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bcbio/bcbio-nextgen | bcbio/structural/regions.py | calculate_sv_coverage | def calculate_sv_coverage(data):
"""Calculate coverage within bins for downstream CNV calling.
Creates corrected cnr files with log2 ratios and depths.
"""
calcfns = {"cnvkit": _calculate_sv_coverage_cnvkit, "gatk-cnv": _calculate_sv_coverage_gatk}
from bcbio.structural import cnvkit
data = uti... | python | def calculate_sv_coverage(data):
"""Calculate coverage within bins for downstream CNV calling.
Creates corrected cnr files with log2 ratios and depths.
"""
calcfns = {"cnvkit": _calculate_sv_coverage_cnvkit, "gatk-cnv": _calculate_sv_coverage_gatk}
from bcbio.structural import cnvkit
data = uti... | [
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | _calculate_sv_coverage_gatk | def _calculate_sv_coverage_gatk(data, work_dir):
"""Calculate coverage in defined regions using GATK tools
TODO: This does double calculations to get GATK4 compatible HDF read counts
and then depth and gene annotations. Both are needed for creating heterogeneity inputs.
Ideally replace with a single mo... | python | def _calculate_sv_coverage_gatk(data, work_dir):
"""Calculate coverage in defined regions using GATK tools
TODO: This does double calculations to get GATK4 compatible HDF read counts
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | _calculate_sv_coverage_cnvkit | def _calculate_sv_coverage_cnvkit(data, work_dir):
"""Calculate coverage in an CNVkit ready format using mosdepth.
"""
from bcbio.variation import coverage
from bcbio.structural import annotate
out_target_file = os.path.join(work_dir, "%s-target-coverage.cnn" % dd.get_sample_name(data))
out_anti... | python | def _calculate_sv_coverage_cnvkit(data, work_dir):
"""Calculate coverage in an CNVkit ready format using mosdepth.
"""
from bcbio.variation import coverage
from bcbio.structural import annotate
out_target_file = os.path.join(work_dir, "%s-target-coverage.cnn" % dd.get_sample_name(data))
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | normalize_sv_coverage | def normalize_sv_coverage(*items):
"""Normalize CNV coverage, providing flexible point for multiple methods.
"""
calcfns = {"cnvkit": _normalize_sv_coverage_cnvkit, "gatk-cnv": _normalize_sv_coverage_gatk}
from bcbio.structural import cnvkit
from bcbio.structural import shared as sshared
items =... | python | def normalize_sv_coverage(*items):
"""Normalize CNV coverage, providing flexible point for multiple methods.
"""
calcfns = {"cnvkit": _normalize_sv_coverage_cnvkit, "gatk-cnv": _normalize_sv_coverage_gatk}
from bcbio.structural import cnvkit
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | _normalize_sv_coverage_gatk | def _normalize_sv_coverage_gatk(group_id, inputs, backgrounds, work_dir, back_files, out_files):
"""Normalize CNV coverage using panel of normals with GATK's de-noise approaches.
"""
input_backs = set(filter(lambda x: x is not None,
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"""Normalize CNV coverage using panel of normals with GATK's de-noise approaches.
"""
input_backs = set(filter(lambda x: x is not None,
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | _normalize_sv_coverage_cnvkit | def _normalize_sv_coverage_cnvkit(group_id, inputs, backgrounds, work_dir, back_files, out_files):
"""Normalize CNV coverage depths by GC, repeats and background using CNVkit
- reference: calculates reference backgrounds from normals and pools
including GC and repeat information
- fix: Uses backgroun... | python | def _normalize_sv_coverage_cnvkit(group_id, inputs, backgrounds, work_dir, back_files, out_files):
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | get_base_cnv_regions | def get_base_cnv_regions(data, work_dir, genome_default="transcripts1e4", include_gene_names=True):
"""Retrieve set of target regions for CNV analysis.
Subsets to extended transcript regions for WGS experiments to avoid
long runtimes.
"""
cov_interval = dd.get_coverage_interval(data)
base_regio... | python | def get_base_cnv_regions(data, work_dir, genome_default="transcripts1e4", include_gene_names=True):
"""Retrieve set of target regions for CNV analysis.
Subsets to extended transcript regions for WGS experiments to avoid
long runtimes.
"""
cov_interval = dd.get_coverage_interval(data)
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | remove_exclude_regions | def remove_exclude_regions(orig_bed, base_file, items, remove_entire_feature=False):
"""Remove centromere and short end regions from an existing BED file of regions to target.
"""
from bcbio.structural import shared as sshared
out_bed = os.path.join("%s-noexclude.bed" % (utils.splitext_plus(base_file)[0... | python | def remove_exclude_regions(orig_bed, base_file, items, remove_entire_feature=False):
"""Remove centromere and short end regions from an existing BED file of regions to target.
"""
from bcbio.structural import shared as sshared
out_bed = os.path.join("%s-noexclude.bed" % (utils.splitext_plus(base_file)[0... | [
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | get_sv_bed | def get_sv_bed(data, method=None, out_dir=None, include_gene_names=True):
"""Retrieve a BED file of regions for SV and heterogeneity calling using the provided method.
method choices:
- exons: Raw BED file of exon regions
- transcripts: Full collapsed regions with the min and max of each transcript... | python | def get_sv_bed(data, method=None, out_dir=None, include_gene_names=True):
"""Retrieve a BED file of regions for SV and heterogeneity calling using the provided method.
