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bcbio/bcbio-nextgen | bcbio/heterogeneity/bubbletree.py | sample_alt_and_depth | def sample_alt_and_depth(rec, sample):
"""Flexibly get ALT allele and depth counts, handling FreeBayes, MuTect and other cases.
"""
if sample and "AD" in sample:
all_counts = [int(x) for x in sample["AD"]]
alt_counts = sum(all_counts[1:])
depth = sum(all_counts)
elif sample and "... | python | def sample_alt_and_depth(rec, sample):
"""Flexibly get ALT allele and depth counts, handling FreeBayes, MuTect and other cases.
"""
if sample and "AD" in sample:
all_counts = [int(x) for x in sample["AD"]]
alt_counts = sum(all_counts[1:])
depth = sum(all_counts)
elif sample and "... | [
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bcbio/bcbio-nextgen | bcbio/bam/ref.py | fasta_idx | def fasta_idx(in_file, config=None):
"""Retrieve samtools style fasta index.
"""
fasta_index = in_file + ".fai"
if not utils.file_exists(fasta_index):
samtools = config_utils.get_program("samtools", config) if config else "samtools"
cmd = "{samtools} faidx {in_file}"
do.run(cmd.f... | python | def fasta_idx(in_file, config=None):
"""Retrieve samtools style fasta index.
"""
fasta_index = in_file + ".fai"
if not utils.file_exists(fasta_index):
samtools = config_utils.get_program("samtools", config) if config else "samtools"
cmd = "{samtools} faidx {in_file}"
do.run(cmd.f... | [
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bcbio/bcbio-nextgen | bcbio/bam/ref.py | file_contigs | def file_contigs(ref_file, config=None):
"""Iterator of reference contigs and lengths from a reference file.
"""
ContigInfo = collections.namedtuple("ContigInfo", "name size")
with open(fasta_idx(ref_file, config)) as in_handle:
for line in (l for l in in_handle if l.strip()):
name, ... | python | def file_contigs(ref_file, config=None):
"""Iterator of reference contigs and lengths from a reference file.
"""
ContigInfo = collections.namedtuple("ContigInfo", "name size")
with open(fasta_idx(ref_file, config)) as in_handle:
for line in (l for l in in_handle if l.strip()):
name, ... | [
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bcbio/bcbio-nextgen | bcbio/variation/smcounter2.py | run | def run(align_bams, items, ref_file, assoc_files, region=None, out_file=None):
"""Run tumor only smCounter2 calling.
"""
paired = vcfutils.get_paired_bams(align_bams, items)
assert paired and not paired.normal_bam, ("smCounter2 supports tumor-only variant calling: %s" %
... | python | def run(align_bams, items, ref_file, assoc_files, region=None, out_file=None):
"""Run tumor only smCounter2 calling.
"""
paired = vcfutils.get_paired_bams(align_bams, items)
assert paired and not paired.normal_bam, ("smCounter2 supports tumor-only variant calling: %s" %
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bcbio/bcbio-nextgen | bcbio/bam/readstats.py | number_of_mapped_reads | def number_of_mapped_reads(data, bam_file, keep_dups=True, bed_file=None, target_name=None):
"""Count mapped reads, allow adjustment for duplicates and BED regions.
Since samtools view does not use indexes for BED files
(https://github.com/samtools/samtools/issues/88)
we loop over regions in a BED file... | python | def number_of_mapped_reads(data, bam_file, keep_dups=True, bed_file=None, target_name=None):
"""Count mapped reads, allow adjustment for duplicates and BED regions.
Since samtools view does not use indexes for BED files
(https://github.com/samtools/samtools/issues/88)
we loop over regions in a BED file... | [
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bcbio/bcbio-nextgen | bcbio/bam/readstats.py | _simple_lock | def _simple_lock(f):
"""Simple file lock, times out after 20 second assuming lock is stale
"""
lock_file = f + ".lock"
timeout = 20
curtime = 0
interval = 2
while os.path.exists(lock_file):
time.sleep(interval)
curtime += interval
if curtime > timeout:
os.... | python | def _simple_lock(f):
"""Simple file lock, times out after 20 second assuming lock is stale
"""
lock_file = f + ".lock"
timeout = 20
curtime = 0
interval = 2
while os.path.exists(lock_file):
time.sleep(interval)
curtime += interval
if curtime > timeout:
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bcbio/bcbio-nextgen | bcbio/pipeline/region.py | get_max_counts | def get_max_counts(samples):
"""Retrieve number of regions that can be processed in parallel from current samples.
"""
counts = []
for data in (x[0] for x in samples):
count = tz.get_in(["config", "algorithm", "callable_count"], data, 1)
vcs = tz.get_in(["config", "algorithm", "variantca... | python | def get_max_counts(samples):
"""Retrieve number of regions that can be processed in parallel from current samples.
"""
counts = []
for data in (x[0] for x in samples):
count = tz.get_in(["config", "algorithm", "callable_count"], data, 1)
vcs = tz.get_in(["config", "algorithm", "variantca... | [
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bcbio/bcbio-nextgen | bcbio/pipeline/region.py | _split_by_regions | def _split_by_regions(dirname, out_ext, in_key):
"""Split a BAM file data analysis into chromosomal regions.
"""
def _do_work(data):
# XXX Need to move retrieval of regions into preparation to avoid
# need for files when running in non-shared filesystems
regions = _get_parallel_regio... | python | def _split_by_regions(dirname, out_ext, in_key):
"""Split a BAM file data analysis into chromosomal regions.
"""
def _do_work(data):
# XXX Need to move retrieval of regions into preparation to avoid
# need for files when running in non-shared filesystems
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bcbio/bcbio-nextgen | bcbio/pipeline/region.py | _get_parallel_regions | def _get_parallel_regions(data):
"""Retrieve regions to run in parallel, putting longest intervals first.
"""
callable_regions = tz.get_in(["config", "algorithm", "callable_regions"], data)
if not callable_regions:
raise ValueError("Did not find any callable regions for sample: %s\n"
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"""Retrieve regions to run in parallel, putting longest intervals first.
"""
callable_regions = tz.get_in(["config", "algorithm", "callable_regions"], data)
if not callable_regions:
raise ValueError("Did not find any callable regions for sample: %s\n"
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bcbio/bcbio-nextgen | bcbio/pipeline/region.py | get_parallel_regions | def get_parallel_regions(batch):
"""CWL target to retrieve a list of callable regions for parallelization.
"""
samples = [utils.to_single_data(d) for d in batch]
regions = _get_parallel_regions(samples[0])
return [{"region": "%s:%s-%s" % (c, s, e)} for c, s, e in regions] | python | def get_parallel_regions(batch):
"""CWL target to retrieve a list of callable regions for parallelization.
"""
samples = [utils.to_single_data(d) for d in batch]
regions = _get_parallel_regions(samples[0])
return [{"region": "%s:%s-%s" % (c, s, e)} for c, s, e in regions] | [
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bcbio/bcbio-nextgen | bcbio/pipeline/region.py | get_parallel_regions_block | def get_parallel_regions_block(batch):
"""CWL target to retrieve block group of callable regions for parallelization.
Uses blocking to handle multicore runs.
"""
samples = [utils.to_single_data(d) for d in batch]
regions = _get_parallel_regions(samples[0])
out = []
# Currently don't have co... | python | def get_parallel_regions_block(batch):
"""CWL target to retrieve block group of callable regions for parallelization.
Uses blocking to handle multicore runs.
"""
samples = [utils.to_single_data(d) for d in batch]
regions = _get_parallel_regions(samples[0])
out = []
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bcbio/bcbio-nextgen | bcbio/pipeline/region.py | _add_combine_info | def _add_combine_info(output, combine_map, file_key):
"""Do not actually combine, but add details for later combining work.
