
if file_exists(target):
return target
shutil.move(origin, target)
return target | python | def move_safe(origin, target):
"""
Move file, skip if exists
"""
if origin == target:
return origin
if file_exists(target):
return target
shutil.move(origin, target)
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bcbio/bcbio-nextgen | bcbio/utils.py | file_plus_index | def file_plus_index(fname):
"""Convert a file name into the file plus required indexes.
"""
exts = {".vcf": ".idx", ".bam": ".bai", ".vcf.gz": ".tbi", ".bed.gz": ".tbi",
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ext = splitext_plus(fname)[-1]
if ext in exts:
return [fname, fname + exts[ext]]
else:
... | python | def file_plus_index(fname):
"""Convert a file name into the file plus required indexes.
"""
exts = {".vcf": ".idx", ".bam": ".bai", ".vcf.gz": ".tbi", ".bed.gz": ".tbi",
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ext = splitext_plus(fname)[-1]
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bcbio/bcbio-nextgen | bcbio/utils.py | remove_plus | def remove_plus(orig):
"""Remove a fils, including biological index files.
"""
for ext in ["", ".idx", ".gbi", ".tbi", ".bai"]:
if os.path.exists(orig + ext):
remove_safe(orig + ext) | python | def remove_plus(orig):
"""Remove a fils, including biological index files.
"""
for ext in ["", ".idx", ".gbi", ".tbi", ".bai"]:
if os.path.exists(orig + ext):
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bcbio/bcbio-nextgen | bcbio/utils.py | copy_plus | def copy_plus(orig, new):
"""Copy a fils, including biological index files.
"""
for ext in ["", ".idx", ".gbi", ".tbi", ".bai"]:
if os.path.exists(orig + ext) and (not os.path.lexists(new + ext) or not os.path.exists(new + ext)):
shutil.copyfile(orig + ext, new + ext) | python | def copy_plus(orig, new):
"""Copy a fils, including biological index files.
"""
for ext in ["", ".idx", ".gbi", ".tbi", ".bai"]:
if os.path.exists(orig + ext) and (not os.path.lexists(new + ext) or not os.path.exists(new + ext)):
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bcbio/bcbio-nextgen | bcbio/utils.py | merge_config_files | def merge_config_files(fnames):
"""Merge configuration files, preferring definitions in latter files.
"""
def _load_yaml(fname):
with open(fname) as in_handle:
config = yaml.safe_load(in_handle)
return config
out = _load_yaml(fnames[0])
for fname in fnames[1:]:
cu... | python | def merge_config_files(fnames):
"""Merge configuration files, preferring definitions in latter files.
"""
def _load_yaml(fname):
with open(fname) as in_handle:
config = yaml.safe_load(in_handle)
return config
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bcbio/bcbio-nextgen | bcbio/utils.py | deepish_copy | def deepish_copy(org):
"""Improved speed deep copy for dictionaries of simple python types.
Thanks to Gregg Lind:
http://writeonly.wordpress.com/2009/05/07/deepcopy-is-a-pig-for-simple-data/
"""
out = dict().fromkeys(org)
for k, v in org.items():
if isinstance(v, dict):
out[... | python | def deepish_copy(org):
"""Improved speed deep copy for dictionaries of simple python types.
Thanks to Gregg Lind:
http://writeonly.wordpress.com/2009/05/07/deepcopy-is-a-pig-for-simple-data/
"""
out = dict().fromkeys(org)
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bcbio/bcbio-nextgen | bcbio/utils.py | reservoir_sample | def reservoir_sample(stream, num_items, item_parser=lambda x: x):
"""
samples num_items from the stream keeping each with equal probability
"""
kept = []
for index, item in enumerate(stream):
if index < num_items:
kept.append(item_parser(item))
else:
r = rando... | python | def reservoir_sample(stream, num_items, item_parser=lambda x: x):
"""
samples num_items from the stream keeping each with equal probability
"""
kept = []
for index, item in enumerate(stream):
if index < num_items:
kept.append(item_parser(item))
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bcbio/bcbio-nextgen | bcbio/utils.py | dictapply | def dictapply(d, fn):
"""
apply a function to all non-dict values in a dictionary
"""
for k, v in d.items():
if isinstance(v, dict):
v = dictapply(v, fn)
else:
d[k] = fn(v)
return d | python | def dictapply(d, fn):
"""
apply a function to all non-dict values in a dictionary
"""
for k, v in d.items():
if isinstance(v, dict):
v = dictapply(v, fn)
else:
d[k] = fn(v)
return d | [
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bcbio/bcbio-nextgen | bcbio/utils.py | Rscript_cmd | def Rscript_cmd():
"""Retrieve path to locally installed Rscript or first in PATH.