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- exons: Raw BED file of exon regions
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | _group_coords | def _group_coords(rs):
"""Organize coordinate regions into groups for each transcript.
Avoids collapsing very large introns or repetitive genes spread across
the chromosome by limiting the intron size to 100kb for creating a single transcript
"""
max_intron_size = 1e5
coords = []
for r in r... | python | def _group_coords(rs):
"""Organize coordinate regions into groups for each transcript.
Avoids collapsing very large introns or repetitive genes spread across
the chromosome by limiting the intron size to 100kb for creating a single transcript
"""
max_intron_size = 1e5
coords = []
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bcbio/bcbio-nextgen | bcbio/structural/regions.py | MemoizedSizes._calc_sizes | def _calc_sizes(self, cnv_file, items):
"""Retrieve target and antitarget bin sizes based on depth.
Similar to CNVkit's do_autobin but tries to have a standard set of
ranges (50bp intervals for target and 10kb intervals for antitarget).
"""
bp_per_bin = 100000 # same target as ... | python | def _calc_sizes(self, cnv_file, items):
"""Retrieve target and antitarget bin sizes based on depth.
Similar to CNVkit's do_autobin but tries to have a standard set of
ranges (50bp intervals for target and 10kb intervals for antitarget).
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bcbio/bcbio-nextgen | bcbio/hmmer/search.py | phmmer | def phmmer(**kwargs):
"""Search a protein sequence against a HMMER sequence database.
Arguments:
seq - The sequence to search -- a Fasta string.
seqdb -- Sequence database to search against.
range -- A string range of results to return (ie. 1,10 for the first ten)
output -- The output f... | python | def phmmer(**kwargs):
"""Search a protein sequence against a HMMER sequence database.
Arguments:
seq - The sequence to search -- a Fasta string.
seqdb -- Sequence database to search against.
range -- A string range of results to return (ie. 1,10 for the first ten)
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | scrnaseq_concatenate_metadata | def scrnaseq_concatenate_metadata(samples):
"""
Create file same dimension than mtx.colnames
with metadata and sample name to help in the
creation of the SC object.
"""
barcodes = {}
counts = ""
metadata = {}
has_sample_barcodes = False
for sample in dd.sample_data_iterator(samp... | python | def scrnaseq_concatenate_metadata(samples):
"""
Create file same dimension than mtx.colnames
with metadata and sample name to help in the
creation of the SC object.
"""
barcodes = {}
counts = ""
metadata = {}
has_sample_barcodes = False
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | rnaseq_variant_calling | def rnaseq_variant_calling(samples, run_parallel):
"""
run RNA-seq variant calling using GATK
"""
samples = run_parallel("run_rnaseq_variant_calling", samples)
variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
if variantcaller and ("gatk-haplotype" in variantcaller):
out =... | python | def rnaseq_variant_calling(samples, run_parallel):
"""
run RNA-seq variant calling using GATK
"""
samples = run_parallel("run_rnaseq_variant_calling", samples)
variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
if variantcaller and ("gatk-haplotype" in variantcaller):
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | run_rnaseq_variant_calling | def run_rnaseq_variant_calling(data):
"""
run RNA-seq variant calling, variation file is stored in `vrn_file`
in the datadict
"""
variantcaller = dd.get_variantcaller(data)
if isinstance(variantcaller, list) and len(variantcaller) > 1:
logger.error("Only one variantcaller can be run for ... | python | def run_rnaseq_variant_calling(data):
"""
run RNA-seq variant calling, variation file is stored in `vrn_file`
in the datadict
"""
variantcaller = dd.get_variantcaller(data)
if isinstance(variantcaller, list) and len(variantcaller) > 1:
logger.error("Only one variantcaller can be run for ... | [
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | run_rnaseq_ann_filter | def run_rnaseq_ann_filter(data):
"""Run RNA-seq annotation and filtering.
"""
data = to_single_data(data)
if dd.get_vrn_file(data):
eff_file = effects.add_to_vcf(dd.get_vrn_file(data), data)[0]
if eff_file:
data = dd.set_vrn_file(data, eff_file)
ann_file = population.... | python | def run_rnaseq_ann_filter(data):
"""Run RNA-seq annotation and filtering.
"""
data = to_single_data(data)
if dd.get_vrn_file(data):
eff_file = effects.add_to_vcf(dd.get_vrn_file(data), data)[0]
if eff_file:
data = dd.set_vrn_file(data, eff_file)
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | quantitate | def quantitate(data):
"""CWL target for quantitation.
XXX Needs to be split and parallelized by expression caller, with merging
of multiple calls.
"""
data = to_single_data(to_single_data(data))
data = generate_transcript_counts(data)[0][0]
data["quant"] = {}
if "sailfish" in dd.get_exp... | python | def quantitate(data):
"""CWL target for quantitation.
XXX Needs to be split and parallelized by expression caller, with merging
of multiple calls.
