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223,100 | bcbio/bcbio-nextgen | bcbio/variation/effects.py | get_db | def get_db(data):
"""Retrieve a snpEff database name and location relative to reference file.
"""
snpeff_db = utils.get_in(data, ("genome_resources", "aliases", "snpeff"))
snpeff_base_dir = None
if snpeff_db:
snpeff_base_dir = utils.get_in(data, ("reference", "snpeff"))
if not (isins... | python | def get_db(data):
"""Retrieve a snpEff database name and location relative to reference file.
"""
snpeff_db = utils.get_in(data, ("genome_resources", "aliases", "snpeff"))
snpeff_base_dir = None
if snpeff_db:
snpeff_base_dir = utils.get_in(data, ("reference", "snpeff"))
if not (isins... | [
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223,101 | bcbio/bcbio-nextgen | bcbio/variation/effects.py | _get_snpeff_cmd | def _get_snpeff_cmd(cmd_name, datadir, data, out_file):
"""Retrieve snpEff base command line.
"""
resources = config_utils.get_resources("snpeff", data["config"])
jvm_opts = resources.get("jvm_opts", ["-Xms750m", "-Xmx3g"])
# scale by cores, defaulting to 2x base usage to ensure we have enough memor... | python | def _get_snpeff_cmd(cmd_name, datadir, data, out_file):
"""Retrieve snpEff base command line.
"""
resources = config_utils.get_resources("snpeff", data["config"])
jvm_opts = resources.get("jvm_opts", ["-Xms750m", "-Xmx3g"])
# scale by cores, defaulting to 2x base usage to ensure we have enough memor... | [
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223,102 | bcbio/bcbio-nextgen | bcbio/variation/effects.py | _run_snpeff | def _run_snpeff(snp_in, out_format, data):
"""Run effects prediction with snpEff, skipping if snpEff database not present.
"""
snpeff_db, datadir = get_db(data)
if not snpeff_db:
return None, None
assert os.path.exists(os.path.join(datadir, snpeff_db)), \
"Did not find %s snpEff gen... | python | def _run_snpeff(snp_in, out_format, data):
"""Run effects prediction with snpEff, skipping if snpEff database not present.
"""
snpeff_db, datadir = get_db(data)
if not snpeff_db:
return None, None
assert os.path.exists(os.path.join(datadir, snpeff_db)), \
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223,103 | bcbio/bcbio-nextgen | bcbio/variation/effects.py | _installed_snpeff_genome | def _installed_snpeff_genome(base_name, config):
"""Find the most recent installed genome for snpEff with the given name.
"""
snpeff_config_file = os.path.join(config_utils.get_program("snpeff", config, "dir"),
"snpEff.config")
if os.path.exists(snpeff_config_file):... | python | def _installed_snpeff_genome(base_name, config):
"""Find the most recent installed genome for snpEff with the given name.
"""
snpeff_config_file = os.path.join(config_utils.get_program("snpeff", config, "dir"),
"snpEff.config")
if os.path.exists(snpeff_config_file):... | [
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223,104 | bcbio/bcbio-nextgen | bcbio/ngsalign/minimap2.py | remap_index_fn | def remap_index_fn(ref_file):
"""minimap2 can build indexes on the fly but will also store commons ones.
"""
index_dir = os.path.join(os.path.dirname(ref_file), os.pardir, "minimap2")
if os.path.exists(index_dir) and os.path.isdir(index_dir):
return index_dir
else:
return os.path.dir... | python | def remap_index_fn(ref_file):
"""minimap2 can build indexes on the fly but will also store commons ones.
"""
index_dir = os.path.join(os.path.dirname(ref_file), os.pardir, "minimap2")
if os.path.exists(index_dir) and os.path.isdir(index_dir):
return index_dir
else:
return os.path.dir... | [
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223,105 | bcbio/bcbio-nextgen | scripts/bcbio_prepare_samples.py | create_new_csv | def create_new_csv(samples, args):
"""create csv file that can be use with bcbio -w template"""
out_fn = os.path.splitext(args.csv)[0] + "-merged.csv"
logger.info("Preparing new csv: %s" % out_fn)
with file_transaction(out_fn) as tx_out:
with open(tx_out, 'w') as handle:
handle.write... | python | def create_new_csv(samples, args):
"""create csv file that can be use with bcbio -w template"""
out_fn = os.path.splitext(args.csv)[0] + "-merged.csv"
logger.info("Preparing new csv: %s" % out_fn)
with file_transaction(out_fn) as tx_out:
with open(tx_out, 'w') as handle:
handle.write... | [
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223,106 | bcbio/bcbio-nextgen | scripts/bcbio_prepare_samples.py | _get_samples_to_process | def _get_samples_to_process(fn, out_dir, config, force_single, separators):
"""parse csv file with one line per file. It will merge
all files that have the same description name"""
out_dir = os.path.abspath(out_dir)
samples = defaultdict(list)
with open(fn) as handle:
for l in handle:
... | python | def _get_samples_to_process(fn, out_dir, config, force_single, separators):
"""parse csv file with one line per file. It will merge
all files that have the same description name"""
out_dir = os.path.abspath(out_dir)
samples = defaultdict(list)
with open(fn) as handle:
for l in handle:
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223,107 | bcbio/bcbio-nextgen | scripts/bcbio_prepare_samples.py | _check_stems | def _check_stems(files):
"""check if stem names are the same and use full path then"""
used = set()
for fn in files:
if os.path.basename(fn) in used:
logger.warning("%s stem is multiple times in your file list, "
"so we don't know "
"how ... | python | def _check_stems(files):
"""check if stem names are the same and use full path then"""
used = set()
for fn in files:
if os.path.basename(fn) in used:
logger.warning("%s stem is multiple times in your file list, "
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223,108 | bcbio/bcbio-nextgen | scripts/bcbio_prepare_samples.py | get_cluster_view | def get_cluster_view(p):
"""get ipython running"""
from cluster_helper import cluster as ipc
return ipc.cluster_view(p['scheduler'], p['queue'], p['num_jobs'], p['cores_per_job'], start_wait=p['timeout'], extra_params={"resources": p['resources'], "mem": p['mem'], "tag": p['tag'], "run_local": False}) | python | def get_cluster_view(p):
"""get ipython running"""
from cluster_helper import cluster as ipc
return ipc.cluster_view(p['scheduler'], p['queue'], p['num_jobs'], p['cores_per_job'], start_wait=p['timeout'], extra_params={"resources": p['resources'], "mem": p['mem'], "tag": p['tag'], "run_local": False}) | [
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223,109 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | from_sample | def from_sample(sample):
"""Upload results of processing from an analysis pipeline sample.
"""
upload_config = sample.get("upload")
if upload_config:
approach = _approaches[upload_config.get("method", "filesystem")]
for finfo in _get_files(sample):
approach.update_file(finfo,... | python | def from_sample(sample):
"""Upload results of processing from an analysis pipeline sample.
"""
upload_config = sample.get("upload")
if upload_config:
approach = _approaches[upload_config.get("method", "filesystem")]
for finfo in _get_files(sample):
approach.update_file(finfo,... | [
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223,110 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | _get_files | def _get_files(sample):
"""Retrieve files for the sample, dispatching by analysis type.
Each file is a dictionary containing the path plus associated
metadata about the file and pipeline versions.
"""
analysis = sample.get("analysis")
if analysis.lower() in ["variant", "snp calling", "variant2"... | python | def _get_files(sample):
"""Retrieve files for the sample, dispatching by analysis type.
Each file is a dictionary containing the path plus associated
metadata about the file and pipeline versions.
"""
analysis = sample.get("analysis")
if analysis.lower() in ["variant", "snp calling", "variant2"... | [
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223,111 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | _add_meta | def _add_meta(xs, sample=None, config=None):
"""Add top level information about the sample or flowcell to output.
Sorts outputs into sample names (sample input) and project (config input).
"""
out = []
for x in xs:
if not isinstance(x["path"], six.string_types) or not os.path.exists(x["path... | python | def _add_meta(xs, sample=None, config=None):
"""Add top level information about the sample or flowcell to output.
Sorts outputs into sample names (sample input) and project (config input).
"""
out = []
for x in xs:
if not isinstance(x["path"], six.string_types) or not os.path.exists(x["path... | [
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223,112 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | _get_files_variantcall | def _get_files_variantcall(sample):
"""Return output files for the variant calling pipeline.