Prefers Rscript version installed via conda to a system version.
"""
rscript = which(os.path.join(get_bcbio_bin(), "Rscript"))
if rscript:
return rscript
else:
return which("Rscript") | python | def Rscript_cmd():
"""Retrieve path to locally installed Rscript or first in PATH.
Prefers Rscript version installed via conda to a system version.
"""
rscript = which(os.path.join(get_bcbio_bin(), "Rscript"))
if rscript:
return rscript
else:
return which("Rscript") | [
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bcbio/bcbio-nextgen | bcbio/utils.py | R_package_resource | def R_package_resource(package, resource):
"""
return a path to an R package resource, if it is available
"""
package_path = R_package_path(package)
if not package_path:
return None
package_resource = os.path.join(package_path, resource)
if not file_exists(package_resource):
... | python | def R_package_resource(package, resource):
"""
return a path to an R package resource, if it is available
"""
package_path = R_package_path(package)
if not package_path:
return None
package_resource = os.path.join(package_path, resource)
if not file_exists(package_resource):
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bcbio/bcbio-nextgen | bcbio/utils.py | get_java_binpath | def get_java_binpath(cmd=None):
"""Retrieve path for java to use, handling custom BCBIO_JAVA_HOME
Defaults to the dirname of cmd, or local anaconda directory
"""
if os.environ.get("BCBIO_JAVA_HOME"):
test_cmd = os.path.join(os.environ["BCBIO_JAVA_HOME"], "bin", "java")
if os.path.exists... | python | def get_java_binpath(cmd=None):
"""Retrieve path for java to use, handling custom BCBIO_JAVA_HOME
Defaults to the dirname of cmd, or local anaconda directory
"""
if os.environ.get("BCBIO_JAVA_HOME"):
test_cmd = os.path.join(os.environ["BCBIO_JAVA_HOME"], "bin", "java")
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bcbio/bcbio-nextgen | bcbio/utils.py | clear_java_home | def clear_java_home():
"""Clear JAVA_HOME environment or reset to BCBIO_JAVA_HOME.
Avoids accidental java injection but respects custom BCBIO_JAVA_HOME
command.
"""
if os.environ.get("BCBIO_JAVA_HOME"):
test_cmd = os.path.join(os.environ["BCBIO_JAVA_HOME"], "bin", "java")
if os.path... | python | def clear_java_home():
"""Clear JAVA_HOME environment or reset to BCBIO_JAVA_HOME.
Avoids accidental java injection but respects custom BCBIO_JAVA_HOME
command.
"""
if os.environ.get("BCBIO_JAVA_HOME"):
test_cmd = os.path.join(os.environ["BCBIO_JAVA_HOME"], "bin", "java")
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bcbio/bcbio-nextgen | bcbio/utils.py | perl_cmd | def perl_cmd():
"""Retrieve path to locally installed conda Perl or first in PATH.
"""
perl = which(os.path.join(get_bcbio_bin(), "perl"))
if perl:
return perl
else:
return which("perl") | python | def perl_cmd():
"""Retrieve path to locally installed conda Perl or first in PATH.
"""
perl = which(os.path.join(get_bcbio_bin(), "perl"))
if perl:
return perl
else:
return which("perl") | [
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bcbio/bcbio-nextgen | bcbio/utils.py | get_perl_exports | def get_perl_exports(tmpdir=None):
"""Environmental exports to use conda installed perl.