"""
data = to_single_data(to_single_data(data))
data = generate_transcript_counts(data)[0][0]
data["quant"] = {}
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | quantitate_expression_parallel | def quantitate_expression_parallel(samples, run_parallel):
"""
quantitate expression, all programs run here should be multithreaded to
take advantage of the threaded run_parallel environment
"""
data = samples[0][0]
samples = run_parallel("generate_transcript_counts", samples)
if "cufflinks"... | python | def quantitate_expression_parallel(samples, run_parallel):
"""
quantitate expression, all programs run here should be multithreaded to
take advantage of the threaded run_parallel environment
"""
data = samples[0][0]
samples = run_parallel("generate_transcript_counts", samples)
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | quantitate_expression_noparallel | def quantitate_expression_noparallel(samples, run_parallel):
"""
run transcript quantitation for algorithms that don't run in parallel
"""
data = samples[0][0]
if "express" in dd.get_expression_caller(data):
samples = run_parallel("run_express", samples)
if "dexseq" in dd.get_expression_... | python | def quantitate_expression_noparallel(samples, run_parallel):
"""
run transcript quantitation for algorithms that don't run in parallel
"""
data = samples[0][0]
if "express" in dd.get_expression_caller(data):
samples = run_parallel("run_express", samples)
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | generate_transcript_counts | def generate_transcript_counts(data):
"""Generate counts per transcript and per exon from an alignment"""
data["count_file"] = featureCounts.count(data)
if dd.get_fusion_mode(data, False) and not dd.get_fusion_caller(data):
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
da... | python | def generate_transcript_counts(data):
"""Generate counts per transcript and per exon from an alignment"""
data["count_file"] = featureCounts.count(data)
if dd.get_fusion_mode(data, False) and not dd.get_fusion_caller(data):
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
da... | [
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | run_dexseq | def run_dexseq(data):
"""Quantitate exon-level counts with DEXSeq"""
if dd.get_dexseq_gff(data, None):
data = dexseq.bcbio_run(data)
return [[data]] | python | def run_dexseq(data):
"""Quantitate exon-level counts with DEXSeq"""
if dd.get_dexseq_gff(data, None):
data = dexseq.bcbio_run(data)
return [[data]] | [
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | combine_express | def combine_express(samples, combined):
"""Combine tpm, effective counts and fpkm from express results"""
if not combined:
return None
to_combine = [dd.get_express_counts(x) for x in
dd.sample_data_iterator(samples) if dd.get_express_counts(x)]
gtf_file = dd.get_gtf_file(sample... | python | def combine_express(samples, combined):
"""Combine tpm, effective counts and fpkm from express results"""
if not combined:
return None
to_combine = [dd.get_express_counts(x) for x in
dd.sample_data_iterator(samples) if dd.get_express_counts(x)]
gtf_file = dd.get_gtf_file(sample... | [
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bcbio/bcbio-nextgen | bcbio/pipeline/rnaseq.py | run_cufflinks | def run_cufflinks(data):
"""Quantitate transcript expression with Cufflinks"""
if "cufflinks" in dd.get_tools_off(data):
return [[data]]
work_bam = dd.get_work_bam(data)
ref_file = dd.get_sam_ref(data)
out_dir, fpkm_file, fpkm_isoform_file = cufflinks.run(work_bam, ref_file, data)
data =... | python | def run_cufflinks(data):
"""Quantitate transcript expression with Cufflinks"""
if "cufflinks" in dd.get_tools_off(data):
return [[data]]
work_bam = dd.get_work_bam(data)
ref_file = dd.get_sam_ref(data)
out_dir, fpkm_file, fpkm_isoform_file = cufflinks.run(work_bam, ref_file, data)
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bcbio/bcbio-nextgen | bcbio/rnaseq/express.py | run | def run(data):
"""Quantitaive isoforms expression by eXpress"""
name = dd.get_sample_name(data)
in_bam = dd.get_transcriptome_bam(data)
config = data['config']
if not in_bam:
logger.info("Transcriptome-mapped BAM file not found, skipping eXpress.")
return data
out_dir = os.path.j... | python | def run(data):
"""Quantitaive isoforms expression by eXpress"""
name = dd.get_sample_name(data)
in_bam = dd.get_transcriptome_bam(data)
config = data['config']
if not in_bam:
logger.info("Transcriptome-mapped BAM file not found, skipping eXpress.")
return data
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bcbio/bcbio-nextgen | bcbio/rnaseq/express.py | _get_column | def _get_column(in_file, out_file, column, data=None):
"""Subset one column from a file
"""
with file_transaction(data, out_file) as tx_out_file:
with open(in_file) as in_handle:
with open(tx_out_file, 'w') as out_handle:
for line in in_handle:
cols = ... | python | def _get_column(in_file, out_file, column, data=None):
"""Subset one column from a file
"""
with file_transaction(data, out_file) as tx_out_file:
with open(in_file) as in_handle:
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bcbio/bcbio-nextgen | bcbio/rnaseq/express.py | _prepare_bam_file | def _prepare_bam_file(bam_file, tmp_dir, config):
"""
Pipe sort by name cmd in case sort by coordinates
"""
sort_mode = _get_sort_order(bam_file, config)
if sort_mode != "queryname":
bam_file = sort(bam_file, config, "queryname")
return bam_file | python | def _prepare_bam_file(bam_file, tmp_dir, config):
"""
Pipe sort by name cmd in case sort by coordinates
"""
sort_mode = _get_sort_order(bam_file, config)
if sort_mode != "queryname":
bam_file = sort(bam_file, config, "queryname")
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bcbio/bcbio-nextgen | bcbio/rnaseq/express.py | isoform_to_gene_name | def isoform_to_gene_name(gtf_file, out_file, data):
"""
produce a table of isoform -> gene mappings for loading into EBSeq
"""
if not out_file:
out_file = tempfile.NamedTemporaryFile(delete=False).name
if file_exists(out_file):
return out_file
db = gtf.get_gtf_db(gtf_file)
l... | python | def isoform_to_gene_name(gtf_file, out_file, data):
"""
produce a table of isoform -> gene mappings for loading into EBSeq
"""
if not out_file:
out_file = tempfile.NamedTemporaryFile(delete=False).name
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bcbio/bcbio-nextgen | bcbio/variation/samtools.py | shared_variantcall | def shared_variantcall(call_fn, name, align_bams, ref_file, items,
assoc_files, region=None, out_file=None):
"""Provide base functionality for prepping and indexing for variant calling.