"""
out = []
algorithm = sample["config"]["algorithm"]
out = _maybe_add_summary(algorithm, sample, out)
out = _maybe_add_alignment(algorithm, sample, out)
out = _maybe_add_callable(sample, out)
o... | python | def _get_files_variantcall(sample):
"""Return output files for the variant calling pipeline.
"""
out = []
algorithm = sample["config"]["algorithm"]
out = _maybe_add_summary(algorithm, sample, out)
out = _maybe_add_alignment(algorithm, sample, out)
out = _maybe_add_callable(sample, out)
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223,113 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | _maybe_add_callable | def _maybe_add_callable(data, out):
"""Add callable and depth regions to output folder.
"""
callable_bed = dd.get_sample_callable(data)
if callable_bed:
out.append({"path": callable_bed, "type": "bed", "ext": "callable"})
perbase_bed = tz.get_in(["depth", "variant_regions", "per_base"], data... | python | def _maybe_add_callable(data, out):
"""Add callable and depth regions to output folder.
"""
callable_bed = dd.get_sample_callable(data)
if callable_bed:
out.append({"path": callable_bed, "type": "bed", "ext": "callable"})
perbase_bed = tz.get_in(["depth", "variant_regions", "per_base"], data... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/upload/__init__.py#L183-L192 |
223,114 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | _get_batch_name | def _get_batch_name(sample):
"""Retrieve batch name for use in SV calling outputs.
Handles multiple batches split via SV calling.
"""
batch = dd.get_batch(sample) or dd.get_sample_name(sample)
if isinstance(batch, (list, tuple)) and len(batch) > 1:
batch = dd.get_sample_name(sample)
ret... | python | def _get_batch_name(sample):
"""Retrieve batch name for use in SV calling outputs.
Handles multiple batches split via SV calling.
"""
batch = dd.get_batch(sample) or dd.get_sample_name(sample)
if isinstance(batch, (list, tuple)) and len(batch) > 1:
batch = dd.get_sample_name(sample)
ret... | [
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223,115 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | _sample_variant_file_in_population | def _sample_variant_file_in_population(x):
"""Check if a sample file is the same as the population file.
This is true for batches where we don't extract into samples and do not
run decomposition for gemini.
'"""
if "population" in x:
a = _get_project_vcf(x)
b = _get_variant_file(x, ... | python | def _sample_variant_file_in_population(x):
"""Check if a sample file is the same as the population file.
This is true for batches where we don't extract into samples and do not
run decomposition for gemini.
'"""
if "population" in x:
a = _get_project_vcf(x)
b = _get_variant_file(x, ... | [
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223,116 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | _get_variant_file | def _get_variant_file(x, key, suffix="", sample=None, ignore_do_upload=False):
"""Retrieve VCF file with the given key if it exists, handling bgzipped.
"""
out = []
fname = utils.get_in(x, key)
upload_key = list(key)
upload_key[-1] = "do_upload"
do_upload = tz.get_in(tuple(upload_key), x, Tr... | python | def _get_variant_file(x, key, suffix="", sample=None, ignore_do_upload=False):
"""Retrieve VCF file with the given key if it exists, handling bgzipped.
"""
out = []
fname = utils.get_in(x, key)
upload_key = list(key)
upload_key[-1] = "do_upload"
do_upload = tz.get_in(tuple(upload_key), x, Tr... | [
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223,117 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | _add_batch | def _add_batch(x, sample):
"""Potentially add batch name to an upload file.
"""
added = False
for batch in sorted(dd.get_batches(sample) or [], key=len, reverse=True):
if batch and os.path.basename(x["path"]).startswith(("%s-" % batch, "%s.vcf" % batch)):
x["batch"] = batch
... | python | def _add_batch(x, sample):
"""Potentially add batch name to an upload file.
"""
added = False
for batch in sorted(dd.get_batches(sample) or [], key=len, reverse=True):
if batch and os.path.basename(x["path"]).startswith(("%s-" % batch, "%s.vcf" % batch)):
x["batch"] = batch
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223,118 | bcbio/bcbio-nextgen | bcbio/upload/__init__.py | _get_project_vcf | def _get_project_vcf(x, suffix=""):
"""Get our project VCF, either from the population or the variant batch file.
"""
vcfs = _get_variant_file(x, ("population", "vcf"), suffix=suffix)
if not vcfs:
vcfs = _get_variant_file(x, ("vrn_file_batch", ), suffix=suffix, ignore_do_upload=True)
if ... | python | def _get_project_vcf(x, suffix=""):
"""Get our project VCF, either from the population or the variant batch file.
"""
vcfs = _get_variant_file(x, ("population", "vcf"), suffix=suffix)
if not vcfs:
vcfs = _get_variant_file(x, ("vrn_file_batch", ), suffix=suffix, ignore_do_upload=True)
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223,119 | bcbio/bcbio-nextgen | scripts/utils/resort_bam_karyotype.py | _id_remapper | def _id_remapper(orig, new):
"""Provide a dictionary remapping original read indexes to new indexes.
When re-ordering the header, the individual read identifiers need to be
updated as well.
"""
new_chrom_to_index = {}
for i_n, (chr_n, _) in enumerate(new):
new_chrom_to_index[chr_n] = i_... | python | def _id_remapper(orig, new):
"""Provide a dictionary remapping original read indexes to new indexes.
When re-ordering the header, the individual read identifiers need to be
updated as well.
"""
new_chrom_to_index = {}
for i_n, (chr_n, _) in enumerate(new):
new_chrom_to_index[chr_n] = i_... | [
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223,120 | bcbio/bcbio-nextgen | scripts/bcbio_setup_genome.py | _clean_rec_name | def _clean_rec_name(rec):
"""Clean illegal characters in input fasta file which cause problems downstream.
"""
out_id = []
for char in list(rec.id):
if char in ALLOWED_CONTIG_NAME_CHARS:
out_id.append(char)
else:
out_id.append("_")
rec.id = "".join(out_id)
... | python | def _clean_rec_name(rec):
"""Clean illegal characters in input fasta file which cause problems downstream.
"""
out_id = []
for char in list(rec.id):
if char in ALLOWED_CONTIG_NAME_CHARS:
out_id.append(char)
else:
out_id.append("_")
rec.id = "".join(out_id)
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223,121 | bcbio/bcbio-nextgen | bcbio/qc/kraken.py | run | def run(_, data, out_dir):
"""Run kraken, generating report in specified directory and parsing metrics.
Using only first paired reads.
"""
# logger.info("Number of aligned reads < than 0.60 in %s: %s" % (dd.get_sample_name(data), ratio))
logger.info("Running kraken to determine contaminant: %s" %... | python | def run(_, data, out_dir):
"""Run kraken, generating report in specified directory and parsing metrics.
Using only first paired reads.
"""
# logger.info("Number of aligned reads < than 0.60 in %s: %s" % (dd.get_sample_name(data), ratio))
logger.info("Running kraken to determine contaminant: %s" %... | [
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223,122 | bcbio/bcbio-nextgen | bcbio/qc/kraken.py | _parse_kraken_output | def _parse_kraken_output(out_dir, db, data):
"""Parse kraken stat info comming from stderr,
generating report with kraken-report
"""
in_file = os.path.join(out_dir, "kraken_out")
stat_file = os.path.join(out_dir, "kraken_stats")
out_file = os.path.join(out_dir, "kraken_summary")
kraken_cm... | python | def _parse_kraken_output(out_dir, db, data):
"""Parse kraken stat info comming from stderr,
generating report with kraken-report
"""
in_file = os.path.join(out_dir, "kraken_out")
stat_file = os.path.join(out_dir, "kraken_stats")
out_file = os.path.join(out_dir, "kraken_summary")
kraken_cm... | [
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223,123 | bcbio/bcbio-nextgen | bcbio/qc/kraken.py | _summarize_kraken | def _summarize_kraken(fn):
"""get the value at species level"""
kraken = {}
list_sp, list_value = [], []
with open(fn) as handle:
for line in handle:
cols = line.strip().split("\t")
sp = cols[5].strip()
if len(sp.split(" ")) > 1 and not sp.startswith("cellular... | python | def _summarize_kraken(fn):
"""get the value at species level"""
kraken = {}
list_sp, list_value = [], []
with open(fn) as handle:
for line in handle:
cols = line.strip().split("\t")
sp = cols[5].strip()
if len(sp.split(" ")) > 1 and not sp.startswith("cellular... | [
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223,124 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _get_main_and_json | def _get_main_and_json(directory):
"""Retrieve the main CWL and sample JSON files from a bcbio generated directory.