"""
perl_path = os.path.dirname(perl_cmd())
out = "unset PERL5LIB && export PATH=%s:\"$PATH\"" % (perl_path)
if tmpdir:
out += " && export TMPDIR=%s" % (tmpdir)
return out | python | def get_perl_exports(tmpdir=None):
"""Environmental exports to use conda installed perl.
"""
perl_path = os.path.dirname(perl_cmd())
out = "unset PERL5LIB && export PATH=%s:\"$PATH\"" % (perl_path)
if tmpdir:
out += " && export TMPDIR=%s" % (tmpdir)
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bcbio/bcbio-nextgen | bcbio/utils.py | get_all_conda_bins | def get_all_conda_bins():
"""Retrieve all possible conda bin directories, including environments.
"""
bcbio_bin = get_bcbio_bin()
conda_dir = os.path.dirname(bcbio_bin)
if os.path.join("anaconda", "envs") in conda_dir:
conda_dir = os.path.join(conda_dir[:conda_dir.rfind(os.path.join("anacond... | python | def get_all_conda_bins():
"""Retrieve all possible conda bin directories, including environments.
"""
bcbio_bin = get_bcbio_bin()
conda_dir = os.path.dirname(bcbio_bin)
if os.path.join("anaconda", "envs") in conda_dir:
conda_dir = os.path.join(conda_dir[:conda_dir.rfind(os.path.join("anacond... | [
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bcbio/bcbio-nextgen | bcbio/utils.py | get_program_python | def get_program_python(cmd):
"""Get the full path to a python version linked to the command.
Allows finding python based programs in python 2 versus python 3
environments.
"""
full_cmd = os.path.realpath(which(cmd))
cmd_python = os.path.join(os.path.dirname(full_cmd), "python")
env_python =... | python | def get_program_python(cmd):
"""Get the full path to a python version linked to the command.
Allows finding python based programs in python 2 versus python 3
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"""
full_cmd = os.path.realpath(which(cmd))
cmd_python = os.path.join(os.path.dirname(full_cmd), "python")
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bcbio/bcbio-nextgen | bcbio/utils.py | local_path_export | def local_path_export(at_start=True, env_cmd=None):
"""Retrieve paths to local install, also including environment paths if env_cmd included.
"""
paths = [get_bcbio_bin()]
if env_cmd:
env_path = os.path.dirname(get_program_python(env_cmd))
if env_path not in paths:
paths.inse... | python | def local_path_export(at_start=True, env_cmd=None):
"""Retrieve paths to local install, also including environment paths if env_cmd included.
"""
paths = [get_bcbio_bin()]
if env_cmd:
env_path = os.path.dirname(get_program_python(env_cmd))
if env_path not in paths:
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bcbio/bcbio-nextgen | bcbio/utils.py | rbind | def rbind(dfs):
"""
acts like rbind for pandas dataframes
"""
if len(dfs) == 1:
return dfs[0]
df = dfs[0]
for d in dfs[1:]:
df = df.append(d)
return df | python | def rbind(dfs):
"""
acts like rbind for pandas dataframes
"""
if len(dfs) == 1:
return dfs[0]
df = dfs[0]
for d in dfs[1:]:
df = df.append(d)
return df | [
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bcbio/bcbio-nextgen | bcbio/utils.py | sort_filenames | def sort_filenames(filenames):
"""
sort a list of files by filename only, ignoring the directory names
"""
basenames = [os.path.basename(x) for x in filenames]
indexes = [i[0] for i in sorted(enumerate(basenames), key=lambda x:x[1])]
return [filenames[x] for x in indexes] | python | def sort_filenames(filenames):
"""
sort a list of files by filename only, ignoring the directory names
"""
basenames = [os.path.basename(x) for x in filenames]
indexes = [i[0] for i in sorted(enumerate(basenames), key=lambda x:x[1])]
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bcbio/bcbio-nextgen | bcbio/utils.py | walk_json | def walk_json(d, func):
""" Walk over a parsed JSON nested structure `d`, apply `func` to each leaf element and replace it with result
"""
if isinstance(d, Mapping):
return OrderedDict((k, walk_json(v, func)) for k, v in d.items())
elif isinstance(d, list):
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""" Walk over a parsed JSON nested structure `d`, apply `func` to each leaf element and replace it with result
"""
if isinstance(d, Mapping):
return OrderedDict((k, walk_json(v, func)) for k, v in d.items())
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | _link_bam_file | def _link_bam_file(in_file, new_dir, data):
"""Provide symlinks of BAM file and existing indexes if needed.