"""
config = items[0]["config"]
if out_file is None:
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assoc_files, region=None, out_file=None):
"""Provide base functionality for prepping and indexing for variant calling.
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config = items[0]["config"]
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bcbio/bcbio-nextgen | bcbio/variation/samtools.py | run_samtools | def run_samtools(align_bams, items, ref_file, assoc_files, region=None,
out_file=None):
"""Detect SNPs and indels with samtools mpileup and bcftools.
"""
return shared_variantcall(_call_variants_samtools, "samtools", align_bams, ref_file,
items, assoc_files, re... | python | def run_samtools(align_bams, items, ref_file, assoc_files, region=None,
out_file=None):
"""Detect SNPs and indels with samtools mpileup and bcftools.
"""
return shared_variantcall(_call_variants_samtools, "samtools", align_bams, ref_file,
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bcbio/bcbio-nextgen | bcbio/variation/samtools.py | _call_variants_samtools | def _call_variants_samtools(align_bams, ref_file, items, target_regions, tx_out_file):
"""Call variants with samtools in target_regions.
Works around a GATK VCF 4.2 compatibility issue in samtools 1.0
by removing addition 4.2-only isms from VCF header lines.
"""
config = items[0]["config"]
mpil... | python | def _call_variants_samtools(align_bams, ref_file, items, target_regions, tx_out_file):
"""Call variants with samtools in target_regions.
Works around a GATK VCF 4.2 compatibility issue in samtools 1.0
by removing addition 4.2-only isms from VCF header lines.
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config = items[0]["config"]
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bcbio/bcbio-nextgen | bcbio/pipeline/sra.py | _convert_fastq | def _convert_fastq(srafn, outdir, single=False):
"convert sra to fastq"
cmd = "fastq-dump --split-files --gzip {srafn}"
cmd = "%s %s" % (utils.local_path_export(), cmd)
sraid = os.path.basename(utils.splitext_plus(srafn)[0])
if not srafn:
return None
if not single:
out_file = [os... | python | def _convert_fastq(srafn, outdir, single=False):
"convert sra to fastq"
cmd = "fastq-dump --split-files --gzip {srafn}"
cmd = "%s %s" % (utils.local_path_export(), cmd)
sraid = os.path.basename(utils.splitext_plus(srafn)[0])
if not srafn:
return None
if not single:
out_file = [os... | [
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bcbio/bcbio-nextgen | bcbio/illumina/machine.py | check_and_postprocess | def check_and_postprocess(args):
"""Check for newly dumped sequencer output, post-processing and transferring.
"""
with open(args.process_config) as in_handle:
config = yaml.safe_load(in_handle)
setup_local_logging(config)
for dname in _find_unprocessed(config):
lane_details = nglims... | python | def check_and_postprocess(args):
"""Check for newly dumped sequencer output, post-processing and transferring.
"""
with open(args.process_config) as in_handle:
config = yaml.safe_load(in_handle)
setup_local_logging(config)
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bcbio/bcbio-nextgen | bcbio/illumina/machine.py | _tweak_lane | def _tweak_lane(lane_details, dname):
"""Potentially tweak lane information to handle custom processing, reading a lane_config.yaml file.
"""
tweak_config_file = os.path.join(dname, "lane_config.yaml")
if os.path.exists(tweak_config_file):
with open(tweak_config_file) as in_handle:
t... | python | def _tweak_lane(lane_details, dname):
"""Potentially tweak lane information to handle custom processing, reading a lane_config.yaml file.
"""
tweak_config_file = os.path.join(dname, "lane_config.yaml")
if os.path.exists(tweak_config_file):
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bcbio/bcbio-nextgen | bcbio/illumina/machine.py | _remap_dirname | def _remap_dirname(local, remote):
"""Remap directory names from local to remote.
"""
def do(x):
return x.replace(local, remote, 1)
return do | python | def _remap_dirname(local, remote):
"""Remap directory names from local to remote.
"""
def do(x):
return x.replace(local, remote, 1)
return do | [
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bcbio/bcbio-nextgen | bcbio/illumina/machine.py | _find_unprocessed | def _find_unprocessed(config):
"""Find any finished directories that have not been processed.
"""
reported = _read_reported(config["msg_db"])
for dname in _get_directories(config):
if os.path.isdir(dname) and dname not in reported:
if _is_finished_dumping(dname):
yiel... | python | def _find_unprocessed(config):
"""Find any finished directories that have not been processed.