Each sample will contain information on the out file and additional files
to merge, enabling other splits and recombines without losing information.
"""
files_per_output = col... | python | def _add_combine_info(output, combine_map, file_key):
"""Do not actually combine, but add details for later combining work.
Each sample will contain information on the out file and additional files
to merge, enabling other splits and recombines without losing information.
"""
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bcbio/bcbio-nextgen | bcbio/pipeline/region.py | parallel_prep_region | def parallel_prep_region(samples, run_parallel):
"""Perform full pre-variant calling BAM prep work on regions.
"""
file_key = "work_bam"
split_fn = _split_by_regions("bamprep", "-prep.bam", file_key)
# identify samples that do not need preparation -- no recalibration or realignment
extras = []
... | python | def parallel_prep_region(samples, run_parallel):
"""Perform full pre-variant calling BAM prep work on regions.
"""
file_key = "work_bam"
split_fn = _split_by_regions("bamprep", "-prep.bam", file_key)
# identify samples that do not need preparation -- no recalibration or realignment
extras = []
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bcbio/bcbio-nextgen | bcbio/pipeline/region.py | delayed_bamprep_merge | def delayed_bamprep_merge(samples, run_parallel):
"""Perform a delayed merge on regional prepared BAM files.
"""
if any("combine" in data[0] for data in samples):
return run_parallel("delayed_bam_merge", samples)
else:
return samples | python | def delayed_bamprep_merge(samples, run_parallel):
"""Perform a delayed merge on regional prepared BAM files.
"""
if any("combine" in data[0] for data in samples):
return run_parallel("delayed_bam_merge", samples)
else:
return samples | [
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bcbio/bcbio-nextgen | bcbio/pipeline/region.py | clean_sample_data | def clean_sample_data(samples):
"""Clean unnecessary information from sample data, reducing size for message passing.
"""
out = []
for data in (utils.to_single_data(x) for x in samples):
if "dirs" in data:
data["dirs"] = {"work": data["dirs"]["work"], "galaxy": data["dirs"]["galaxy"]... | python | def clean_sample_data(samples):
"""Clean unnecessary information from sample data, reducing size for message passing.
"""
out = []
for data in (utils.to_single_data(x) for x in samples):
if "dirs" in data:
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bcbio/bcbio-nextgen | bcbio/ngsalign/star.py | _add_sj_index_commands | def _add_sj_index_commands(fq1, ref_file, gtf_file):
"""
newer versions of STAR can generate splice junction databases on thephfly
this is preferable since we can tailor it to the read lengths
"""
if _has_sj_index(ref_file):
return ""
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"""
newer versions of STAR can generate splice junction databases on thephfly
this is preferable since we can tailor it to the read lengths
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if _has_sj_index(ref_file):
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bcbio/bcbio-nextgen | bcbio/ngsalign/star.py | _has_sj_index | def _has_sj_index(ref_file):
"""this file won't exist if we can do on the fly splice junction indexing"""
return (file_exists(os.path.join(ref_file, "sjdbInfo.txt")) and
(file_exists(os.path.join(ref_file, "transcriptInfo.tab")))) | python | def _has_sj_index(ref_file):
"""this file won't exist if we can do on the fly splice junction indexing"""
return (file_exists(os.path.join(ref_file, "sjdbInfo.txt")) and
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bcbio/bcbio-nextgen | bcbio/ngsalign/star.py | remap_index_fn | def remap_index_fn(ref_file):
"""Map sequence references to equivalent star indexes
"""
return os.path.join(os.path.dirname(os.path.dirname(ref_file)), "star") | python | def remap_index_fn(ref_file):
"""Map sequence references to equivalent star indexes
"""
return os.path.join(os.path.dirname(os.path.dirname(ref_file)), "star") | [
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bcbio/bcbio-nextgen | bcbio/ngsalign/star.py | index | def index(ref_file, out_dir, data):
"""Create a STAR index in the defined reference directory.
"""
(ref_dir, local_file) = os.path.split(ref_file)
gtf_file = dd.get_gtf_file(data)
if not utils.file_exists(gtf_file):
raise ValueError("%s not found, could not create a star index." % (gtf_file)... | python | def index(ref_file, out_dir, data):
"""Create a STAR index in the defined reference directory.
"""
(ref_dir, local_file) = os.path.split(ref_file)
gtf_file = dd.get_gtf_file(data)
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bcbio/bcbio-nextgen | bcbio/ngsalign/star.py | get_splicejunction_file | def get_splicejunction_file(out_dir, data):
"""
locate the splicejunction file starting from the alignment directory
"""
samplename = dd.get_sample_name(data)
sjfile = os.path.join(out_dir, os.pardir, "{0}SJ.out.tab").format(samplename)
if file_exists(sjfile):
return sjfile
else:
... | python | def get_splicejunction_file(out_dir, data):
"""
locate the splicejunction file starting from the alignment directory
"""
samplename = dd.get_sample_name(data)
sjfile = os.path.join(out_dir, os.pardir, "{0}SJ.out.tab").format(samplename)
if file_exists(sjfile):
return sjfile
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bcbio/bcbio-nextgen | bcbio/ngsalign/star.py | junction2bed | def junction2bed(junction_file):
"""
reformat the STAR junction file to BED3 format, one end of the splice junction per line
"""
base, _ = os.path.splitext(junction_file)
out_file = base + "-minimized.bed"
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return out_file
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... | python | def junction2bed(junction_file):
"""
reformat the STAR junction file to BED3 format, one end of the splice junction per line
"""
base, _ = os.path.splitext(junction_file)
out_file = base + "-minimized.bed"
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bcbio/bcbio-nextgen | bcbio/hla/optitype.py | run | def run(data):
"""HLA typing with OptiType, parsing output from called genotype files.
"""
hlas = []
for hla_fq in tz.get_in(["hla", "fastq"], data, []):
hla_type = re.search("[.-](?P<hlatype>HLA-[\w-]+).fq", hla_fq).group("hlatype")
if hla_type in SUPPORTED_HLAS:
if utils.fi... | python | def run(data):
"""HLA typing with OptiType, parsing output from called genotype files.
"""
hlas = []
for hla_fq in tz.get_in(["hla", "fastq"], data, []):
hla_type = re.search("[.-](?P<hlatype>HLA-[\w-]+).fq", hla_fq).group("hlatype")
if hla_type in SUPPORTED_HLAS:
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bcbio/bcbio-nextgen | bcbio/hla/optitype.py | combine_hla_fqs | def combine_hla_fqs(hlas, out_file, data):
"""OptiType performs best on a combination of all extracted HLAs.
"""
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
for hla_type, hla_fq in hl... | python | def combine_hla_fqs(hlas, out_file, data):
"""OptiType performs best on a combination of all extracted HLAs.
"""
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
for hla_type, hla_fq in hl... | [
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bcbio/bcbio-nextgen | bcbio/hla/optitype.py | _prepare_calls | def _prepare_calls(result_file, out_dir, data):
"""Write summary file of results of HLA typing by allele.
"""
sample = dd.get_sample_name(data)
out_file = os.path.join(out_dir, "%s-optitype.csv" % (sample))
if not utils.file_uptodate(out_file, result_file):
hla_truth = bwakit.get_hla_truthse... | python | def _prepare_calls(result_file, out_dir, data):
"""Write summary file of results of HLA typing by allele.
"""
sample = dd.get_sample_name(data)
out_file = os.path.join(out_dir, "%s-optitype.csv" % (sample))
if not utils.file_uptodate(out_file, result_file):
hla_truth = bwakit.get_hla_truthse... | [
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bcbio/bcbio-nextgen | bcbio/hla/optitype.py | _call_hla | def _call_hla(hla_fq, out_dir, data):
"""Run OptiType HLA calling for a specific fastq input.