"""
new_dir = utils.safe_makedir(new_dir)
out_file = os.path.join(new_dir, os.path.basename(in_file))
if not utils.file_exists(out_file):
out_file = os.path.join(new_dir, "%s-prealign.... | python | def _link_bam_file(in_file, new_dir, data):
"""Provide symlinks of BAM file and existing indexes if needed.
"""
new_dir = utils.safe_makedir(new_dir)
out_file = os.path.join(new_dir, os.path.basename(in_file))
if not utils.file_exists(out_file):
out_file = os.path.join(new_dir, "%s-prealign.... | [
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | _add_supplemental_bams | def _add_supplemental_bams(data):
"""Add supplemental files produced by alignment, useful for structural
variant calling.
"""
file_key = "work_bam"
if data.get(file_key):
for supext in ["disc", "sr"]:
base, ext = os.path.splitext(data[file_key])
test_file = "%s-%s%s" ... | python | def _add_supplemental_bams(data):
"""Add supplemental files produced by alignment, useful for structural
variant calling.
"""
file_key = "work_bam"
if data.get(file_key):
for supext in ["disc", "sr"]:
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | _add_hla_files | def _add_hla_files(data):
"""Add extracted fastq files of HLA alleles for typing.
"""
if "hla" not in data:
data["hla"] = {}
align_file = dd.get_align_bam(data)
hla_dir = os.path.join(os.path.dirname(align_file), "hla")
if not os.path.exists(hla_dir):
hla_files = None
else:
... | python | def _add_hla_files(data):
"""Add extracted fastq files of HLA alleles for typing.
"""
if "hla" not in data:
data["hla"] = {}
align_file = dd.get_align_bam(data)
hla_dir = os.path.join(os.path.dirname(align_file), "hla")
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | prep_samples | def prep_samples(*items):
"""Handle any global preparatory steps for samples with potentially shared data.
Avoids race conditions in postprocess alignment when performing prep tasks
on shared files between multiple similar samples.
Cleans input BED files to avoid issues with overlapping input segments... | python | def prep_samples(*items):
"""Handle any global preparatory steps for samples with potentially shared data.
Avoids race conditions in postprocess alignment when performing prep tasks
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | clean_inputs | def clean_inputs(data):
"""Clean BED input files to avoid overlapping segments that cause downstream issues.
Per-merges inputs to avoid needing to call multiple times during later parallel steps.
"""
if not utils.get_in(data, ("config", "algorithm", "variant_regions_orig")):
data["config"]["alg... | python | def clean_inputs(data):
"""Clean BED input files to avoid overlapping segments that cause downstream issues.
Per-merges inputs to avoid needing to call multiple times during later parallel steps.
"""
if not utils.get_in(data, ("config", "algorithm", "variant_regions_orig")):
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | postprocess_alignment | def postprocess_alignment(data):
"""Perform post-processing steps required on full BAM files.
Prepares list of callable genome regions allowing subsequent parallelization.
"""
data = cwlutils.normalize_missing(utils.to_single_data(data))
data = cwlutils.unpack_tarballs(data, data)
bam_file = dat... | python | def postprocess_alignment(data):
"""Perform post-processing steps required on full BAM files.
Prepares list of callable genome regions allowing subsequent parallelization.
"""
data = cwlutils.normalize_missing(utils.to_single_data(data))
data = cwlutils.unpack_tarballs(data, data)
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | _merge_out_from_infiles | def _merge_out_from_infiles(in_files):
"""Generate output merged file name from set of input files.
Handles non-shared filesystems where we don't know output path when setting
up split parts.