"""
reported = _read_reported(config["msg_db"])
for dname in _get_directories(config):
if os.path.isdir(dname) and dname not in reported:
if _is_finished_dumping(dname):
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bcbio/bcbio-nextgen | bcbio/illumina/machine.py | _is_finished_dumping | def _is_finished_dumping(directory):
"""Determine if the sequencing directory has all files.
The final checkpoint file will differ depending if we are a
single or paired end run.
"""
#if _is_finished_dumping_checkpoint(directory):
# return True
# Check final output files; handles both Hi... | python | def _is_finished_dumping(directory):
"""Determine if the sequencing directory has all files.
The final checkpoint file will differ depending if we are a
single or paired end run.
"""
#if _is_finished_dumping_checkpoint(directory):
# return True
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bcbio/bcbio-nextgen | bcbio/illumina/machine.py | _expected_reads | def _expected_reads(run_info_file):
"""Parse the number of expected reads from the RunInfo.xml file.
"""
reads = []
if os.path.exists(run_info_file):
tree = ElementTree()
tree.parse(run_info_file)
read_elem = tree.find("Run/Reads")
reads = read_elem.findall("Read")
re... | python | def _expected_reads(run_info_file):
"""Parse the number of expected reads from the RunInfo.xml file.
"""
reads = []
if os.path.exists(run_info_file):
tree = ElementTree()
tree.parse(run_info_file)
read_elem = tree.find("Run/Reads")
reads = read_elem.findall("Read")
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bcbio/bcbio-nextgen | bcbio/illumina/machine.py | _read_reported | def _read_reported(msg_db):
"""Retrieve a list of directories previous reported.
"""
reported = []
if os.path.exists(msg_db):
with open(msg_db) as in_handle:
for line in in_handle:
reported.append(line.strip())
return reported | python | def _read_reported(msg_db):
"""Retrieve a list of directories previous reported.
"""
reported = []
if os.path.exists(msg_db):
with open(msg_db) as in_handle:
for line in in_handle:
reported.append(line.strip())
return reported | [
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bcbio/bcbio-nextgen | bcbio/qc/viral.py | get_files | def get_files(data):
"""Retrieve pre-installed viral reference files.
"""
all_files = glob.glob(os.path.normpath(os.path.join(os.path.dirname(dd.get_ref_file(data)),
os.pardir, "viral", "*")))
return sorted(all_files) | python | def get_files(data):
"""Retrieve pre-installed viral reference files.
"""
all_files = glob.glob(os.path.normpath(os.path.join(os.path.dirname(dd.get_ref_file(data)),
os.pardir, "viral", "*")))
return sorted(all_files) | [
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bcbio/bcbio-nextgen | bcbio/rnaseq/variation.py | gatk_splitreads | def gatk_splitreads(data):
"""
use GATK to split reads with Ns in the CIGAR string, hard clipping regions
that end up in introns
"""
broad_runner = broad.runner_from_config(dd.get_config(data))
ref_file = dd.get_ref_file(data)
deduped_bam = dd.get_deduped_bam(data)
base, ext = os.path.sp... | python | def gatk_splitreads(data):
"""
use GATK to split reads with Ns in the CIGAR string, hard clipping regions
that end up in introns
"""
broad_runner = broad.runner_from_config(dd.get_config(data))
ref_file = dd.get_ref_file(data)
deduped_bam = dd.get_deduped_bam(data)
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bcbio/bcbio-nextgen | bcbio/rnaseq/variation.py | _setup_variant_regions | def _setup_variant_regions(data, out_dir):
"""Ensure we have variant regions for calling, using transcript if not present.
Respects noalt_calling by removing additional contigs to improve
speeds.
"""
vr_file = dd.get_variant_regions(data)
if not vr_file:
vr_file = regions.get_sv_bed(dat... | python | def _setup_variant_regions(data, out_dir):
"""Ensure we have variant regions for calling, using transcript if not present.
Respects noalt_calling by removing additional contigs to improve
speeds.
"""
vr_file = dd.get_variant_regions(data)
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bcbio/bcbio-nextgen | bcbio/rnaseq/variation.py | gatk_rnaseq_calling | def gatk_rnaseq_calling(data):
"""Use GATK to perform gVCF variant calling on RNA-seq data
"""
from bcbio.bam import callable
data = utils.deepish_copy(data)
tools_on = dd.get_tools_on(data)
if not tools_on:
tools_on = []
tools_on.append("gvcf")
data = dd.set_tools_on(data, tools... | python | def gatk_rnaseq_calling(data):
"""Use GATK to perform gVCF variant calling on RNA-seq data
"""
from bcbio.bam import callable
data = utils.deepish_copy(data)
tools_on = dd.get_tools_on(data)
if not tools_on:
tools_on = []
tools_on.append("gvcf")
data = dd.set_tools_on(data, tools... | [
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bcbio/bcbio-nextgen | bcbio/rnaseq/variation.py | filter_junction_variants | def filter_junction_variants(vrn_file, data):
"""
filter out variants within 10 basepairs of a splice junction, these are
very prone to being false positives with RNA-seq data
"""
SJ_BP_MASK = 10
vrn_dir = os.path.dirname(vrn_file)
splicebed = dd.get_junction_bed(data)
if not file_exists... | python | def filter_junction_variants(vrn_file, data):
"""
filter out variants within 10 basepairs of a splice junction, these are
very prone to being false positives with RNA-seq data
"""
SJ_BP_MASK = 10
vrn_dir = os.path.dirname(vrn_file)
splicebed = dd.get_junction_bed(data)
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bcbio/bcbio-nextgen | scripts/bcbio_nextgen_install.py | _clean_args | def _clean_args(sys_argv, args):
"""Remove data directory from arguments to pass to upgrade function.