"""
bin_dir = os.path.dirname(os.path.realpath(sys.executable))
out_dir = utils.safe_makedir(out_dir)
with tx_tmpdir(data, os.path.dirname(out_dir)) as tx_out_dir:
config_file = os.path.join(tx_out_... | python | def _call_hla(hla_fq, out_dir, data):
"""Run OptiType HLA calling for a specific fastq input.
"""
bin_dir = os.path.dirname(os.path.realpath(sys.executable))
out_dir = utils.safe_makedir(out_dir)
with tx_tmpdir(data, os.path.dirname(out_dir)) as tx_out_dir:
config_file = os.path.join(tx_out_... | [
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bcbio/bcbio-nextgen | bcbio/heterogeneity/chromhacks.py | is_autosomal | def is_autosomal(chrom):
"""Keep chromosomes that are a digit 1-22, or chr prefixed digit chr1-chr22
"""
try:
int(chrom)
return True
except ValueError:
try:
int(str(chrom.lower().replace("chr", "").replace("_", "").replace("-", "")))
return True
ex... | python | def is_autosomal(chrom):
"""Keep chromosomes that are a digit 1-22, or chr prefixed digit chr1-chr22
"""
try:
int(chrom)
return True
except ValueError:
try:
int(str(chrom.lower().replace("chr", "").replace("_", "").replace("-", "")))
return True
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bcbio/bcbio-nextgen | bcbio/qc/variant.py | _bcftools_stats | def _bcftools_stats(data, out_dir, vcf_file_key=None, germline=False):
"""Run bcftools stats.
"""
vcinfo = get_active_vcinfo(data)
if vcinfo:
out_dir = utils.safe_makedir(out_dir)
vcf_file = vcinfo[vcf_file_key or "vrn_file"]
if dd.get_jointcaller(data) or "gvcf" in dd.get_tools_... | python | def _bcftools_stats(data, out_dir, vcf_file_key=None, germline=False):
"""Run bcftools stats.
"""
vcinfo = get_active_vcinfo(data)
if vcinfo:
out_dir = utils.safe_makedir(out_dir)
vcf_file = vcinfo[vcf_file_key or "vrn_file"]
if dd.get_jointcaller(data) or "gvcf" in dd.get_tools_... | [
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bcbio/bcbio-nextgen | bcbio/qc/variant.py | _add_filename_details | def _add_filename_details(full_f):
"""Add variant callers and germline information standard CWL filenames.
This is an ugly way of working around not having metadata with calls.
"""
out = {"vrn_file": full_f}
f = os.path.basename(full_f)
for vc in list(genotype.get_variantcallers().keys()) + ["e... | python | def _add_filename_details(full_f):
"""Add variant callers and germline information standard CWL filenames.
This is an ugly way of working around not having metadata with calls.
"""
out = {"vrn_file": full_f}
f = os.path.basename(full_f)
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bcbio/bcbio-nextgen | bcbio/qc/variant.py | _get_variants | def _get_variants(data):
"""Retrieve variants from CWL and standard inputs for organizing variants.
"""
active_vs = []
if "variants" in data:
variants = data["variants"]
# CWL based list of variants
if isinstance(variants, dict) and "samples" in variants:
variants = v... | python | def _get_variants(data):
"""Retrieve variants from CWL and standard inputs for organizing variants.
"""
active_vs = []
if "variants" in data:
variants = data["variants"]
# CWL based list of variants
if isinstance(variants, dict) and "samples" in variants:
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bcbio/bcbio-nextgen | bcbio/qc/variant.py | get_active_vcinfo | def get_active_vcinfo(data, use_ensemble=True):
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active_vs = _get_variants(data)
if len(active_vs) > 0:
e_active_vs = []
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"""Use first caller if ensemble is not active
"""
active_vs = _get_variants(data)
if len(active_vs) > 0:
e_active_vs = []
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bcbio/bcbio-nextgen | bcbio/qc/variant.py | extract_germline_vcinfo | def extract_germline_vcinfo(data, out_dir):
"""Extract germline VCFs from existing tumor inputs.
"""
supported_germline = set(["vardict", "octopus", "freebayes"])
if dd.get_phenotype(data) in ["tumor"]:
for v in _get_variants(data):
if v.get("variantcaller") in supported_germline:
... | python | def extract_germline_vcinfo(data, out_dir):
"""Extract germline VCFs from existing tumor inputs.
"""
supported_germline = set(["vardict", "octopus", "freebayes"])
if dd.get_phenotype(data) in ["tumor"]:
for v in _get_variants(data):
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bcbio/bcbio-nextgen | bcbio/pipeline/merge.py | merge_bam_files | def merge_bam_files(bam_files, work_dir, data, out_file=None, batch=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Checks system open file limit and merges in batches if necessary to avoid
file handle limits.
"""
out_file = _merge_outfile_fname(out_file, bam_file... | python | def merge_bam_files(bam_files, work_dir, data, out_file=None, batch=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Checks system open file limit and merges in batches if necessary to avoid
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bcbio/bcbio-nextgen | bcbio/pipeline/merge.py | _create_merge_filelist | def _create_merge_filelist(bam_files, base_file, config):
"""Create list of input files for merge, ensuring all files are valid.
"""
bam_file_list = "%s.list" % os.path.splitext(base_file)[0]
samtools = config_utils.get_program("samtools", config)
with open(bam_file_list, "w") as out_handle:
... | python | def _create_merge_filelist(bam_files, base_file, config):
"""Create list of input files for merge, ensuring all files are valid.
"""
bam_file_list = "%s.list" % os.path.splitext(base_file)[0]
samtools = config_utils.get_program("samtools", config)
with open(bam_file_list, "w") as out_handle:
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bcbio/bcbio-nextgen | bcbio/pipeline/merge.py | _merge_outfile_fname | def _merge_outfile_fname(out_file, bam_files, work_dir, batch):
"""Derive correct name of BAM file based on batching.
"""
if out_file is None:
out_file = os.path.join(work_dir, os.path.basename(sorted(bam_files)[0]))
if batch is not None:
base, ext = os.path.splitext(out_file)
ou... | python | def _merge_outfile_fname(out_file, bam_files, work_dir, batch):
"""Derive correct name of BAM file based on batching.
"""
if out_file is None:
out_file = os.path.join(work_dir, os.path.basename(sorted(bam_files)[0]))
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base, ext = os.path.splitext(out_file)
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bcbio/bcbio-nextgen | bcbio/pipeline/merge.py | _finalize_merge | def _finalize_merge(out_file, bam_files, config):
"""Handle indexes and cleanups of merged BAM and input files.
"""
# Ensure timestamps are up to date on output file and index
# Works around issues on systems with inconsistent times
for ext in ["", ".bai"]:
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# Ensure timestamps are up to date on output file and index
# Works around issues on systems with inconsistent times
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _cwl_workflow_template | def _cwl_workflow_template(inputs, top_level=False):
"""Retrieve CWL inputs shared amongst different workflows.
"""
ready_inputs = []
for inp in inputs:
cur_inp = copy.deepcopy(inp)
for attr in ["source", "valueFrom", "wf_duplicate"]:
cur_inp.pop(attr, None)
if top_le... | python | def _cwl_workflow_template(inputs, top_level=False):
"""Retrieve CWL inputs shared amongst different workflows.
"""
ready_inputs = []
for inp in inputs:
cur_inp = copy.deepcopy(inp)
for attr in ["source", "valueFrom", "wf_duplicate"]:
cur_inp.pop(attr, None)
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _get_disk_estimates | def _get_disk_estimates(name, parallel, inputs, file_estimates, samples, disk,
cur_remotes, no_files):
"""Retrieve disk usage estimates as CWL ResourceRequirement and hint.