"""
fname = os.path.commonprefix([os.path.basename(f) for f in in_files])
while fname.endswith(("-", "_... | python | def _merge_out_from_infiles(in_files):
"""Generate output merged file name from set of input files.
Handles non-shared filesystems where we don't know output path when setting
up split parts.
"""
fname = os.path.commonprefix([os.path.basename(f) for f in in_files])
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | delayed_bam_merge | def delayed_bam_merge(data):
"""Perform a merge on previously prepped files, delayed in processing.
Handles merging of associated split read and discordant files if present.
"""
if data.get("combine"):
assert len(data["combine"].keys()) == 1
file_key = list(data["combine"].keys())[0]
... | python | def delayed_bam_merge(data):
"""Perform a merge on previously prepped files, delayed in processing.
Handles merging of associated split read and discordant files if present.
"""
if data.get("combine"):
assert len(data["combine"].keys()) == 1
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | merge_split_alignments | def merge_split_alignments(data):
"""Merge split BAM inputs generated by common workflow language runs.
"""
data = utils.to_single_data(data)
data = _merge_align_bams(data)
data = _merge_hla_fastq_inputs(data)
return [[data]] | python | def merge_split_alignments(data):
"""Merge split BAM inputs generated by common workflow language runs.
"""
data = utils.to_single_data(data)
data = _merge_align_bams(data)
data = _merge_hla_fastq_inputs(data)
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | _merge_align_bams | def _merge_align_bams(data):
"""Merge multiple alignment BAMs, including split and discordant reads.
"""
for key in (["work_bam"], ["work_bam_plus", "disc"], ["work_bam_plus", "sr"], ["umi_bam"]):
in_files = tz.get_in(key, data, [])
if not isinstance(in_files, (list, tuple)):
in_... | python | def _merge_align_bams(data):
"""Merge multiple alignment BAMs, including split and discordant reads.
"""
for key in (["work_bam"], ["work_bam_plus", "disc"], ["work_bam_plus", "sr"], ["umi_bam"]):
in_files = tz.get_in(key, data, [])
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | _merge_hla_fastq_inputs | def _merge_hla_fastq_inputs(data):
"""Merge HLA inputs from a split initial alignment.
"""
hla_key = ["hla", "fastq"]
hla_sample_files = [x for x in (tz.get_in(hla_key, data) or []) if x and x != "None"]
merged_hlas = None
if hla_sample_files:
out_files = collections.defaultdict(list)
... | python | def _merge_hla_fastq_inputs(data):
"""Merge HLA inputs from a split initial alignment.
"""
hla_key = ["hla", "fastq"]
hla_sample_files = [x for x in (tz.get_in(hla_key, data) or []) if x and x != "None"]
merged_hlas = None
if hla_sample_files:
out_files = collections.defaultdict(list)
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bcbio/bcbio-nextgen | bcbio/pipeline/sample.py | prepare_bcbio_samples | def prepare_bcbio_samples(sample):
"""
Function that will use specific function to merge input files
"""
logger.info("Preparing %s files %s to merge into %s." % (sample['name'], sample['files'], sample['out_file']))
if sample['fn'] == "fq_merge":
out_file = fq_merge(sample['files'], sample['... | python | def prepare_bcbio_samples(sample):
"""
Function that will use specific function to merge input files
"""
logger.info("Preparing %s files %s to merge into %s." % (sample['name'], sample['files'], sample['out_file']))
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bcbio/bcbio-nextgen | bcbio/heterogeneity/__init__.py | _get_calls | def _get_calls(data, cnv_only=False):
"""Retrieve calls, organized by name, to use for heterogeneity analysis.
"""
cnvs_supported = set(["cnvkit", "battenberg"])
out = {}
for sv in data.get("sv", []):
if not cnv_only or sv["variantcaller"] in cnvs_supported:
out[sv["variantcaller... | python | def _get_calls(data, cnv_only=False):
"""Retrieve calls, organized by name, to use for heterogeneity analysis.