"""
base = [x for x in sys_argv if
x.startswith("-") or not args.datadir == os.path.abspath(os.path.expanduser(x))]
# Remove installer only options we don't pass on
base = [x for x in ba... | python | def _clean_args(sys_argv, args):
"""Remove data directory from arguments to pass to upgrade function.
"""
base = [x for x in sys_argv if
x.startswith("-") or not args.datadir == os.path.abspath(os.path.expanduser(x))]
# Remove installer only options we don't pass on
base = [x for x in ba... | [
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bcbio/bcbio-nextgen | scripts/bcbio_nextgen_install.py | setup_manifest | def setup_manifest(datadir):
"""Create barebones manifest to be filled in during update
"""
manifest_dir = os.path.join(datadir, "manifest")
if not os.path.exists(manifest_dir):
os.makedirs(manifest_dir) | python | def setup_manifest(datadir):
"""Create barebones manifest to be filled in during update
"""
manifest_dir = os.path.join(datadir, "manifest")
if not os.path.exists(manifest_dir):
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bcbio/bcbio-nextgen | scripts/bcbio_nextgen_install.py | write_system_config | def write_system_config(base_url, datadir, tooldir):
"""Write a bcbio_system.yaml configuration file with tool information.
"""
out_file = os.path.join(datadir, "galaxy", os.path.basename(base_url))
if not os.path.exists(os.path.dirname(out_file)):
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if o... | python | def write_system_config(base_url, datadir, tooldir):
"""Write a bcbio_system.yaml configuration file with tool information.
"""
out_file = os.path.join(datadir, "galaxy", os.path.basename(base_url))
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bcbio/bcbio-nextgen | scripts/bcbio_nextgen_install.py | check_dependencies | def check_dependencies():
"""Ensure required tools for installation are present.
"""
print("Checking required dependencies")
for dep, msg in [(["git", "--version"], "Git (http://git-scm.com/)"),
(["wget", "--version"], "wget"),
(["bzip2", "-h"], "bzip2")]:
... | python | def check_dependencies():
"""Ensure required tools for installation are present.
"""
print("Checking required dependencies")
for dep, msg in [(["git", "--version"], "Git (http://git-scm.com/)"),
(["wget", "--version"], "wget"),
(["bzip2", "-h"], "bzip2")]:
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | process | def process(args):
"""Run the function in args.name given arguments in args.argfile.
"""
# Set environment to standard to use periods for decimals and avoid localization
os.environ["LC_ALL"] = "C"
os.environ["LC"] = "C"
os.environ["LANG"] = "C"
setpath.prepend_bcbiopath()
try:
fn... | python | def process(args):
"""Run the function in args.name given arguments in args.argfile.
"""
# Set environment to standard to use periods for decimals and avoid localization
os.environ["LC_ALL"] = "C"
os.environ["LC"] = "C"
os.environ["LANG"] = "C"
setpath.prepend_bcbiopath()
try:
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _cwlvar_to_wdl | def _cwlvar_to_wdl(var):
"""Convert a CWL output object into a WDL output.
This flattens files and other special CWL outputs that are
plain strings in WDL.
"""
if isinstance(var, (list, tuple)):
return [_cwlvar_to_wdl(x) for x in var]
elif isinstance(var, dict):
assert var.get("... | python | def _cwlvar_to_wdl(var):
"""Convert a CWL output object into a WDL output.
This flattens files and other special CWL outputs that are
plain strings in WDL.
"""
if isinstance(var, (list, tuple)):
return [_cwlvar_to_wdl(x) for x in var]
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _write_out_argfile | def _write_out_argfile(argfile, out, fnargs, parallel, out_keys, input_files, work_dir):
"""Write output argfile, preparing a CWL ready JSON or YAML representation of the world.
"""
with open(argfile, "w") as out_handle:
if argfile.endswith(".json"):
record_name, record_attrs = _get_reco... | python | def _write_out_argfile(argfile, out, fnargs, parallel, out_keys, input_files, work_dir):
"""Write output argfile, preparing a CWL ready JSON or YAML representation of the world.
"""
with open(argfile, "w") as out_handle:
if argfile.endswith(".json"):
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _get_record_attrs | def _get_record_attrs(out_keys):
"""Check for records, a single key plus output attributes.
"""
if len(out_keys) == 1:
attr = list(out_keys.keys())[0]
if out_keys[attr]:
return attr, out_keys[attr]
return None, None | python | def _get_record_attrs(out_keys):
"""Check for records, a single key plus output attributes.
"""
if len(out_keys) == 1:
attr = list(out_keys.keys())[0]
if out_keys[attr]:
return attr, out_keys[attr]
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _add_resources | def _add_resources(data, runtime):
"""Merge input resources with current CWL runtime parameters.
"""
if "config" not in data:
data["config"] = {}
# Convert input resources, which may be a JSON string
resources = data.get("resources", {}) or {}
if isinstance(resources, six.string_types) a... | python | def _add_resources(data, runtime):
"""Merge input resources with current CWL runtime parameters.