"""
directory = os.path.normpath(os.path.abspath(directory))
checker_main = os.path.normpath(os.path.join(directory, os.path.pardir, "checker-workflow-wrapping-tool.cwl"))
if checker_m... | python | def _get_main_and_json(directory):
"""Retrieve the main CWL and sample JSON files from a bcbio generated directory.
"""
directory = os.path.normpath(os.path.abspath(directory))
checker_main = os.path.normpath(os.path.join(directory, os.path.pardir, "checker-workflow-wrapping-tool.cwl"))
if checker_m... | [
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223,125 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _run_tool | def _run_tool(cmd, use_container=True, work_dir=None, log_file=None):
"""Run with injection of bcbio path.
Place at end for runs without containers to avoid overriding other
bcbio installations.
"""
if isinstance(cmd, (list, tuple)):
cmd = " ".join([str(x) for x in cmd])
cmd = utils.loc... | python | def _run_tool(cmd, use_container=True, work_dir=None, log_file=None):
"""Run with injection of bcbio path.
Place at end for runs without containers to avoid overriding other
bcbio installations.
"""
if isinstance(cmd, (list, tuple)):
cmd = " ".join([str(x) for x in cmd])
cmd = utils.loc... | [
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223,126 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _pack_cwl | def _pack_cwl(unpacked_cwl):
"""Pack CWL into a single document for submission.
"""
out_file = "%s-pack%s" % os.path.splitext(unpacked_cwl)
cmd = "cwltool --pack {unpacked_cwl} > {out_file}"
_run_tool(cmd.format(**locals()))
return out_file | python | def _pack_cwl(unpacked_cwl):
"""Pack CWL into a single document for submission.
"""
out_file = "%s-pack%s" % os.path.splitext(unpacked_cwl)
cmd = "cwltool --pack {unpacked_cwl} > {out_file}"
_run_tool(cmd.format(**locals()))
return out_file | [
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223,127 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _remove_bcbiovm_path | def _remove_bcbiovm_path():
"""Avoid referencing minimal bcbio_nextgen in bcbio_vm installation.
"""
cur_path = os.path.dirname(os.path.realpath(sys.executable))
paths = os.environ["PATH"].split(":")
if cur_path in paths:
paths.remove(cur_path)
os.environ["PATH"] = ":".join(paths) | python | def _remove_bcbiovm_path():
"""Avoid referencing minimal bcbio_nextgen in bcbio_vm installation.
"""
cur_path = os.path.dirname(os.path.realpath(sys.executable))
paths = os.environ["PATH"].split(":")
if cur_path in paths:
paths.remove(cur_path)
os.environ["PATH"] = ":".join(paths) | [
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223,128 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _run_arvados | def _run_arvados(args):
"""Run CWL on Arvados.
"""
assert not args.no_container, "Arvados runs require containers"
assert "ARVADOS_API_TOKEN" in os.environ and "ARVADOS_API_HOST" in os.environ, \
"Need to set ARVADOS_API_TOKEN and ARVADOS_API_HOST in environment to run"
main_file, json_file,... | python | def _run_arvados(args):
"""Run CWL on Arvados.
"""
assert not args.no_container, "Arvados runs require containers"
assert "ARVADOS_API_TOKEN" in os.environ and "ARVADOS_API_HOST" in os.environ, \
"Need to set ARVADOS_API_TOKEN and ARVADOS_API_HOST in environment to run"
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223,129 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _run_toil | def _run_toil(args):
"""Run CWL with Toil.
"""
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "toil_work"))
tmp_dir = utils.safe_makedir(os.path.join(work_dir, "tmpdir"))
os.environ["TMPDIR"] = tmp_dir
log_file ... | python | def _run_toil(args):
"""Run CWL with Toil.
"""
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "toil_work"))
tmp_dir = utils.safe_makedir(os.path.join(work_dir, "tmpdir"))
os.environ["TMPDIR"] = tmp_dir
log_file ... | [
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223,130 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _run_bunny | def _run_bunny(args):
"""Run CWL with rabix bunny.
"""
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "bunny_work"))
flags = ["-b", work_dir]
log_file = os.path.join(work_dir, "%s-bunny.log" % project_name)
if o... | python | def _run_bunny(args):
"""Run CWL with rabix bunny.
"""
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "bunny_work"))
flags = ["-b", work_dir]
log_file = os.path.join(work_dir, "%s-bunny.log" % project_name)
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223,131 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _run_wes_stratus | def _run_wes_stratus(args, main_file, json_file):
"""Run WES on Illumina stratus endpoint server, which wes-client doesn't support.
https://stratus-docs.readme.io/docs/quick-start-4
"""
import requests
base_url = args.host
if not base_url.startswith("http"):
base_url = "https://%s" % ba... | python | def _run_wes_stratus(args, main_file, json_file):
"""Run WES on Illumina stratus endpoint server, which wes-client doesn't support.
https://stratus-docs.readme.io/docs/quick-start-4
"""
import requests
base_url = args.host
if not base_url.startswith("http"):
base_url = "https://%s" % ba... | [
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223,132 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _estimate_runner_memory | def _estimate_runner_memory(json_file):
"""Estimate Java memory requirements based on number of samples.
A rough approach to selecting correct allocated memory for Cromwell.
"""
with open(json_file) as in_handle:
sinfo = json.load(in_handle)
num_parallel = 1
for key in ["config__algorit... | python | def _estimate_runner_memory(json_file):
"""Estimate Java memory requirements based on number of samples.
A rough approach to selecting correct allocated memory for Cromwell.
"""
with open(json_file) as in_handle:
sinfo = json.load(in_handle)
num_parallel = 1
for key in ["config__algorit... | [
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223,133 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _run_cromwell | def _run_cromwell(args):
"""Run CWL with Cromwell.
"""
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "cromwell_work"))
final_dir = utils.safe_makedir(os.path.join(work_dir, "final"))
if args.no_container:
_... | python | def _run_cromwell(args):
"""Run CWL with Cromwell.
"""
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "cromwell_work"))
final_dir = utils.safe_makedir(os.path.join(work_dir, "final"))
if args.no_container:
_... | [
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223,134 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _cromwell_debug | def _cromwell_debug(metadata):
"""Format Cromwell failures to make debugging easier.
"""
def get_failed_calls(cur, key=None):
if key is None: key = []
out = []
if isinstance(cur, dict) and "failures" in cur and "callRoot" in cur:
out.append((key, cur))
elif isinst... | python | def _cromwell_debug(metadata):
"""Format Cromwell failures to make debugging easier.
"""
def get_failed_calls(cur, key=None):
if key is None: key = []
out = []
if isinstance(cur, dict) and "failures" in cur and "callRoot" in cur:
out.append((key, cur))
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223,135 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _cromwell_move_outputs | def _cromwell_move_outputs(metadata, final_dir):
"""Move Cromwell outputs to the final upload directory.
"""
sample_key = [k for k in metadata["outputs"].keys() if k.endswith(("rgnames__sample", "rgnames__sample_out"))][0]
project_dir = utils.safe_makedir(os.path.join(final_dir, "project"))
samples ... | python | def _cromwell_move_outputs(metadata, final_dir):
"""Move Cromwell outputs to the final upload directory.
"""
sample_key = [k for k in metadata["outputs"].keys() if k.endswith(("rgnames__sample", "rgnames__sample_out"))][0]
project_dir = utils.safe_makedir(os.path.join(final_dir, "project"))
samples ... | [
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223,136 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _run_sbgenomics | def _run_sbgenomics(args):
"""Run CWL on SevenBridges platform and Cancer Genomics Cloud.
"""
assert not args.no_container, "Seven Bridges runs require containers"
main_file, json_file, project_name = _get_main_and_json(args.directory)
flags = []
cmd = ["sbg-cwl-runner"] + flags + args.toolargs ... | python | def _run_sbgenomics(args):
"""Run CWL on SevenBridges platform and Cancer Genomics Cloud.
"""
assert not args.no_container, "Seven Bridges runs require containers"
main_file, json_file, project_name = _get_main_and_json(args.directory)
flags = []
cmd = ["sbg-cwl-runner"] + flags + args.toolargs ... | [
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223,137 | bcbio/bcbio-nextgen | bcbio/cwl/tool.py | _run_funnel | def _run_funnel(args):
"""Run funnel TES server with rabix bunny for CWL.