"""
cnvs_supported = set(["cnvkit", "battenberg"])
out = {}
for sv in data.get("sv", []):
if not cnv_only or sv["variantcaller"] in cnvs_supported:
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bcbio/bcbio-nextgen | bcbio/heterogeneity/__init__.py | get_variants | def get_variants(data, include_germline=False):
"""Retrieve set of variant calls to use for heterogeneity analysis.
"""
data = utils.deepish_copy(data)
supported = ["precalled", "vardict", "vardict-java", "vardict-perl",
"freebayes", "octopus", "strelka2"]
# Right now mutect2 and mu... | python | def get_variants(data, include_germline=False):
"""Retrieve set of variant calls to use for heterogeneity analysis.
"""
data = utils.deepish_copy(data)
supported = ["precalled", "vardict", "vardict-java", "vardict-perl",
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bcbio/bcbio-nextgen | bcbio/heterogeneity/__init__.py | _ready_for_het_analysis | def _ready_for_het_analysis(items):
"""Check if a sample has input information for heterogeneity analysis.
We currently require a tumor/normal sample containing both CNV and variant calls.
"""
paired = vcfutils.get_paired_bams([dd.get_align_bam(d) for d in items], items)
has_het = any(dd.get_hetcal... | python | def _ready_for_het_analysis(items):
"""Check if a sample has input information for heterogeneity analysis.
We currently require a tumor/normal sample containing both CNV and variant calls.
"""
paired = vcfutils.get_paired_bams([dd.get_align_bam(d) for d in items], items)
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bcbio/bcbio-nextgen | bcbio/heterogeneity/__init__.py | run | def run(items, run_parallel):
"""Top level entry point for calculating heterogeneity, handles organization and job distribution.
"""
to_process = []
extras = []
for batch, cur_items in _group_by_batches(items).items():
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"""Top level entry point for calculating heterogeneity, handles organization and job distribution.
"""
to_process = []
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | create_inputs | def create_inputs(data):
"""Index input reads and prepare groups of reads to process concurrently.
Allows parallelization of alignment beyond processors available on a single
machine. Prepares a bgzip and grabix indexed file for retrieving sections
of files.
"""
from bcbio.pipeline import sampl... | python | def create_inputs(data):
"""Index input reads and prepare groups of reads to process concurrently.
Allows parallelization of alignment beyond processors available on a single
machine. Prepares a bgzip and grabix indexed file for retrieving sections
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"""
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | _set_align_split_size | def _set_align_split_size(data):
"""Set useful align_split_size, generating an estimate if it doesn't exist.
We try to split on larger inputs and avoid too many pieces, aiming for size
chunks of 5Gb or at most 50 maximum splits.
The size estimate used in calculations is 20 million reads for ~5Gb.
... | python | def _set_align_split_size(data):
"""Set useful align_split_size, generating an estimate if it doesn't exist.
We try to split on larger inputs and avoid too many pieces, aiming for size
chunks of 5Gb or at most 50 maximum splits.
The size estimate used in calculations is 20 million reads for ~5Gb.
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | _pick_align_split_size | def _pick_align_split_size(total_size, target_size, target_size_reads, max_splits):
"""Do the work of picking an alignment split size for the given criteria.
"""
# Too many pieces, increase our target size to get max_splits pieces
if total_size // target_size > max_splits:
piece_size = total_siz... | python | def _pick_align_split_size(total_size, target_size, target_size_reads, max_splits):
"""Do the work of picking an alignment split size for the given criteria.
"""
# Too many pieces, increase our target size to get max_splits pieces
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | split_namedpipe_cls | def split_namedpipe_cls(pair1_file, pair2_file, data):
"""Create a commandline suitable for use as a named pipe with reads in a given region.
"""
if "align_split" in data:
start, end = [int(x) for x in data["align_split"].split("-")]
else:
start, end = None, None
if pair1_file.endswi... | python | def split_namedpipe_cls(pair1_file, pair2_file, data):
"""Create a commandline suitable for use as a named pipe with reads in a given region.