Disk specification for temporary files and outputs.
Also optionally includes disk input estimates as a custom... | python | def _get_disk_estimates(name, parallel, inputs, file_estimates, samples, disk,
cur_remotes, no_files):
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _add_current_quay_tag | def _add_current_quay_tag(repo, container_tags):
"""Lookup the current quay tag for the repository, adding to repo string.
Enables generation of CWL explicitly tied to revisions.
"""
if ':' in repo:
return repo, container_tags
try:
latest_tag = container_tags[repo]
except KeyErr... | python | def _add_current_quay_tag(repo, container_tags):
"""Lookup the current quay tag for the repository, adding to repo string.
Enables generation of CWL explicitly tied to revisions.
"""
if ':' in repo:
return repo, container_tags
try:
latest_tag = container_tags[repo]
except KeyErr... | [
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _write_expressiontool | def _write_expressiontool(step_dir, name, inputs, outputs, expression, parallel):
"""Create an ExpressionTool output for the given inputs
"""
out_file = os.path.join(step_dir, "%s.cwl" % name)
out = {"class": "ExpressionTool",
"cwlVersion": "v1.0",
"requirements": [{"class": "Inlin... | python | def _write_expressiontool(step_dir, name, inputs, outputs, expression, parallel):
"""Create an ExpressionTool output for the given inputs
"""
out_file = os.path.join(step_dir, "%s.cwl" % name)
out = {"class": "ExpressionTool",
"cwlVersion": "v1.0",
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _clean_record | def _clean_record(rec):
"""Remove secondary files from record fields, which are currently not supported.
To be removed later when secondaryFiles added to records.
"""
if workflow.is_cwl_record(rec):
def _clean_fields(d):
if isinstance(d, dict):
if "fields" in d:
... | python | def _clean_record(rec):
"""Remove secondary files from record fields, which are currently not supported.
To be removed later when secondaryFiles added to records.
"""
if workflow.is_cwl_record(rec):
def _clean_fields(d):
if isinstance(d, dict):
if "fields" in d:
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _get_record_fields | def _get_record_fields(d):
"""Get field names from a potentially nested record.
"""
if isinstance(d, dict):
if "fields" in d:
return d["fields"]
else:
for v in d.values():
fields = _get_record_fields(v)
if fields:
re... | python | def _get_record_fields(d):
"""Get field names from a potentially nested record.
"""
if isinstance(d, dict):
if "fields" in d:
return d["fields"]
else:
for v in d.values():
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _get_sentinel_val | def _get_sentinel_val(v):
"""Retrieve expected sentinel value for an output, expanding records.
"""
out = workflow.get_base_id(v["id"])
if workflow.is_cwl_record(v):
out += ":%s" % ";".join([x["name"] for x in _get_record_fields(v)])
return out | python | def _get_sentinel_val(v):
"""Retrieve expected sentinel value for an output, expanding records.
"""
out = workflow.get_base_id(v["id"])
if workflow.is_cwl_record(v):
out += ":%s" % ";".join([x["name"] for x in _get_record_fields(v)])
return out | [
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _place_input_binding | def _place_input_binding(inp_tool, inp_binding, parallel):
"""Check nesting of variables to determine where to place the input binding.
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _place_secondary_files | def _place_secondary_files(inp_tool, inp_binding=None):
"""Put secondaryFiles at the level of the File item to ensure indexes get passed.
"""
def _is_file(val):
return (val == "File" or (isinstance(val, (list, tuple)) and
("File" in val or any(isinstance(x, dict) an... | python | def _place_secondary_files(inp_tool, inp_binding=None):
"""Put secondaryFiles at the level of the File item to ensure indexes get passed.
"""
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return (val == "File" or (isinstance(val, (list, tuple)) and
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _do_scatter_var | def _do_scatter_var(v, parallel):
"""Logic for scattering a variable.
"""
# For batches, scatter records only at the top level (double nested)
if parallel.startswith("batch") and workflow.is_cwl_record(v):
return (tz.get_in(["type", "type"], v) == "array" and
tz.get_in(["type", "... | python | def _do_scatter_var(v, parallel):
"""Logic for scattering a variable.
"""
# For batches, scatter records only at the top level (double nested)
if parallel.startswith("batch") and workflow.is_cwl_record(v):
return (tz.get_in(["type", "type"], v) == "array" and
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _step_template | def _step_template(name, run_file, inputs, outputs, parallel, step_parallelism, scatter=None):
"""Templating function for writing a step to avoid repeating namespaces.
"""
scatter_inputs = []
sinputs = []
for inp in inputs:
step_inp = {"id": workflow.get_base_id(inp["id"]), "source": inp["id... | python | def _step_template(name, run_file, inputs, outputs, parallel, step_parallelism, scatter=None):
"""Templating function for writing a step to avoid repeating namespaces.
"""
scatter_inputs = []
sinputs = []
for inp in inputs:
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _get_cur_remotes | def _get_cur_remotes(path):
"""Retrieve remote references defined in the CWL.
"""
cur_remotes = set([])
if isinstance(path, (list, tuple)):
for v in path:
cur_remotes |= _get_cur_remotes(v)
elif isinstance(path, dict):
for v in path.values():
cur_remotes |= _g... | python | def _get_cur_remotes(path):
"""Retrieve remote references defined in the CWL.
"""
cur_remotes = set([])
if isinstance(path, (list, tuple)):
for v in path:
cur_remotes |= _get_cur_remotes(v)
elif isinstance(path, dict):
for v in path.values():
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _flatten_samples | def _flatten_samples(samples, base_file, get_retriever):
"""Create a flattened JSON representation of data from the bcbio world map.
"""
flat_data = []
for data in samples:
data["reference"] = _indexes_to_secondary_files(data["reference"], data["genome_build"])
cur_flat = {}
for ... | python | def _flatten_samples(samples, base_file, get_retriever):
"""Create a flattened JSON representation of data from the bcbio world map.
"""
flat_data = []
for data in samples:
data["reference"] = _indexes_to_secondary_files(data["reference"], data["genome_build"])
cur_flat = {}
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _indexes_to_secondary_files | def _indexes_to_secondary_files(gresources, genome_build):
"""Convert a list of genome indexes into a single file plus secondary files.
This ensures that all indices are staged together in a single directory.
"""
out = {}
for refname, val in gresources.items():
if isinstance(val, dict) and ... | python | def _indexes_to_secondary_files(gresources, genome_build):
"""Convert a list of genome indexes into a single file plus secondary files.
This ensures that all indices are staged together in a single directory.
"""
out = {}
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _add_suppl_info | def _add_suppl_info(inp, val):
"""Add supplementary information to inputs from file values.
"""
inp["type"] = _get_avro_type(val)
secondary = _get_secondary_files(val)
if secondary:
inp["secondaryFiles"] = secondary
return inp | python | def _add_suppl_info(inp, val):
"""Add supplementary information to inputs from file values.
"""
inp["type"] = _get_avro_type(val)
secondary = _get_secondary_files(val)
if secondary:
inp["secondaryFiles"] = secondary
return inp | [
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _get_secondary_files | def _get_secondary_files(val):
"""Retrieve associated secondary files.
Normalizes input values into definitions of available secondary files.
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files are not optional. So if we have a mix of BAM (bai) and fastq (gbi) we
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"""Retrieve associated secondary files.
Normalizes input values into definitions of available secondary files.
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _get_relative_ext | def _get_relative_ext(of, sf):
"""Retrieve relative extension given the original and secondary files.