"""
host = "localhost"
port = "8088"
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "funnel_work"))
log_file = os.path.join(work_dir, "%s... | python | def _run_funnel(args):
"""Run funnel TES server with rabix bunny for CWL.
"""
host = "localhost"
port = "8088"
main_file, json_file, project_name = _get_main_and_json(args.directory)
work_dir = utils.safe_makedir(os.path.join(os.getcwd(), "funnel_work"))
log_file = os.path.join(work_dir, "%s... | [
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223,138 | bcbio/bcbio-nextgen | bcbio/qc/qualimap.py | _parse_qualimap_globals_inregion | def _parse_qualimap_globals_inregion(table):
"""Retrieve metrics from the global targeted region table.
"""
out = {}
for row in table.find_all("tr"):
col, val = [x.text for x in row.find_all("td")]
if col == "Mapped reads":
out.update(_parse_num_pct("%s (in regions)" % col, v... | python | def _parse_qualimap_globals_inregion(table):
"""Retrieve metrics from the global targeted region table.
"""
out = {}
for row in table.find_all("tr"):
col, val = [x.text for x in row.find_all("td")]
if col == "Mapped reads":
out.update(_parse_num_pct("%s (in regions)" % col, v... | [
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223,139 | bcbio/bcbio-nextgen | bcbio/qc/qualimap.py | _parse_qualimap_coverage | def _parse_qualimap_coverage(table):
"""Parse summary qualimap coverage metrics.
"""
out = {}
for row in table.find_all("tr"):
col, val = [x.text for x in row.find_all("td")]
if col == "Mean":
out["Coverage (Mean)"] = val
return out | python | def _parse_qualimap_coverage(table):
"""Parse summary qualimap coverage metrics.
"""
out = {}
for row in table.find_all("tr"):
col, val = [x.text for x in row.find_all("td")]
if col == "Mean":
out["Coverage (Mean)"] = val
return out | [
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223,140 | bcbio/bcbio-nextgen | bcbio/qc/qualimap.py | _bed_to_bed6 | def _bed_to_bed6(orig_file, out_dir):
"""Convert bed to required bed6 inputs.
"""
bed6_file = os.path.join(out_dir, "%s-bed6%s" % os.path.splitext(os.path.basename(orig_file)))
if not utils.file_exists(bed6_file):
with open(bed6_file, "w") as out_handle:
for i, region in enumerate(li... | python | def _bed_to_bed6(orig_file, out_dir):
"""Convert bed to required bed6 inputs.
"""
bed6_file = os.path.join(out_dir, "%s-bed6%s" % os.path.splitext(os.path.basename(orig_file)))
if not utils.file_exists(bed6_file):
with open(bed6_file, "w") as out_handle:
for i, region in enumerate(li... | [
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223,141 | bcbio/bcbio-nextgen | bcbio/qc/qualimap.py | _detect_duplicates | def _detect_duplicates(bam_file, out_dir, data):
"""
count duplicate percentage
"""
out_file = os.path.join(out_dir, "dup_metrics.txt")
if not utils.file_exists(out_file):
dup_align_bam = postalign.dedup_bam(bam_file, data)
logger.info("Detecting duplicates in %s." % dup_align_bam)
... | python | def _detect_duplicates(bam_file, out_dir, data):
"""
count duplicate percentage
"""
out_file = os.path.join(out_dir, "dup_metrics.txt")
if not utils.file_exists(out_file):
dup_align_bam = postalign.dedup_bam(bam_file, data)
logger.info("Detecting duplicates in %s." % dup_align_bam)
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223,142 | bcbio/bcbio-nextgen | bcbio/qc/qualimap.py | run_rnaseq | def run_rnaseq(bam_file, data, out_dir):
"""
Run qualimap for a rnaseq bam file and parse results
"""
strandedness = {"firststrand": "strand-specific-reverse",
"secondstrand": "strand-specific-forward",
"unstranded": "non-strand-specific"}
# Qualimap results ... | python | def run_rnaseq(bam_file, data, out_dir):
"""
Run qualimap for a rnaseq bam file and parse results
"""
strandedness = {"firststrand": "strand-specific-reverse",
"secondstrand": "strand-specific-forward",
"unstranded": "non-strand-specific"}
# Qualimap results ... | [
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223,143 | bcbio/bcbio-nextgen | bcbio/qc/qualimap.py | _rnaseq_qualimap_cmd | def _rnaseq_qualimap_cmd(data, bam_file, out_dir, gtf_file=None, library="non-strand-specific"):
"""
Create command lines for qualimap
"""
config = data["config"]
qualimap = config_utils.get_program("qualimap", config)
resources = config_utils.get_resources("qualimap", config)
num_cores = re... | python | def _rnaseq_qualimap_cmd(data, bam_file, out_dir, gtf_file=None, library="non-strand-specific"):
"""
Create command lines for qualimap
"""
config = data["config"]
qualimap = config_utils.get_program("qualimap", config)
resources = config_utils.get_resources("qualimap", config)
num_cores = re... | [
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223,144 | bcbio/bcbio-nextgen | bcbio/qc/qualimap.py | _find_qualimap_secondary_files | def _find_qualimap_secondary_files(results_dir, base_file):
"""Retrieve additional files, avoiding double uploading the base file.
"""
def not_dup(x):
is_dup = (os.path.basename(x) == os.path.basename(base_file) and
os.path.getsize(x) == os.path.getsize(base_file))
return n... | python | def _find_qualimap_secondary_files(results_dir, base_file):
"""Retrieve additional files, avoiding double uploading the base file.
"""
def not_dup(x):
is_dup = (os.path.basename(x) == os.path.basename(base_file) and
os.path.getsize(x) == os.path.getsize(base_file))
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223,145 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | classifyplot_from_plotfiles | def classifyplot_from_plotfiles(plot_files, out_csv, outtype="png", title=None, size=None):
"""Create a plot from individual summary csv files with classification metrics.
"""
dfs = [pd.read_csv(x) for x in plot_files]
samples = []
for df in dfs:
for sample in df["sample"].unique():
... | python | def classifyplot_from_plotfiles(plot_files, out_csv, outtype="png", title=None, size=None):
"""Create a plot from individual summary csv files with classification metrics.
"""
dfs = [pd.read_csv(x) for x in plot_files]
samples = []
for df in dfs:
for sample in df["sample"].unique():
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223,146 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | classifyplot_from_valfile | def classifyplot_from_valfile(val_file, outtype="png", title=None, size=None,
samples=None, callers=None):
"""Create a plot from a summarized validation file.
Does new-style plotting of summarized metrics of
false negative rate and false discovery rate.
https://en.wikipedi... | python | def classifyplot_from_valfile(val_file, outtype="png", title=None, size=None,
samples=None, callers=None):
"""Create a plot from a summarized validation file.
Does new-style plotting of summarized metrics of
false negative rate and false discovery rate.
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223,147 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | create | def create(plot_data, header, ploti, sample_config, out_file_base, outtype="png",
title=None, size=None):
"""Create plots of validation results for a sample, labeling prep strategies.
"""
if mpl is None or plt is None or sns is None:
not_found = ", ".join([x for x in ['mpl', 'plt', 'sns']... | python | def create(plot_data, header, ploti, sample_config, out_file_base, outtype="png",
title=None, size=None):
"""Create plots of validation results for a sample, labeling prep strategies.
"""
if mpl is None or plt is None or sns is None:
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223,148 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | plot_prep_methods | def plot_prep_methods(df, prep, prepi, out_file_base, outtype, title=None,
size=None):
"""Plot comparison between BAM preparation methods.
"""
samples = df[(df["bamprep"] == prep)]["sample"].unique()
assert len(samples) >= 1, samples
out_file = "%s-%s.%s" % (out_file_base, samp... | python | def plot_prep_methods(df, prep, prepi, out_file_base, outtype, title=None,
size=None):
"""Plot comparison between BAM preparation methods.
"""
samples = df[(df["bamprep"] == prep)]["sample"].unique()
assert len(samples) >= 1, samples
out_file = "%s-%s.%s" % (out_file_base, samp... | [
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223,149 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | _seaborn | def _seaborn(df, prep, prepi, out_file, title=None, size=None):
"""Plot using seaborn wrapper around matplotlib.