"""
if "align_split" in data:
start, end = [int(x) for x in data["align_split"].split("-")]
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | _seqtk_fastq_prep_cl | def _seqtk_fastq_prep_cl(data, in_file=None, read_num=0):
"""Provide a commandline for prep of fastq inputs with seqtk.
Handles fast conversion of fastq quality scores and trimming.
"""
needs_convert = dd.get_quality_format(data).lower() == "illumina"
trim_ends = dd.get_trim_ends(data)
seqtk = ... | python | def _seqtk_fastq_prep_cl(data, in_file=None, read_num=0):
"""Provide a commandline for prep of fastq inputs with seqtk.
Handles fast conversion of fastq quality scores and trimming.
"""
needs_convert = dd.get_quality_format(data).lower() == "illumina"
trim_ends = dd.get_trim_ends(data)
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | fastq_convert_pipe_cl | def fastq_convert_pipe_cl(in_file, data):
"""Create an anonymous pipe converting Illumina 1.3-1.7 to Sanger.
Uses seqtk: https://github.com/lh3/seqt
"""
cmd = _seqtk_fastq_prep_cl(data, in_file)
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cat_cmd = "zcat" if in_file.endswith(".gz") else "cat"
cmd = cat_cmd + " " +... | python | def fastq_convert_pipe_cl(in_file, data):
"""Create an anonymous pipe converting Illumina 1.3-1.7 to Sanger.
Uses seqtk: https://github.com/lh3/seqt
"""
cmd = _seqtk_fastq_prep_cl(data, in_file)
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | parallel_multiplier | def parallel_multiplier(items):
"""Determine if we will be parallelizing items during processing.
"""
multiplier = 1
for data in (x[0] for x in items):
if (tz.get_in(["config", "algorithm", "align_split_size"], data) is not False and
tz.get_in(["algorithm", "align_split_size"], dat... | python | def parallel_multiplier(items):
"""Determine if we will be parallelizing items during processing.
"""
multiplier = 1
for data in (x[0] for x in items):
if (tz.get_in(["config", "algorithm", "align_split_size"], data) is not False and
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | setup_combine | def setup_combine(final_file, data):
"""Setup the data and outputs to allow merging data back together.
"""
if "align_split" not in data:
return final_file, data
align_dir = os.path.dirname(final_file)
base, ext = os.path.splitext(os.path.basename(final_file))
start, end = [int(x) for x ... | python | def setup_combine(final_file, data):
"""Setup the data and outputs to allow merging data back together.
"""
if "align_split" not in data:
return final_file, data
align_dir = os.path.dirname(final_file)
base, ext = os.path.splitext(os.path.basename(final_file))
start, end = [int(x) for x ... | [
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | merge_split_alignments | def merge_split_alignments(samples, run_parallel):
"""Manage merging split alignments back into a final working BAM file.
Perform de-duplication on the final merged file.
"""
ready = []
file_key = "work_bam"
to_merge = collections.defaultdict(list)
for data in (xs[0] for xs in samples):
... | python | def merge_split_alignments(samples, run_parallel):
"""Manage merging split alignments back into a final working BAM file.
Perform de-duplication on the final merged file.
"""
ready = []
file_key = "work_bam"
to_merge = collections.defaultdict(list)
for data in (xs[0] for xs in samples):
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | _save_fastq_space | def _save_fastq_space(items):
"""Potentially save fastq space prior to merging, since alignments done.
"""
to_cleanup = {}
for data in (utils.to_single_data(x) for x in items):
for fname in data.get("files", []):
if os.path.realpath(fname).startswith(dd.get_work_dir(data)):
... | python | def _save_fastq_space(items):
"""Potentially save fastq space prior to merging, since alignments done.
"""
to_cleanup = {}
for data in (utils.to_single_data(x) for x in items):
for fname in data.get("files", []):
if os.path.realpath(fname).startswith(dd.get_work_dir(data)):
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | total_reads_from_grabix | def total_reads_from_grabix(in_file):
"""Retrieve total reads in a fastq file from grabix index.