"""
if "config" not in data:
data["config"] = {}
# Convert input resources, which may be a JSON string
resources = data.get("resources", {}) or {}
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _world_from_cwl | def _world_from_cwl(fn_name, fnargs, work_dir):
"""Reconstitute a bcbio world data object from flattened CWL-compatible inputs.
Converts the flat CWL representation into a nested bcbio world dictionary.
Handles single sample inputs (returning a single world object) and multi-sample
runs (returning a l... | python | def _world_from_cwl(fn_name, fnargs, work_dir):
"""Reconstitute a bcbio world data object from flattened CWL-compatible inputs.
Converts the flat CWL representation into a nested bcbio world dictionary.
Handles single sample inputs (returning a single world object) and multi-sample
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _parse_output_keys | def _parse_output_keys(val):
"""Parse expected output keys from string, handling records.
"""
out = {}
for k in val.split(","):
# record output
if ":" in k:
name, attrs = k.split(":")
out[name] = attrs.split(";")
else:
out[k] = None
return ... | python | def _parse_output_keys(val):
"""Parse expected output keys from string, handling records.
"""
out = {}
for k in val.split(","):
# record output
if ":" in k:
name, attrs = k.split(":")
out[name] = attrs.split(";")
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out[k] = None
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _find_input_files | def _find_input_files(var, out):
"""Find input files within the given CWL object.
"""
if isinstance(var, (list, tuple)):
for x in var:
out = _find_input_files(x, out)
elif isinstance(var, dict):
if var.get("class") == "File":
out.append(var["path"])
ou... | python | def _find_input_files(var, out):
"""Find input files within the given CWL object.
"""
if isinstance(var, (list, tuple)):
for x in var:
out = _find_input_files(x, out)
elif isinstance(var, dict):
if var.get("class") == "File":
out.append(var["path"])
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _read_from_cwlinput | def _read_from_cwlinput(in_file, work_dir, runtime, parallel, input_order, output_cwl_keys):
"""Read data records from a JSON dump of inputs. Avoids command line flattening of records.
"""
with open(in_file) as in_handle:
inputs = json.load(in_handle)
items_by_key = {}
input_files = []
p... | python | def _read_from_cwlinput(in_file, work_dir, runtime, parallel, input_order, output_cwl_keys):
"""Read data records from a JSON dump of inputs. Avoids command line flattening of records.
"""
with open(in_file) as in_handle:
inputs = json.load(in_handle)
items_by_key = {}
input_files = []
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _maybe_nest_bare_single | def _maybe_nest_bare_single(items_by_key, parallel):
"""Nest single inputs to avoid confusing single items and lists like files.
"""
if (parallel == "multi-parallel" and
(sum([1 for x in items_by_key.values() if not _is_nested_item(x)]) >=
sum([1 for x in items_by_key.values() if _is_ne... | python | def _maybe_nest_bare_single(items_by_key, parallel):
"""Nest single inputs to avoid confusing single items and lists like files.
"""
if (parallel == "multi-parallel" and
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _check_for_single_nested | def _check_for_single_nested(target, items_by_key, input_order):
"""Check for single nested inputs that match our target count and unnest.
Handles complex var inputs where some have an extra layer of nesting.
"""
out = utils.deepish_copy(items_by_key)
for (k, t) in input_order.items():
if t... | python | def _check_for_single_nested(target, items_by_key, input_order):
"""Check for single nested inputs that match our target count and unnest.
Handles complex var inputs where some have an extra layer of nesting.
"""
out = utils.deepish_copy(items_by_key)
for (k, t) in input_order.items():
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _concat_records | def _concat_records(items_by_key, input_order):
"""Concatenate records into a single key to avoid merging.
Handles heterogeneous records that will then be sorted out in
the processing fuction.
"""
all_records = []
for (k, t) in input_order.items():
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all_reco... | python | def _concat_records(items_by_key, input_order):
"""Concatenate records into a single key to avoid merging.
Handles heterogeneous records that will then be sorted out in
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _nest_vars_in_rec | def _nest_vars_in_rec(var_items, rec_items, input_order, items_by_key, parallel):
"""Nest multiple variable inputs into a single record or list of batch records.
Custom CWL implementations extract and merge these.
"""
num_items = var_items
var_items = list(var_items)[0]
if rec_items:
re... | python | def _nest_vars_in_rec(var_items, rec_items, input_order, items_by_key, parallel):
"""Nest multiple variable inputs into a single record or list of batch records.
Custom CWL implementations extract and merge these.
"""
num_items = var_items
var_items = list(var_items)[0]
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _expand_rec_to_vars | def _expand_rec_to_vars(var_items, rec_items, input_order, items_by_key, parallel):
"""Expand record to apply to number of variants.
Alternative approach to _nest_vars_in_rec
to combining a single record with multiple variants.
"""
num_items = var_items
var_items = list(var_items)[0]
if rec... | python | def _expand_rec_to_vars(var_items, rec_items, input_order, items_by_key, parallel):
"""Expand record to apply to number of variants.
Alternative approach to _nest_vars_in_rec
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _read_cwl_record | def _read_cwl_record(rec):
"""Read CWL records, handling multiple nesting and batching cases.