"""
plt.ioff()
sns.set(style='dark')
vtypes = df["variant.type"].unique()
callers = sorted(df["caller"].unique())
cats = _check_cats(["concordant", "discordant-missing-total",
... | python | def _seaborn(df, prep, prepi, out_file, title=None, size=None):
"""Plot using seaborn wrapper around matplotlib.
"""
plt.ioff()
sns.set(style='dark')
vtypes = df["variant.type"].unique()
callers = sorted(df["caller"].unique())
cats = _check_cats(["concordant", "discordant-missing-total",
... | [
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223,150 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | _check_cats | def _check_cats(cats, vtypes, df, prep, callers):
"""Only include categories in the final output if they have values.
"""
out = []
for cat in cats:
all_vals = []
for vtype in vtypes:
vals, labels, maxval = _get_chart_info(df, vtype, cat, prep, callers)
all_vals.ex... | python | def _check_cats(cats, vtypes, df, prep, callers):
"""Only include categories in the final output if they have values.
"""
out = []
for cat in cats:
all_vals = []
for vtype in vtypes:
vals, labels, maxval = _get_chart_info(df, vtype, cat, prep, callers)
all_vals.ex... | [
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223,151 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | _get_chart_info | def _get_chart_info(df, vtype, cat, prep, callers):
"""Retrieve values for a specific variant type, category and prep method.
"""
maxval_raw = max(list(df["value.floor"]))
curdf = df[(df["variant.type"] == vtype) & (df["category"] == cat)
& (df["bamprep"] == prep)]
vals = []
label... | python | def _get_chart_info(df, vtype, cat, prep, callers):
"""Retrieve values for a specific variant type, category and prep method.
"""
maxval_raw = max(list(df["value.floor"]))
curdf = df[(df["variant.type"] == vtype) & (df["category"] == cat)
& (df["bamprep"] == prep)]
vals = []
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223,152 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | _annotate | def _annotate(ax, annotate, height, left, width):
"""Annotate axis with labels.
"""
annotate_yrange_factor = 0.010
xticks = np.array(left) + width / 2.0
ymin, ymax = ax.get_ylim()
yrange = ymax - ymin
# Reset ymax and ymin so there's enough room to see the annotation of
# the top-most
... | python | def _annotate(ax, annotate, height, left, width):
"""Annotate axis with labels.
"""
annotate_yrange_factor = 0.010
xticks = np.array(left) + width / 2.0
ymin, ymax = ax.get_ylim()
yrange = ymax - ymin
# Reset ymax and ymin so there's enough room to see the annotation of
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223,153 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | _ggplot | def _ggplot(df, out_file):
"""Plot faceted items with ggplot wrapper on top of matplotlib.
XXX Not yet functional
"""
import ggplot as gg
df["variant.type"] = [vtype_labels[x] for x in df["variant.type"]]
df["category"] = [cat_labels[x] for x in df["category"]]
df["caller"] = [caller_labels.... | python | def _ggplot(df, out_file):
"""Plot faceted items with ggplot wrapper on top of matplotlib.
XXX Not yet functional
"""
import ggplot as gg
df["variant.type"] = [vtype_labels[x] for x in df["variant.type"]]
df["category"] = [cat_labels[x] for x in df["category"]]
df["caller"] = [caller_labels.... | [
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223,154 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | get_floor_value | def get_floor_value(x, cat, vartype, floors):
"""Modify values so all have the same relative scale for differences.
Using the chosen base heights, adjusts an individual sub-plot to be consistent
relative to that height.
"""
all_base = floors[vartype]
cur_max = floors[(cat, vartype)]
if cur_... | python | def get_floor_value(x, cat, vartype, floors):
"""Modify values so all have the same relative scale for differences.
Using the chosen base heights, adjusts an individual sub-plot to be consistent
relative to that height.
"""
all_base = floors[vartype]
cur_max = floors[(cat, vartype)]
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223,155 | bcbio/bcbio-nextgen | bcbio/variation/validateplot.py | get_group_floors | def get_group_floors(df, cat_labels):
"""Retrieve the floor for a given row of comparisons, creating a normalized set of differences.
We need to set non-zero floors so large numbers (like concordance) don't drown out small
numbers (like discordance). This defines the height for a row of comparisons as eith... | python | def get_group_floors(df, cat_labels):
"""Retrieve the floor for a given row of comparisons, creating a normalized set of differences.
We need to set non-zero floors so large numbers (like concordance) don't drown out small
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223,156 | bcbio/bcbio-nextgen | scripts/bcbio_nextgen.py | _sanity_check_args | def _sanity_check_args(args):
"""Ensure dependent arguments are correctly specified
"""
if "scheduler" in args and "queue" in args:
if args.scheduler and not args.queue:
if args.scheduler != "sge":
return "IPython parallel scheduler (-s) specified. This also requires a qu... | python | def _sanity_check_args(args):
"""Ensure dependent arguments are correctly specified
"""
if "scheduler" in args and "queue" in args:
if args.scheduler and not args.queue:
if args.scheduler != "sge":
return "IPython parallel scheduler (-s) specified. This also requires a qu... | [
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223,157 | bcbio/bcbio-nextgen | scripts/bcbio_nextgen.py | _add_inputs_to_kwargs | def _add_inputs_to_kwargs(args, kwargs, parser):
"""Convert input system config, flow cell directory and sample yaml to kwargs.
Handles back compatibility with previous commandlines while allowing flexible
specification of input parameters.
"""
inputs = [x for x in [args.global_config, args.fc_dir]... | python | def _add_inputs_to_kwargs(args, kwargs, parser):
"""Convert input system config, flow cell directory and sample yaml to kwargs.
Handles back compatibility with previous commandlines while allowing flexible
specification of input parameters.
"""
inputs = [x for x in [args.global_config, args.fc_dir]... | [
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223,158 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | _add_commas | def _add_commas(s, sep=','):
"""Add commas to output counts.
From: http://code.activestate.com/recipes/498181
"""
if len(s) <= 3:
return s
return _add_commas(s[:-3], sep) + sep + s[-3:] | python | def _add_commas(s, sep=','):
"""Add commas to output counts.
From: http://code.activestate.com/recipes/498181
"""
if len(s) <= 3:
return s
return _add_commas(s[:-3], sep) + sep + s[-3:] | [
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223,159 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | bed_to_interval | def bed_to_interval(orig_bed, bam_file):
"""Add header and format BED bait and target files for Picard if necessary.
"""
with open(orig_bed) as in_handle:
line = in_handle.readline()
if line.startswith("@"):
yield orig_bed
else:
with pysam.Samfile(bam_file, "rb") as bam_handl... | python | def bed_to_interval(orig_bed, bam_file):
"""Add header and format BED bait and target files for Picard if necessary.
"""
with open(orig_bed) as in_handle:
line = in_handle.readline()
if line.startswith("@"):
yield orig_bed
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223,160 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | PicardMetricsParser.get_summary_metrics | def get_summary_metrics(self, align_metrics, dup_metrics,
insert_metrics=None, hybrid_metrics=None, vrn_vals=None,
rnaseq_metrics=None):
"""Retrieve a high level summary of interesting metrics.
"""
with open(align_metrics) as in_handle:
align_vals = self._pars... | python | def get_summary_metrics(self, align_metrics, dup_metrics,
insert_metrics=None, hybrid_metrics=None, vrn_vals=None,
rnaseq_metrics=None):
"""Retrieve a high level summary of interesting metrics.
"""
with open(align_metrics) as in_handle:
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223,161 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | PicardMetricsParser.extract_metrics | def extract_metrics(self, metrics_files):
"""Return summary information for a lane of metrics files.
"""
extension_maps = dict(
align_metrics=(self._parse_align_metrics, "AL"),
dup_metrics=(self._parse_dup_metrics, "DUP"),
hs_metrics=(self._parse_hybrid_metric... | python | def extract_metrics(self, metrics_files):
"""Return summary information for a lane of metrics files.
"""
extension_maps = dict(
align_metrics=(self._parse_align_metrics, "AL"),
dup_metrics=(self._parse_dup_metrics, "DUP"),
hs_metrics=(self._parse_hybrid_metric... | [
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223,162 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | PicardMetrics.report | def report(self, align_bam, ref_file, is_paired, bait_file, target_file,
variant_region_file, config):
"""Produce report metrics using Picard with sorted aligned BAM file.