"""
gbi_file = _get_grabix_index(in_file)
if gbi_file:
with open(gbi_file) as in_handle:
next(in_handle) # throw away
num_lines = int(next(in_handle).strip())
assert ... | python | def total_reads_from_grabix(in_file):
"""Retrieve total reads in a fastq file from grabix index.
"""
gbi_file = _get_grabix_index(in_file)
if gbi_file:
with open(gbi_file) as in_handle:
next(in_handle) # throw away
num_lines = int(next(in_handle).strip())
assert ... | [
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | _find_read_splits | def _find_read_splits(in_file, split_size):
"""Determine sections of fastq files to process in splits.
Assumes a 4 line order to input files (name, read, name, quality).
grabix is 1-based inclusive, so return coordinates in that format.
"""
num_lines = total_reads_from_grabix(in_file) * 4
asser... | python | def _find_read_splits(in_file, split_size):
"""Determine sections of fastq files to process in splits.
Assumes a 4 line order to input files (name, read, name, quality).
grabix is 1-based inclusive, so return coordinates in that format.
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num_lines = total_reads_from_grabix(in_file) * 4
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | _ready_gzip_fastq | def _ready_gzip_fastq(in_files, data, require_bgzip=False):
"""Check if we have gzipped fastq and don't need format conversion or splitting.
Avoid forcing bgzip if we don't need indexed files.
"""
all_gzipped = all([not x or x.endswith(".gz") for x in in_files])
if require_bgzip and all_gzipped:
... | python | def _ready_gzip_fastq(in_files, data, require_bgzip=False):
"""Check if we have gzipped fastq and don't need format conversion or splitting.
Avoid forcing bgzip if we don't need indexed files.
"""
all_gzipped = all([not x or x.endswith(".gz") for x in in_files])
if require_bgzip and all_gzipped:
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | prep_fastq_inputs | def prep_fastq_inputs(in_files, data):
"""Prepare bgzipped fastq inputs
"""
if len(in_files) == 1 and _is_bam_input(in_files):
out = _bgzip_from_bam(in_files[0], data["dirs"], data)
elif len(in_files) == 1 and _is_cram_input(in_files):
out = _bgzip_from_cram(in_files[0], data["dirs"], da... | python | def prep_fastq_inputs(in_files, data):
"""Prepare bgzipped fastq inputs
"""
if len(in_files) == 1 and _is_bam_input(in_files):
out = _bgzip_from_bam(in_files[0], data["dirs"], data)
elif len(in_files) == 1 and _is_cram_input(in_files):
out = _bgzip_from_cram(in_files[0], data["dirs"], da... | [
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bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | _symlink_or_copy_grabix | def _symlink_or_copy_grabix(in_file, out_file, data):
"""We cannot symlink in CWL, but may be able to use inputs or copy
"""
if cwlutils.is_cwl_run(data):
# Has grabix indexes, we're okay to go
if utils.file_exists(in_file + ".gbi"):
out_file = in_file
else:
u... | python | def _symlink_or_copy_grabix(in_file, out_file, data):
"""We cannot symlink in CWL, but may be able to use inputs or copy
"""
if cwlutils.is_cwl_run(data):
# Has grabix indexes, we're okay to go
if utils.file_exists(in_file + ".gbi"):
out_file = in_file
else:
u... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/ngsalign/alignprep.py#L372-L383 | train |
bcbio/bcbio-nextgen | bcbio/ngsalign/alignprep.py | _prep_grabix_indexes | def _prep_grabix_indexes(in_files, data):
"""Parallel preparation of grabix indexes for files.
"""
# if we have gzipped but not bgzipped, add a fake index for CWL support
# Also skips bgzip indexing if we don't need alignment splitting
if _ready_gzip_fastq(in_files, data) and (not _ready_gzip_fastq(... | python | def _prep_grabix_indexes(in_files, data):
"""Parallel preparation of grabix indexes for files.
"""
# if we have gzipped but not bgzipped, add a fake index for CWL support
# Also skips bgzip indexing if we don't need alignment splitting
if _ready_gzip_fastq(in_files, data) and (not _ready_gzip_fastq(... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/ngsalign/alignprep.py#L385-L400 | train |
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