"""
def half_finished_trim(orig, prefix):
return (os.path.basename(prefix).count(".") > 0 and
os.path.basename(orig).count(".") == os.path.basename(prefix).count("."))
# Handle r... | python | def _get_relative_ext(of, sf):
"""Retrieve relative extension given the original and secondary files.
"""
def half_finished_trim(orig, prefix):
return (os.path.basename(prefix).count(".") > 0 and
os.path.basename(orig).count(".") == os.path.basename(prefix).count("."))
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _get_avro_type | def _get_avro_type(val):
"""Infer avro type for the current input.
"""
if isinstance(val, dict):
assert val.get("class") == "File" or "File" in val.get("class")
return "File"
elif isinstance(val, (tuple, list)):
types = []
for ctype in [_get_avro_type(v) for v in val]:
... | python | def _get_avro_type(val):
"""Infer avro type for the current input.
"""
if isinstance(val, dict):
assert val.get("class") == "File" or "File" in val.get("class")
return "File"
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types = []
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _avoid_duplicate_arrays | def _avoid_duplicate_arrays(types):
"""Collapse arrays when we have multiple types.
"""
arrays = [t for t in types if isinstance(t, dict) and t["type"] == "array"]
others = [t for t in types if not (isinstance(t, dict) and t["type"] == "array")]
if arrays:
items = set([])
for t in ar... | python | def _avoid_duplicate_arrays(types):
"""Collapse arrays when we have multiple types.
"""
arrays = [t for t in types if isinstance(t, dict) and t["type"] == "array"]
others = [t for t in types if not (isinstance(t, dict) and t["type"] == "array")]
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items = set([])
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _samplejson_to_inputs | def _samplejson_to_inputs(svals):
"""Convert sample output into inputs for CWL configuration files, with types.
"""
out = []
for key, val in svals.items():
out.append(_add_suppl_info({"id": "%s" % key}, val))
return out | python | def _samplejson_to_inputs(svals):
"""Convert sample output into inputs for CWL configuration files, with types.
"""
out = []
for key, val in svals.items():
out.append(_add_suppl_info({"id": "%s" % key}, val))
return out | [
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _to_cwldata | def _to_cwldata(key, val, get_retriever):
"""Convert nested dictionary into CWL data, flatening and marking up files.
Moves file objects to the top level, enabling insertion in CWL inputs/outputs.
"""
out = []
if isinstance(val, dict):
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"""Convert nested dictionary into CWL data, flatening and marking up files.
Moves file objects to the top level, enabling insertion in CWL inputs/outputs.
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _to_cwlfile_with_indexes | def _to_cwlfile_with_indexes(val, get_retriever):
"""Convert reads with ready to go indexes into the right CWL object.
Identifies the top level directory and creates a tarball, avoiding
trying to handle complex secondary setups which are not cross platform.
Skips doing this for reference files and sta... | python | def _to_cwlfile_with_indexes(val, get_retriever):
"""Convert reads with ready to go indexes into the right CWL object.
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _add_secondary_if_exists | def _add_secondary_if_exists(secondary, out, get_retriever):
"""Add secondary files only if present locally or remotely.
"""
secondary = [_file_local_or_remote(y, get_retriever) for y in secondary]
secondary = [z for z in secondary if z]
if secondary:
out["secondaryFiles"] = [{"class": "File... | python | def _add_secondary_if_exists(secondary, out, get_retriever):
"""Add secondary files only if present locally or remotely.
"""
secondary = [_file_local_or_remote(y, get_retriever) for y in secondary]
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _item_to_cwldata | def _item_to_cwldata(x, get_retriever, indexes=None):
""""Markup an item with CWL specific metadata.
"""
if isinstance(x, (list, tuple)):
return [_item_to_cwldata(subx, get_retriever) for subx in x]
elif (x and isinstance(x, six.string_types) and
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""""Markup an item with CWL specific metadata.
"""
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return [_item_to_cwldata(subx, get_retriever) for subx in x]
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _file_local_or_remote | def _file_local_or_remote(f, get_retriever):
"""Check for presence of a local or remote file.
"""
if os.path.exists(f):
return f
integration, config = get_retriever.integration_and_config(f)
if integration:
return integration.file_exists(f, config) | python | def _file_local_or_remote(f, get_retriever):
"""Check for presence of a local or remote file.
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if os.path.exists(f):
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | directory_tarball | def directory_tarball(dirname):
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to WDL, so for now we create a tarball that workers will unpack.
"""
assert os.path.isdir(dirname), dirname
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"""Create a tarball of a complex directory, avoiding complex secondaryFiles.
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _calc_input_estimates | def _calc_input_estimates(keyvals, get_retriever):
"""Calculate estimations of input file sizes for disk usage approximation.
These are current dominated by fastq/BAM sizes, so estimate based on that.
"""
out = {}
for key, val in keyvals.items():
size = _calc_file_size(val, 0, get_retriever... | python | def _calc_input_estimates(keyvals, get_retriever):
"""Calculate estimations of input file sizes for disk usage approximation.
These are current dominated by fastq/BAM sizes, so estimate based on that.
"""
out = {}
for key, val in keyvals.items():
size = _calc_file_size(val, 0, get_retriever... | [
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | _get_file_size | def _get_file_size(path, get_retriever):
"""Return file size in megabytes, including querying remote integrations
"""
integration, config = get_retriever.integration_and_config(path)
if integration:
return integration.file_size(path, config)
elif os.path.exists(path):
return os.path.... | python | def _get_file_size(path, get_retriever):
"""Return file size in megabytes, including querying remote integrations
"""
integration, config = get_retriever.integration_and_config(path)
if integration:
return integration.file_size(path, config)
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bcbio/bcbio-nextgen | bcbio/cwl/create.py | GetRetriever.integration_and_config | def integration_and_config(self, path):
"""Get a retriever and configuration for the given file path.
"""
if path.startswith(tuple(INTEGRATION_MAP.keys())):
key = INTEGRATION_MAP[path.split(":")[0] + ":"]
integration = self._integrations.get(key)
config = {}
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"""Get a retriever and configuration for the given file path.
"""
if path.startswith(tuple(INTEGRATION_MAP.keys())):
key = INTEGRATION_MAP[path.split(":")[0] + ":"]
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bcbio/bcbio-nextgen | bcbio/rnaseq/singlecellexperiment.py | make_scrnaseq_object | def make_scrnaseq_object(samples):
"""
load the initial se.rda object using sinclecell-experiment
"""
local_sitelib = R_sitelib()
counts_dir = os.path.dirname(dd.get_in_samples(samples, dd.get_combined_counts))
gtf_file = dd.get_in_samples(samples, dd.get_transcriptome_gtf)
if not gtf_file:
... | python | def make_scrnaseq_object(samples):
"""
load the initial se.rda object using sinclecell-experiment
"""
local_sitelib = R_sitelib()
counts_dir = os.path.dirname(dd.get_in_samples(samples, dd.get_combined_counts))
gtf_file = dd.get_in_samples(samples, dd.get_transcriptome_gtf)
if not gtf_file:
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bcbio/bcbio-nextgen | bcbio/distributed/multi.py | runner | def runner(parallel, config):
"""Run functions, provided by string name, on multiple cores on the current machine.
"""
def run_parallel(fn_name, items):
items = [x for x in items if x is not None]
if len(items) == 0:
return []
items = diagnostics.track_parallel(items, fn_... | python | def runner(parallel, config):
"""Run functions, provided by string name, on multiple cores on the current machine.
"""
def run_parallel(fn_name, items):
items = [x for x in items if x is not None]
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bcbio/bcbio-nextgen | bcbio/distributed/multi.py | zeromq_aware_logging | def zeromq_aware_logging(f):
"""Ensure multiprocessing logging uses ZeroMQ queues.