"""
dup_metrics = self._get_current_dup_metrics(align_bam)
align_metrics = self._collect_align_metric... | python | def report(self, align_bam, ref_file, is_paired, bait_file, target_file,
variant_region_file, config):
"""Produce report metrics using Picard with sorted aligned BAM file.
"""
dup_metrics = self._get_current_dup_metrics(align_bam)
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223,163 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | PicardMetrics._get_current_dup_metrics | def _get_current_dup_metrics(self, align_bam):
"""Retrieve duplicate information from input BAM file.
"""
metrics_file = "%s.dup_metrics" % os.path.splitext(align_bam)[0]
if not file_exists(metrics_file):
dups = 0
with pysam.Samfile(align_bam, "rb") as bam_handle:... | python | def _get_current_dup_metrics(self, align_bam):
"""Retrieve duplicate information from input BAM file.
"""
metrics_file = "%s.dup_metrics" % os.path.splitext(align_bam)[0]
if not file_exists(metrics_file):
dups = 0
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223,164 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | PicardMetrics._check_metrics_file | def _check_metrics_file(self, bam_name, metrics_ext):
"""Check for an existing metrics file for the given BAM.
"""
base, _ = os.path.splitext(bam_name)
try:
int(base[-1])
can_glob = False
except ValueError:
can_glob = True
check_fname =... | python | def _check_metrics_file(self, bam_name, metrics_ext):
"""Check for an existing metrics file for the given BAM.
"""
base, _ = os.path.splitext(bam_name)
try:
int(base[-1])
can_glob = False
except ValueError:
can_glob = True
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223,165 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | PicardMetrics._hybrid_select_metrics | def _hybrid_select_metrics(self, dup_bam, bait_file, target_file):
"""Generate metrics for hybrid selection efficiency.
"""
metrics = self._check_metrics_file(dup_bam, "hs_metrics")
if not file_exists(metrics):
with bed_to_interval(bait_file, dup_bam) as ready_bait:
... | python | def _hybrid_select_metrics(self, dup_bam, bait_file, target_file):
"""Generate metrics for hybrid selection efficiency.
"""
metrics = self._check_metrics_file(dup_bam, "hs_metrics")
if not file_exists(metrics):
with bed_to_interval(bait_file, dup_bam) as ready_bait:
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223,166 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | PicardMetrics._variant_eval_metrics | def _variant_eval_metrics(self, dup_bam):
"""Find metrics for evaluating variant effectiveness.
"""
base, ext = os.path.splitext(dup_bam)
end_strip = "-dup"
base = base[:-len(end_strip)] if base.endswith(end_strip) else base
mfiles = glob.glob("%s*eval_metrics" % base)
... | python | def _variant_eval_metrics(self, dup_bam):
"""Find metrics for evaluating variant effectiveness.
"""
base, ext = os.path.splitext(dup_bam)
end_strip = "-dup"
base = base[:-len(end_strip)] if base.endswith(end_strip) else base
mfiles = glob.glob("%s*eval_metrics" % base)
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223,167 | bcbio/bcbio-nextgen | bcbio/broad/metrics.py | RNASeqPicardMetrics.report | def report(self, align_bam, ref_file, gtf_file, is_paired=False, rrna_file="null"):
"""Produce report metrics for a RNASeq experiment using Picard
with a sorted aligned BAM file.
"""
# collect duplication metrics
dup_metrics = self._get_current_dup_metrics(align_bam)
al... | python | def report(self, align_bam, ref_file, gtf_file, is_paired=False, rrna_file="null"):
"""Produce report metrics for a RNASeq experiment using Picard
with a sorted aligned BAM file.
"""
# collect duplication metrics
dup_metrics = self._get_current_dup_metrics(align_bam)
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223,168 | bcbio/bcbio-nextgen | bcbio/variation/gatk.py | standard_cl_params | def standard_cl_params(items):
"""Shared command line parameters for GATK programs.
Handles no removal of duplicate reads for amplicon or
non mark duplicate experiments. If we have pre-aligned inputs we
ignore the value or mark duplicates (since they may already be
marked in the input BAM).
"""... | python | def standard_cl_params(items):
"""Shared command line parameters for GATK programs.
Handles no removal of duplicate reads for amplicon or
non mark duplicate experiments. If we have pre-aligned inputs we
ignore the value or mark duplicates (since they may already be
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223,169 | bcbio/bcbio-nextgen | bcbio/variation/gatk.py | _shared_gatk_call_prep | def _shared_gatk_call_prep(align_bams, items, ref_file, region, out_file, num_cores=1):
"""Shared preparation work for GATK variant calling.
"""
data = items[0]
config = data["config"]
broad_runner = broad.runner_from_config(config)
gatk_type = broad_runner.gatk_type()
for x in align_bams:
... | python | def _shared_gatk_call_prep(align_bams, items, ref_file, region, out_file, num_cores=1):
"""Shared preparation work for GATK variant calling.
"""
data = items[0]
config = data["config"]
broad_runner = broad.runner_from_config(config)
gatk_type = broad_runner.gatk_type()
for x in align_bams:
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223,170 | bcbio/bcbio-nextgen | bcbio/variation/gatk.py | unified_genotyper | def unified_genotyper(align_bams, items, ref_file, assoc_files,
region=None, out_file=None):
"""Perform SNP genotyping on the given alignment file.
"""
if out_file is None:
out_file = "%s-variants.vcf.gz" % utils.splitext_plus(align_bams[0])[0]
if not utils.file_exists(out... | python | def unified_genotyper(align_bams, items, ref_file, assoc_files,
region=None, out_file=None):
"""Perform SNP genotyping on the given alignment file.
"""
if out_file is None:
out_file = "%s-variants.vcf.gz" % utils.splitext_plus(align_bams[0])[0]
if not utils.file_exists(out... | [
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223,171 | bcbio/bcbio-nextgen | bcbio/variation/gatk.py | _joint_calling | def _joint_calling(items):
"""Determine if this call feeds downstream into joint calls.
"""
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), items[0])
if jointcaller:
assert len(items) == 1, "Can only do joint calling preparation with GATK with single samples"
assert tz.ge... | python | def _joint_calling(items):
"""Determine if this call feeds downstream into joint calls.
"""
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), items[0])
if jointcaller:
assert len(items) == 1, "Can only do joint calling preparation with GATK with single samples"
assert tz.ge... | [
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223,172 | bcbio/bcbio-nextgen | bcbio/variation/gatk.py | _supports_avx | def _supports_avx():
"""Check for support for Intel AVX acceleration."""
if os.path.exists("/proc/cpuinfo"):
with open("/proc/cpuinfo") as in_handle:
for line in in_handle:
if line.startswith("flags") and line.find("avx") > 0:
return True | python | def _supports_avx():
"""Check for support for Intel AVX acceleration."""
if os.path.exists("/proc/cpuinfo"):
with open("/proc/cpuinfo") as in_handle:
for line in in_handle:
if line.startswith("flags") and line.find("avx") > 0:
return True | [
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223,173 | bcbio/bcbio-nextgen | bcbio/provenance/programs.py | jar_versioner | def jar_versioner(program_name, jar_name):
"""Retrieve version information based on jar file.
"""
def get_version(config):
try:
pdir = config_utils.get_program(program_name, config, "dir")
# not configured
except ValueError:
return ""
jar = os.path.bas... | python | def jar_versioner(program_name, jar_name):
"""Retrieve version information based on jar file.
"""
def get_version(config):
try:
pdir = config_utils.get_program(program_name, config, "dir")
# not configured
except ValueError:
return ""
jar = os.path.bas... | [
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223,174 | bcbio/bcbio-nextgen | bcbio/provenance/programs.py | _get_cl_version | def _get_cl_version(p, config):
"""Retrieve version of a single commandline program.
"""
if not p.get("has_cl_version", True):
return ""
try:
prog = config_utils.get_program(p["cmd"], config)
except config_utils.CmdNotFound:
localpy_cmd = os.path.join(os.path.dirname(sys.exe... | python | def _get_cl_version(p, config):
"""Retrieve version of a single commandline program.
"""
if not p.get("has_cl_version", True):
return ""
try:
prog = config_utils.get_program(p["cmd"], config)
except config_utils.CmdNotFound:
localpy_cmd = os.path.join(os.path.dirname(sys.exe... | [
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223,175 | bcbio/bcbio-nextgen | bcbio/provenance/programs.py | _get_brew_versions | def _get_brew_versions():
"""Retrieve versions of tools installed via brew.