ZeroMQ and local stdout/stderr do not behave nicely when intertwined. This
ensures the local logging uses existing ZeroMQ logging queues.
"""
@functools.wraps(f)
def wrapper(*args, **kwargs):
config = Non... | python | def zeromq_aware_logging(f):
"""Ensure multiprocessing logging uses ZeroMQ queues.
ZeroMQ and local stdout/stderr do not behave nicely when intertwined. This
ensures the local logging uses existing ZeroMQ logging queues.
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@functools.wraps(f)
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bcbio/bcbio-nextgen | bcbio/distributed/multi.py | run_multicore | def run_multicore(fn, items, config, parallel=None):
"""Run the function using multiple cores on the given items to process.
"""
if len(items) == 0:
return []
if parallel is None or "num_jobs" not in parallel:
if parallel is None:
parallel = {"type": "local", "cores": config[... | python | def run_multicore(fn, items, config, parallel=None):
"""Run the function using multiple cores on the given items to process.
"""
if len(items) == 0:
return []
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bcbio/bcbio-nextgen | scripts/bcbio_fastq_umi_prep.py | _add_umis_with_fastp | def _add_umis_with_fastp(read_fq, umi_fq, out_fq, cores):
"""Add UMIs to reads from separate UMI file using fastp.
"""
with utils.open_gzipsafe(umi_fq) as in_handle:
in_handle.readline() # name
umi_size = len(in_handle.readline().strip())
cmd = ("fastp -Q -A -L -G -w 1 --in1 {read_fq} -... | python | def _add_umis_with_fastp(read_fq, umi_fq, out_fq, cores):
"""Add UMIs to reads from separate UMI file using fastp.
"""
with utils.open_gzipsafe(umi_fq) as in_handle:
in_handle.readline() # name
umi_size = len(in_handle.readline().strip())
cmd = ("fastp -Q -A -L -G -w 1 --in1 {read_fq} -... | [
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bcbio/bcbio-nextgen | scripts/bcbio_fastq_umi_prep.py | _find_umi | def _find_umi(files):
"""Find UMI file using different naming schemes.
R1/R2/R3 => R1/R3 with R2 UMI
R1/R2/I1 => R1/R2 with I1 UMI
"""
base = os.path.basename(_commonprefix(files))
def _file_ext(f):
exts = utils.splitext_plus(os.path.basename(f).replace(base, ""))[0].split("_")
... | python | def _find_umi(files):
"""Find UMI file using different naming schemes.
R1/R2/R3 => R1/R3 with R2 UMI
R1/R2/I1 => R1/R2 with I1 UMI
"""
base = os.path.basename(_commonprefix(files))
def _file_ext(f):
exts = utils.splitext_plus(os.path.basename(f).replace(base, ""))[0].split("_")
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bcbio/bcbio-nextgen | scripts/bcbio_fastq_umi_prep.py | _commonprefix | def _commonprefix(files):
"""Retrieve a common prefix for files without extra _R1 _I1 extensions.
Allows alternative naming schemes (R1/R2/R3) (R1/R2/I1).
"""
out = os.path.commonprefix(files)
out = out.rstrip("_R")
out = out.rstrip("_I")
out = out.rstrip("_")
return out | python | def _commonprefix(files):
"""Retrieve a common prefix for files without extra _R1 _I1 extensions.
Allows alternative naming schemes (R1/R2/R3) (R1/R2/I1).
"""
out = os.path.commonprefix(files)
out = out.rstrip("_R")
out = out.rstrip("_I")
out = out.rstrip("_")
return out | [
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bcbio/bcbio-nextgen | bcbio/variation/vfilter.py | cutoff_w_expression | def cutoff_w_expression(vcf_file, expression, data, name="+", filterext="",
extra_cmd="", limit_regions="variant_regions"):
"""Perform cutoff-based soft filtering using bcftools expressions like %QUAL < 20 || DP < 4.
"""
base, ext = utils.splitext_plus(vcf_file)
out_file = "{base}-... | python | def cutoff_w_expression(vcf_file, expression, data, name="+", filterext="",
extra_cmd="", limit_regions="variant_regions"):
"""Perform cutoff-based soft filtering using bcftools expressions like %QUAL < 20 || DP < 4.
"""
base, ext = utils.splitext_plus(vcf_file)
out_file = "{base}-... | [
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bcbio/bcbio-nextgen | bcbio/variation/vfilter.py | _freebayes_custom | def _freebayes_custom(in_file, ref_file, data):
"""Custom FreeBayes filtering using bcbio.variation, tuned to human NA12878 results.
Experimental: for testing new methods.
"""
if vcfutils.get_paired_phenotype(data):
return None
config = data["config"]
bv_ver = programs.get_version("bcbi... | python | def _freebayes_custom(in_file, ref_file, data):
"""Custom FreeBayes filtering using bcbio.variation, tuned to human NA12878 results.
Experimental: for testing new methods.
"""
if vcfutils.get_paired_phenotype(data):
return None
config = data["config"]
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bcbio/bcbio-nextgen | bcbio/variation/vfilter.py | _freebayes_cutoff | def _freebayes_cutoff(in_file, data):
"""Perform filtering of FreeBayes results, flagging low confidence calls.
Filters using cutoffs on low depth based on Meynert et al's work modeling sensitivity
of homozygote and heterozygote calling on depth:
http://www.ncbi.nlm.nih.gov/pubmed/23773188
and hi... | python | def _freebayes_cutoff(in_file, data):
"""Perform filtering of FreeBayes results, flagging low confidence calls.
Filters using cutoffs on low depth based on Meynert et al's work modeling sensitivity
of homozygote and heterozygote calling on depth:
http://www.ncbi.nlm.nih.gov/pubmed/23773188
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bcbio/bcbio-nextgen | bcbio/variation/vfilter.py | _calc_vcf_stats | def _calc_vcf_stats(in_file):
"""Calculate statistics on VCF for filtering, saving to a file for quick re-runs.
"""
out_file = "%s-stats.yaml" % utils.splitext_plus(in_file)[0]
if not utils.file_exists(out_file):
stats = {"avg_depth": _average_called_depth(in_file)}
with open(out_file, "... | python | def _calc_vcf_stats(in_file):
"""Calculate statistics on VCF for filtering, saving to a file for quick re-runs.
"""
out_file = "%s-stats.yaml" % utils.splitext_plus(in_file)[0]
if not utils.file_exists(out_file):
stats = {"avg_depth": _average_called_depth(in_file)}
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bcbio/bcbio-nextgen | bcbio/variation/vfilter.py | _average_called_depth | def _average_called_depth(in_file):
"""Retrieve the average depth of called reads in the provided VCF.
"""
import cyvcf2
depths = []
for rec in cyvcf2.VCF(str(in_file)):
d = rec.INFO.get("DP")
if d is not None:
depths.append(int(d))
if len(depths) > 0:
return ... | python | def _average_called_depth(in_file):
"""Retrieve the average depth of called reads in the provided VCF.
"""
import cyvcf2
depths = []
for rec in cyvcf2.VCF(str(in_file)):
d = rec.INFO.get("DP")
if d is not None:
depths.append(int(d))
if len(depths) > 0:
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bcbio/bcbio-nextgen | bcbio/variation/vfilter.py | platypus | def platypus(in_file, data):
"""Filter Platypus calls, removing Q20 filter and replacing with depth and quality based filter.
Platypus uses its own VCF nomenclature: TC == DP, FR == AF
Platypus gVCF output appears to have an 0/1 index problem so the reference block
regions are 1 base outside regions o... | python | def platypus(in_file, data):
"""Filter Platypus calls, removing Q20 filter and replacing with depth and quality based filter.