"""
from bcbio import install
tooldir = install.get_defaults().get("tooldir")
brew_cmd = os.path.join(tooldir, "bin", "brew") if tooldir else "brew"
try:
vout = subprocess.check_output([brew_cmd, "list", "--versi... | python | def _get_brew_versions():
"""Retrieve versions of tools installed via brew.
"""
from bcbio import install
tooldir = install.get_defaults().get("tooldir")
brew_cmd = os.path.join(tooldir, "bin", "brew") if tooldir else "brew"
try:
vout = subprocess.check_output([brew_cmd, "list", "--versi... | [
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223,176 | bcbio/bcbio-nextgen | bcbio/provenance/programs.py | _get_versions | def _get_versions(config=None):
"""Retrieve details on all programs available on the system.
"""
try:
from bcbio.pipeline import version
if hasattr(version, "__version__"):
bcbio_version = ("%s-%s" % (version.__version__, version.__git_revision__)
if ... | python | def _get_versions(config=None):
"""Retrieve details on all programs available on the system.
"""
try:
from bcbio.pipeline import version
if hasattr(version, "__version__"):
bcbio_version = ("%s-%s" % (version.__version__, version.__git_revision__)
if ... | [
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223,177 | bcbio/bcbio-nextgen | bcbio/provenance/programs.py | _get_versions_manifest | def _get_versions_manifest(manifest_dir):
"""Retrieve versions from a pre-existing manifest of installed software.
"""
all_pkgs = _manifest_progs + [p.get("name", p["cmd"]) for p in _cl_progs] + [p["name"] for p in _alt_progs]
if os.path.exists(manifest_dir):
out = []
for plist in ["tool... | python | def _get_versions_manifest(manifest_dir):
"""Retrieve versions from a pre-existing manifest of installed software.
"""
all_pkgs = _manifest_progs + [p.get("name", p["cmd"]) for p in _cl_progs] + [p["name"] for p in _alt_progs]
if os.path.exists(manifest_dir):
out = []
for plist in ["tool... | [
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223,178 | bcbio/bcbio-nextgen | bcbio/provenance/programs.py | write_versions | def write_versions(dirs, config=None, is_wrapper=False):
"""Write CSV file with versions used in analysis pipeline.
"""
out_file = _get_program_file(dirs)
if is_wrapper:
assert utils.file_exists(out_file), "Failed to create program versions from VM"
elif out_file is None:
for p in _g... | python | def write_versions(dirs, config=None, is_wrapper=False):
"""Write CSV file with versions used in analysis pipeline.
"""
out_file = _get_program_file(dirs)
if is_wrapper:
assert utils.file_exists(out_file), "Failed to create program versions from VM"
elif out_file is None:
for p in _g... | [
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223,179 | bcbio/bcbio-nextgen | bcbio/provenance/programs.py | get_version_manifest | def get_version_manifest(name, data=None, required=False):
"""Retrieve a version from the currently installed manifest.
"""
manifest_dir = _get_manifest_dir(data, name)
manifest_vs = _get_versions_manifest(manifest_dir) or []
for x in manifest_vs:
if x["program"] == name:
v = x.g... | python | def get_version_manifest(name, data=None, required=False):
"""Retrieve a version from the currently installed manifest.
"""
manifest_dir = _get_manifest_dir(data, name)
manifest_vs = _get_versions_manifest(manifest_dir) or []
for x in manifest_vs:
if x["program"] == name:
v = x.g... | [
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223,180 | bcbio/bcbio-nextgen | bcbio/provenance/programs.py | add_subparser | def add_subparser(subparsers):
"""Add command line option for exporting version information.
"""
parser = subparsers.add_parser("version",
help="Export versions of used software to stdout or a file ")
parser.add_argument("--workdir", help="Directory export programs to ... | python | def add_subparser(subparsers):
"""Add command line option for exporting version information.
"""
parser = subparsers.add_parser("version",
help="Export versions of used software to stdout or a file ")
parser.add_argument("--workdir", help="Directory export programs to ... | [
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223,181 | bcbio/bcbio-nextgen | bcbio/provenance/programs.py | get_version | def get_version(name, dirs=None, config=None):
"""Retrieve the current version of the given program from cached names.
"""
if dirs:
p = _get_program_file(dirs)
else:
p = tz.get_in(["resources", "program_versions"], config)
if p:
with open(p) as in_handle:
for line... | python | def get_version(name, dirs=None, config=None):
"""Retrieve the current version of the given program from cached names.
"""
if dirs:
p = _get_program_file(dirs)
else:
p = tz.get_in(["resources", "program_versions"], config)
if p:
with open(p) as in_handle:
for line... | [
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223,182 | bcbio/bcbio-nextgen | scripts/utils/hlas_to_pgroups.py | hla_choices | def hla_choices(orig_hla, min_parts=2):
"""Provide a range of options for HLA type, with decreasing resolution.
"""
yield orig_hla
try:
int(orig_hla[-1])
except ValueError:
yield orig_hla[:-1]
hla_parts = orig_hla.split(":")
for sub_i in range(len(hla_parts) - min_parts + 1):... | python | def hla_choices(orig_hla, min_parts=2):
"""Provide a range of options for HLA type, with decreasing resolution.
"""
yield orig_hla
try:
int(orig_hla[-1])
except ValueError:
yield orig_hla[:-1]
hla_parts = orig_hla.split(":")
for sub_i in range(len(hla_parts) - min_parts + 1):... | [
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223,183 | bcbio/bcbio-nextgen | scripts/utils/hlas_to_pgroups.py | read_pgroups | def read_pgroups(in_file):
"""Read HLAs and the pgroups they fall in.
"""
out = {}
with open(in_file) as in_handle:
for line in (l for l in in_handle if not l.startswith("#")):
locus, alleles, group = line.strip().split(";")
for allele in alleles.split("/"):
... | python | def read_pgroups(in_file):
"""Read HLAs and the pgroups they fall in.
"""
out = {}
with open(in_file) as in_handle:
for line in (l for l in in_handle if not l.startswith("#")):
locus, alleles, group = line.strip().split(";")
for allele in alleles.split("/"):
... | [
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223,184 | bcbio/bcbio-nextgen | scripts/utils/hlas_to_pgroups.py | read_hlas | def read_hlas(fasta_fai):
"""Get HLA alleles from the hg38 fasta fai file.
"""
out = []
with open(fasta_fai) as in_handle:
for line in in_handle:
if line.startswith("HLA"):
out.append(line.split()[0])
return out | python | def read_hlas(fasta_fai):
"""Get HLA alleles from the hg38 fasta fai file.
"""
out = []
with open(fasta_fai) as in_handle:
for line in in_handle:
if line.startswith("HLA"):
out.append(line.split()[0])
return out | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/scripts/utils/hlas_to_pgroups.py#L58-L66 |
223,185 | bcbio/bcbio-nextgen | bcbio/variation/split.py | split_vcf | def split_vcf(in_file, ref_file, config, out_dir=None):
"""Split a VCF file into separate files by chromosome.
"""
if out_dir is None:
out_dir = os.path.join(os.path.dirname(in_file), "split")
out_files = []
with open(ref.fasta_idx(ref_file, config)) as in_handle:
for line in in_hand... | python | def split_vcf(in_file, ref_file, config, out_dir=None):
"""Split a VCF file into separate files by chromosome.
"""
if out_dir is None:
out_dir = os.path.join(os.path.dirname(in_file), "split")
out_files = []
with open(ref.fasta_idx(ref_file, config)) as in_handle:
for line in in_hand... | [
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223,186 | bcbio/bcbio-nextgen | bcbio/variation/split.py | subset_vcf | def subset_vcf(in_file, region, out_file, config):
"""Subset VCF in the given region, handling bgzip and indexing of input.
"""
work_file = vcfutils.bgzip_and_index(in_file, config)
if not file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
bcftools = confi... | python | def subset_vcf(in_file, region, out_file, config):
"""Subset VCF in the given region, handling bgzip and indexing of input.
"""
work_file = vcfutils.bgzip_and_index(in_file, config)
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223,187 | bcbio/bcbio-nextgen | bcbio/variation/recalibrate.py | prep_recal | def prep_recal(data):
"""Do pre-BQSR recalibration, calculation of recalibration tables.
"""
if dd.get_recalibrate(data) in [True, "gatk"]:
logger.info("Prepare BQSR tables with GATK: %s " % str(dd.get_sample_name(data)))
dbsnp_file = tz.get_in(("genome_resources", "variation", "dbsnp"), dat... | python | def prep_recal(data):
"""Do pre-BQSR recalibration, calculation of recalibration tables.
"""
if dd.get_recalibrate(data) in [True, "gatk"]:
logger.info("Prepare BQSR tables with GATK: %s " % str(dd.get_sample_name(data)))
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223,188 | bcbio/bcbio-nextgen | bcbio/variation/recalibrate.py | apply_recal | def apply_recal(data):
"""Apply recalibration tables to the sorted aligned BAM, producing recalibrated BAM.
"""
orig_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
had_work_bam = "work_bam" in data
if dd.get_recalibrate(data) in [True, "gatk"]:
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l... | python | def apply_recal(data):
"""Apply recalibration tables to the sorted aligned BAM, producing recalibrated BAM.
"""
orig_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
had_work_bam = "work_bam" in data
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223,189 | bcbio/bcbio-nextgen | bcbio/variation/recalibrate.py | _gatk_base_recalibrator | def _gatk_base_recalibrator(broad_runner, dup_align_bam, ref_file, platform,
dbsnp_file, intervals, data):
"""Step 1 of GATK recalibration process, producing table of covariates.
For GATK 4 we use local multicore spark runs:
https://github.com/broadinstitute/gatk/issues/2345
... | python | def _gatk_base_recalibrator(broad_runner, dup_align_bam, ref_file, platform,
dbsnp_file, intervals, data):
"""Step 1 of GATK recalibration process, producing table of covariates.
For GATK 4 we use local multicore spark runs:
https://github.com/broadinstitute/gatk/issues/2345
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223,190 | bcbio/bcbio-nextgen | bcbio/variation/recalibrate.py | _gatk_apply_bqsr | def _gatk_apply_bqsr(data):
"""Parallel BQSR support for GATK4.
Normalized qualities to 3 bin outputs at 10, 20 and 30 based on pipeline standard
recommendations, which will help with output file sizes:
https://github.com/CCDG/Pipeline-Standardization/blob/master/PipelineStandard.md#base-quality-score-... | python | def _gatk_apply_bqsr(data):
"""Parallel BQSR support for GATK4.
Normalized qualities to 3 bin outputs at 10, 20 and 30 based on pipeline standard
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https://github.com/CCDG/Pipeline-Standardization/blob/master/PipelineStandard.md#base-quality-score-... | [
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223,191 | bcbio/bcbio-nextgen | bcbio/log/__init__.py | create_base_logger | def create_base_logger(config=None, parallel=None):
"""Setup base logging configuration, also handling remote logging.
Correctly sets up for local, multiprocessing and distributed runs.
Creates subscribers for non-local runs that will be references from
local logging.
Retrieves IP address using ti... | python | def create_base_logger(config=None, parallel=None):
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Correctly sets up for local, multiprocessing and distributed runs.
Creates subscribers for non-local runs that will be references from
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223,192 | bcbio/bcbio-nextgen | bcbio/log/__init__.py | setup_local_logging | def setup_local_logging(config=None, parallel=None):
"""Setup logging for a local context, directing messages to appropriate base loggers.
Handles local, multiprocessing and distributed setup, connecting
to handlers created by the base logger.
"""
if config is None: config = {}
if parallel is N... | python | def setup_local_logging(config=None, parallel=None):
"""Setup logging for a local context, directing messages to appropriate base loggers.
Handles local, multiprocessing and distributed setup, connecting
to handlers created by the base logger.
"""
if config is None: config = {}
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223,193 | bcbio/bcbio-nextgen | bcbio/log/__init__.py | setup_script_logging | def setup_script_logging():
"""
Use this logger for standalone scripts, or script-like subcommands,
such as bcbio_prepare_samples and bcbio_nextgen.py -w template.
"""
handlers = [logbook.NullHandler()]
format_str = ("[{record.time:%Y-%m-%dT%H:%MZ}] "
"{record.level_name}: {rec... | python | def setup_script_logging():
"""
Use this logger for standalone scripts, or script-like subcommands,
such as bcbio_prepare_samples and bcbio_nextgen.py -w template.
"""
handlers = [logbook.NullHandler()]
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223,194 | bcbio/bcbio-nextgen | scripts/cwltool2wdl.py | _validate | def _validate(wdl_file):
"""Run validation on the generated WDL output using wdltool.
"""
start_dir = os.getcwd()
os.chdir(os.path.dirname(wdl_file))
print("Validating", wdl_file)
subprocess.check_call(["wdltool", "validate", wdl_file])
os.chdir(start_dir) | python | def _validate(wdl_file):
"""Run validation on the generated WDL output using wdltool.
"""
start_dir = os.getcwd()
os.chdir(os.path.dirname(wdl_file))
print("Validating", wdl_file)
subprocess.check_call(["wdltool", "validate", wdl_file])
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223,195 | bcbio/bcbio-nextgen | scripts/cwltool2wdl.py | _wf_to_dict | def _wf_to_dict(wf, records):
"""Parse a workflow into cwl2wdl style dictionaries for base and sub-workflows.
"""
inputs, outputs, records = _get_wf_inout(wf, records)
out = {"name": _id_to_name(_clean_id(wf.tool["id"])), "inputs": inputs,
"outputs": outputs, "steps": [], "subworkflows": [],
... | python | def _wf_to_dict(wf, records):
"""Parse a workflow into cwl2wdl style dictionaries for base and sub-workflows.
"""
inputs, outputs, records = _get_wf_inout(wf, records)
out = {"name": _id_to_name(_clean_id(wf.tool["id"])), "inputs": inputs,
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223,196 | bcbio/bcbio-nextgen | scripts/cwltool2wdl.py | _organize_step_scatter | def _organize_step_scatter(step, inputs, remapped):
"""Add scattering information from inputs, remapping input variables.
"""
def extract_scatter_id(inp):
_, ns_var = inp.split("#")
_, var = ns_var.split("/")
return var
scatter_local = {}
if "scatter" in step.tool:
as... | python | def _organize_step_scatter(step, inputs, remapped):
"""Add scattering information from inputs, remapping input variables.
"""
def extract_scatter_id(inp):
_, ns_var = inp.split("#")
_, var = ns_var.split("/")
return var
scatter_local = {}
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223,197 | bcbio/bcbio-nextgen | scripts/cwltool2wdl.py | _variable_type_to_read_fn | def _variable_type_to_read_fn(vartype, records):
"""Convert variant types into corresponding WDL standard library functions.
"""
fn_map = {"String": "read_string", "Array[String]": "read_lines",
"Array[Array[String]]": "read_tsv",
"Object": "read_object", "Array[Object]": "read_o... | python | def _variable_type_to_read_fn(vartype, records):
"""Convert variant types into corresponding WDL standard library functions.
"""
fn_map = {"String": "read_string", "Array[String]": "read_lines",
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223,198 | bcbio/bcbio-nextgen | scripts/cwltool2wdl.py | _requirements_to_dict | def _requirements_to_dict(rs):
"""Convert supported requirements into dictionary for output.
"""
out = []
added = set([])
for r in rs:
if r["class"] == "DockerRequirement" and "docker" not in added:
added.add("docker")
out.append({"requirement_type": "docker", "value"... | python | def _requirements_to_dict(rs):
"""Convert supported requirements into dictionary for output.
"""
out = []
added = set([])
for r in rs:
if r["class"] == "DockerRequirement" and "docker" not in added:
added.add("docker")
out.append({"requirement_type": "docker", "value"... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/scripts/cwltool2wdl.py#L306-L325 |
223,199 | bcbio/bcbio-nextgen | bcbio/structural/purple.py | _get_jvm_opts | def _get_jvm_opts(out_file, data):
"""Retrieve Java options, adjusting memory for available cores.
"""
resources = config_utils.get_resources("purple", data["config"])
jvm_opts = resources.get("jvm_opts", ["-Xms750m", "-Xmx3500m"])
jvm_opts = config_utils.adjust_opts(jvm_opts, {"algorithm": {"memory... | python | def _get_jvm_opts(out_file, data):
"""Retrieve Java options, adjusting memory for available cores.
"""
resources = config_utils.get_resources("purple", data["config"])
jvm_opts = resources.get("jvm_opts", ["-Xms750m", "-Xmx3500m"])
jvm_opts = config_utils.adjust_opts(jvm_opts, {"algorithm": {"memory... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/purple.py#L43-L53 |
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