Platypus uses its own VCF nomenclature: TC == DP, FR == AF
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bcbio/bcbio-nextgen | bcbio/variation/vfilter.py | gatk_snp_cutoff | def gatk_snp_cutoff(in_file, data):
"""Perform cutoff-based soft filtering on GATK SNPs using best-practice recommendations.
We have a more lenient mapping quality (MQ) filter compared to GATK defaults.
The recommended filter (MQ < 40) is too stringent, so we adjust to 30:
http://imgur.com/a/oHRVB
... | python | def gatk_snp_cutoff(in_file, data):
"""Perform cutoff-based soft filtering on GATK SNPs using best-practice recommendations.
We have a more lenient mapping quality (MQ) filter compared to GATK defaults.
The recommended filter (MQ < 40) is too stringent, so we adjust to 30:
http://imgur.com/a/oHRVB
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bcbio/bcbio-nextgen | bcbio/bam/counts.py | random_regions | def random_regions(base, n, size):
"""Generate n random regions of 'size' in the provided base spread.
"""
spread = size // 2
base_info = collections.defaultdict(list)
for space, start, end in base:
base_info[space].append(start + spread)
base_info[space].append(end - spread)
reg... | python | def random_regions(base, n, size):
"""Generate n random regions of 'size' in the provided base spread.
"""
spread = size // 2
base_info = collections.defaultdict(list)
for space, start, end in base:
base_info[space].append(start + spread)
base_info[space].append(end - spread)
reg... | [
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bcbio/bcbio-nextgen | bcbio/bam/counts.py | NormalizedBam.all_regions | def all_regions(self):
"""Get a tuple of all chromosome, start and end regions.
"""
regions = []
for sq in self._bam.header["SQ"]:
regions.append((sq["SN"], 1, int(sq["LN"])))
return regions | python | def all_regions(self):
"""Get a tuple of all chromosome, start and end regions.
"""
regions = []
for sq in self._bam.header["SQ"]:
regions.append((sq["SN"], 1, int(sq["LN"])))
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bcbio/bcbio-nextgen | bcbio/bam/counts.py | NormalizedBam.read_count | def read_count(self, space, start, end):
"""Retrieve the normalized read count in the provided region.
"""
read_counts = 0
for read in self._bam.fetch(space, start, end):
read_counts += 1
return self._normalize(read_counts, self._total) | python | def read_count(self, space, start, end):
"""Retrieve the normalized read count in the provided region.
"""
read_counts = 0
for read in self._bam.fetch(space, start, end):
read_counts += 1
return self._normalize(read_counts, self._total) | [
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bcbio/bcbio-nextgen | bcbio/bam/counts.py | NormalizedBam.coverage_pileup | def coverage_pileup(self, space, start, end):
"""Retrieve pileup coverage across a specified region.
"""
return ((col.pos, self._normalize(col.n, self._total))
for col in self._bam.pileup(space, start, end)) | python | def coverage_pileup(self, space, start, end):
"""Retrieve pileup coverage across a specified region.
"""
return ((col.pos, self._normalize(col.n, self._total))
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bcbio/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | _prepare_summary | def _prepare_summary(evolve_file, ssm_file, cnv_file, work_dir, somatic_info):
"""Prepare a summary with gene-labelled heterogeneity from PhyloWGS predictions.
"""
out_file = os.path.join(work_dir, "%s-phylowgs.txt" % somatic_info.tumor_name)
if not utils.file_uptodate(out_file, evolve_file):
wi... | python | def _prepare_summary(evolve_file, ssm_file, cnv_file, work_dir, somatic_info):
"""Prepare a summary with gene-labelled heterogeneity from PhyloWGS predictions.
"""
out_file = os.path.join(work_dir, "%s-phylowgs.txt" % somatic_info.tumor_name)
if not utils.file_uptodate(out_file, evolve_file):
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bcbio/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | _gids_to_genes | def _gids_to_genes(gids, ssm_locs, cnv_ssms, data):
"""Convert support ids for SNPs and SSMs into associated genes.
"""
locs = collections.defaultdict(set)
for gid in gids:
cur_locs = []
try:
cur_locs.append(ssm_locs[gid])
except KeyError:
for ssm_loc in c... | python | def _gids_to_genes(gids, ssm_locs, cnv_ssms, data):
"""Convert support ids for SNPs and SSMs into associated genes.
"""
locs = collections.defaultdict(set)
for gid in gids:
cur_locs = []
try:
cur_locs.append(ssm_locs[gid])
except KeyError:
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bcbio/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | _evolve_reader | def _evolve_reader(in_file):
"""Generate a list of region IDs and trees from a top_k_trees evolve.py file.
"""
cur_id_list = None
cur_tree = None
with open(in_file) as in_handle:
for line in in_handle:
if line.startswith("id,"):
if cur_id_list:
... | python | def _evolve_reader(in_file):
"""Generate a list of region IDs and trees from a top_k_trees evolve.py file.
"""
cur_id_list = None
cur_tree = None
with open(in_file) as in_handle:
for line in in_handle:
if line.startswith("id,"):
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bcbio/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | _read_cnv_ssms | def _read_cnv_ssms(in_file):
"""Map CNVs to associated SSMs
"""
out = {}
with open(in_file) as in_handle:
in_handle.readline() # header
for line in in_handle:
parts = line.strip().split()
if len(parts) > 3:
cnvid, _, _, ssms = parts
... | python | def _read_cnv_ssms(in_file):
"""Map CNVs to associated SSMs
"""
out = {}
with open(in_file) as in_handle:
in_handle.readline() # header
for line in in_handle:
parts = line.strip().split()
if len(parts) > 3:
cnvid, _, _, ssms = parts
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bcbio/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | _read_ssm_locs | def _read_ssm_locs(in_file):
"""Map SSMs to chromosomal locations.
"""
out = {}
with open(in_file) as in_handle:
in_handle.readline() # header
for line in in_handle:
sid, loc = line.split()[:2]
chrom, pos = loc.split("_")
out[sid] = (chrom, int(pos))
... | python | def _read_ssm_locs(in_file):
"""Map SSMs to chromosomal locations.
"""
out = {}
with open(in_file) as in_handle:
in_handle.readline() # header
for line in in_handle:
sid, loc = line.split()[:2]
chrom, pos = loc.split("_")
out[sid] = (chrom, int(pos))
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bcbio/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | _run_evolve | def _run_evolve(ssm_file, cnv_file, work_dir, data):
"""Run evolve.py to infer subclonal composition.
"""
exe = os.path.join(os.path.dirname(sys.executable), "evolve.py")
assert os.path.exists(exe), "Could not find evolve script for PhyloWGS runs."
out_dir = os.path.join(work_dir, "evolve")
out_... | python | def _run_evolve(ssm_file, cnv_file, work_dir, data):
"""Run evolve.py to infer subclonal composition.
"""
exe = os.path.join(os.path.dirname(sys.executable), "evolve.py")
assert os.path.exists(exe), "Could not find evolve script for PhyloWGS runs."
out_dir = os.path.join(work_dir, "evolve")
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bcbio/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | _prep_inputs | def _prep_inputs(vrn_info, cnv_info, somatic_info, work_dir, config):
"""Prepare inputs for running PhyloWGS from variant and CNV calls.
"""
exe = os.path.join(os.path.dirname(sys.executable), "create_phylowgs_inputs.py")
assert os.path.exists(exe), "Could not find input prep script for PhyloWGS runs."
... | python | def _prep_inputs(vrn_info, cnv_info, somatic_info, work_dir, config):
"""Prepare inputs for running PhyloWGS from variant and CNV calls.
"""
exe = os.path.join(os.path.dirname(sys.executable), "create_phylowgs_inputs.py")
assert os.path.exists(exe), "Could not find input prep script for PhyloWGS runs."
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bcbio/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | _prep_cnv_file | def _prep_cnv_file(in_file, work_dir, somatic_info):
"""Prepare Battenberg CNV file for ingest by PhyloWGS.
The PhyloWGS preparation script does not handle 'chr' prefixed chromosomes (hg19 style)
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work in _prep_vrn_file.
... | python | def _prep_cnv_file(in_file, work_dir, somatic_info):
"""Prepare Battenberg CNV file for ingest by PhyloWGS.
The PhyloWGS preparation script does not handle 'chr' prefixed chromosomes (hg19 style)
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work in _prep_vrn_file.
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bcbio/bcbio-nextgen | bcbio/heterogeneity/phylowgs.py | _prep_vrn_file | def _prep_vrn_file(in_file, vcaller, work_dir, somatic_info, ignore_file, config):
"""Create a variant file to feed into the PhyloWGS prep script, limiting records.
Sorts by depth, adding top covered samples up to the sample_size supported
by PhyloWGS. The logic is that the higher depth samples will have b... | python | def _prep_vrn_file(in_file, vcaller, work_dir, somatic_info, ignore_file, config):
"""Create a variant file to feed into the PhyloWGS prep script, limiting records.
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bcbio/bcbio-nextgen | bcbio/srna/group.py | run_prepare | def run_prepare(*data):
"""
Run seqcluster prepare to merge all samples in one file
"""
out_dir = os.path.join(dd.get_work_dir(data[0][0]), "seqcluster", "prepare")
out_dir = os.path.abspath(safe_makedir(out_dir))
prepare_dir = os.path.join(out_dir, "prepare")
tools = dd.get_expression_calle... | python | def run_prepare(*data):
"""
Run seqcluster prepare to merge all samples in one file
"""
out_dir = os.path.join(dd.get_work_dir(data[0][0]), "seqcluster", "prepare")
out_dir = os.path.abspath(safe_makedir(out_dir))
prepare_dir = os.path.join(out_dir, "prepare")
tools = dd.get_expression_calle... | [
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bcbio/bcbio-nextgen | bcbio/srna/group.py | run_align | def run_align(*data):
"""
Prepare data to run alignment step, only once for each project
"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = op.join(work_dir, "seqcluster", "prepare")
seq_out = op.join(out_dir, "seqs.fastq")
bam_dir = op.join(work_dir, "align")
new_bam_file = op.join(ba... | python | def run_align(*data):
"""
Prepare data to run alignment step, only once for each project
"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = op.join(work_dir, "seqcluster", "prepare")
seq_out = op.join(out_dir, "seqs.fastq")
bam_dir = op.join(work_dir, "align")
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bcbio/bcbio-nextgen | bcbio/srna/group.py | run_cluster | def run_cluster(*data):
"""
Run seqcluster cluster to detect smallRNA clusters
"""
sample = data[0][0]
tools = dd.get_expression_caller(data[0][0])
work_dir = dd.get_work_dir(sample)
out_dir = op.join(work_dir, "seqcluster", "cluster")
out_dir = op.abspath(safe_makedir(out_dir))
prep... | python | def run_cluster(*data):
"""
Run seqcluster cluster to detect smallRNA clusters
"""
sample = data[0][0]
tools = dd.get_expression_caller(data[0][0])
work_dir = dd.get_work_dir(sample)
out_dir = op.join(work_dir, "seqcluster", "cluster")
out_dir = op.abspath(safe_makedir(out_dir))
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bcbio/bcbio-nextgen | bcbio/srna/group.py | _cluster | def _cluster(bam_file, ma_file, out_dir, reference, annotation_file=None):
"""
Connect to seqcluster to run cluster with python directly
"""
seqcluster = op.join(get_bcbio_bin(), "seqcluster")
# cl = ["cluster", "-o", out_dir, "-m", ma_file, "-a", bam_file, "-r", reference]
if annotation_file:
... | python | def _cluster(bam_file, ma_file, out_dir, reference, annotation_file=None):
"""
Connect to seqcluster to run cluster with python directly
"""
seqcluster = op.join(get_bcbio_bin(), "seqcluster")
# cl = ["cluster", "-o", out_dir, "-m", ma_file, "-a", bam_file, "-r", reference]
if annotation_file:
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bcbio/bcbio-nextgen | bcbio/srna/group.py | _report | def _report(data, reference):
"""
Run report of seqcluster to get browser options for results
"""
seqcluster = op.join(get_bcbio_bin(), "seqcluster")
work_dir = dd.get_work_dir(data)
out_dir = safe_makedir(os.path.join(work_dir, "seqcluster", "report"))
out_file = op.join(out_dir, "seqcluste... | python | def _report(data, reference):
"""
Run report of seqcluster to get browser options for results
"""
seqcluster = op.join(get_bcbio_bin(), "seqcluster")
work_dir = dd.get_work_dir(data)
out_dir = safe_makedir(os.path.join(work_dir, "seqcluster", "report"))
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bcbio/bcbio-nextgen | bcbio/srna/group.py | report | def report(data):
"""Create a Rmd report for small RNAseq analysis"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = op.join(work_dir, "report")
safe_makedir(out_dir)
summary_file = op.join(out_dir, "summary.csv")
with file_transaction(summary_file) as out_tx:
with open(out_tx, 'w') as... | python | def report(data):
"""Create a Rmd report for small RNAseq analysis"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = op.join(work_dir, "report")
safe_makedir(out_dir)
summary_file = op.join(out_dir, "summary.csv")
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bcbio/bcbio-nextgen | bcbio/srna/group.py | _modify_report | def _modify_report(summary_path, out_dir):
"""Read Rmd template and dump with project path."""
summary_path = op.abspath(summary_path)
template = op.normpath(op.join(op.dirname(op.realpath(template_seqcluster.__file__)), "report.rmd"))
content = open(template).read()
out_content = string.Template(co... | python | def _modify_report(summary_path, out_dir):
"""Read Rmd template and dump with project path."""
summary_path = op.abspath(summary_path)
template = op.normpath(op.join(op.dirname(op.realpath(template_seqcluster.__file__)), "report.rmd"))
content = open(template).read()
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bcbio/bcbio-nextgen | bcbio/srna/group.py | _make_isomir_counts | def _make_isomir_counts(data, srna_type="seqbuster", out_dir=None, stem=""):
"""
Parse miraligner files to create count matrix.
"""
work_dir = dd.get_work_dir(data[0][0])
if not out_dir:
out_dir = op.join(work_dir, "mirbase")
out_novel_isomir = append_stem(op.join(out_dir, "counts.tsv"),... | python | def _make_isomir_counts(data, srna_type="seqbuster", out_dir=None, stem=""):
"""
Parse miraligner files to create count matrix.
"""
work_dir = dd.get_work_dir(data[0][0])
if not out_dir:
out_dir = op.join(work_dir, "mirbase")
out_novel_isomir = append_stem(op.join(out_dir, "counts.tsv"),... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/srna/group.py#L194-L221 | train |
bcbio/bcbio-nextgen | bcbio/bam/coverage.py | _split_regions | def _split_regions(chrom, start, end):
"""Split regions longer than 100kb into smaller sections.
"""
window_size = 1e5
if end - start < window_size * 5:
return [(chrom, start, end)]
else:
out = []
for r in pybedtools.BedTool().window_maker(w=window_size,
... | python | def _split_regions(chrom, start, end):
"""Split regions longer than 100kb into smaller sections.
"""
window_size = 1e5
if end - start < window_size * 5:
return [(chrom, start, end)]
else:
out = []
for r in pybedtools.BedTool().window_maker(w=window_size,
... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/bam/coverage.py#L96-L108 | train |
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