"""
keys = set([])
out = []
if isinstance(rec, dict):
is_batched = all([isinstance(v, (list, tuple)) for v in rec.values()])
cur = [{} for _ in range(len(rec.values()[0]) if is_batched else ... | python | def _read_cwl_record(rec):
"""Read CWL records, handling multiple nesting and batching cases.
"""
keys = set([])
out = []
if isinstance(rec, dict):
is_batched = all([isinstance(v, (list, tuple)) for v in rec.values()])
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _finalize_cwl_in | def _finalize_cwl_in(data, work_dir, passed_keys, output_cwl_keys, runtime):
"""Finalize data object with inputs from CWL.
"""
data["dirs"] = {"work": work_dir}
if not tz.get_in(["config", "algorithm"], data):
if "config" not in data:
data["config"] = {}
data["config"]["algor... | python | def _finalize_cwl_in(data, work_dir, passed_keys, output_cwl_keys, runtime):
"""Finalize data object with inputs from CWL.
"""
data["dirs"] = {"work": work_dir}
if not tz.get_in(["config", "algorithm"], data):
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data["config"] = {}
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _convert_value | def _convert_value(val):
"""Handle multiple input type values.
"""
def _is_number(x, op):
try:
op(x)
return True
except ValueError:
return False
if isinstance(val, (list, tuple)):
return [_convert_value(x) for x in val]
elif val is None:
... | python | def _convert_value(val):
"""Handle multiple input type values.
"""
def _is_number(x, op):
try:
op(x)
return True
except ValueError:
return False
if isinstance(val, (list, tuple)):
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _get_output_cwl_keys | def _get_output_cwl_keys(fnargs):
"""Retrieve output_cwl_keys from potentially nested input arguments.
"""
for d in utils.flatten(fnargs):
if isinstance(d, dict) and d.get("output_cwl_keys"):
return d["output_cwl_keys"]
raise ValueError("Did not find output_cwl_keys in %s" % (pprint.... | python | def _get_output_cwl_keys(fnargs):
"""Retrieve output_cwl_keys from potentially nested input arguments.
"""
for d in utils.flatten(fnargs):
if isinstance(d, dict) and d.get("output_cwl_keys"):
return d["output_cwl_keys"]
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _combine_cwl_records | def _combine_cwl_records(recs, record_name, parallel):
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Handles batches, where we return a list of records, and single items
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"""
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"""Provide a list of nexted CWL records keyed by output key.
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _collapse_to_cwl_record_single | def _collapse_to_cwl_record_single(data, want_attrs, input_files):
"""Convert a single sample into a CWL record.
"""
out = {}
for key in want_attrs:
key_parts = key.split("__")
out[key] = _to_cwl(tz.get_in(key_parts, data), input_files)
return out | python | def _collapse_to_cwl_record_single(data, want_attrs, input_files):
"""Convert a single sample into a CWL record.
"""
out = {}
for key in want_attrs:
key_parts = key.split("__")
out[key] = _to_cwl(tz.get_in(key_parts, data), input_files)
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _nested_cwl_record | def _nested_cwl_record(xs, want_attrs, input_files):
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"""
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"""Convert arbitrarily nested samples into a nested list of dictionaries.
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _collapse_to_cwl_record | def _collapse_to_cwl_record(samples, want_attrs, input_files):
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"""
input_keys = sorted(list(set().union(*[d["cwl_keys"] for d in samples])), key=lambda x: (-len(x), tuple(x)))
out = {}
for key in input_keys:
if ke... | python | def _collapse_to_cwl_record(samples, want_attrs, input_files):
"""Convert nested samples from batches into a CWL record, based on input keys.
"""
input_keys = sorted(list(set().union(*[d["cwl_keys"] for d in samples])), key=lambda x: (-len(x), tuple(x)))
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _file_and_exists | def _file_and_exists(val, input_files):
"""Check if an input is a file and exists.
Checks both locally (staged) and from input files (re-passed but never localized).
"""
return ((os.path.exists(val) and os.path.isfile(val)) or
val in input_files) | python | def _file_and_exists(val, input_files):
"""Check if an input is a file and exists.
Checks both locally (staged) and from input files (re-passed but never localized).
"""
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _to_cwl | def _to_cwl(val, input_files):
"""Convert a value into CWL formatted JSON, handling files and complex things.
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"""Convert a value into CWL formatted JSON, handling files and complex things.
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bcbio/bcbio-nextgen | bcbio/distributed/runfn.py | _remove_duplicate_files | def _remove_duplicate_files(xs):
"""Remove files specified multiple times in a list.
"""
seen = set([])
out = []
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return out | python | def _remove_duplicate_files(xs):
"""Remove files specified multiple times in a list.
"""
seen = set([])
out = []
for x in xs:
if x["path"] not in seen:
out.append(x)
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bcbio/bcbio-nextgen | bcbio/server/main.py | start | def start(args):
"""Run server with provided command line arguments.
"""
application = tornado.web.Application([(r"/run", run.get_handler(args)),
(r"/status", run.StatusHandler)])
application.runmonitor = RunMonitor()
application.listen(args.port)
torna... | python | def start(args):
"""Run server with provided command line arguments.
"""
application = tornado.web.Application([(r"/run", run.get_handler(args)),
(r"/status", run.StatusHandler)])
application.runmonitor = RunMonitor()
application.listen(args.port)
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bcbio/bcbio-nextgen | bcbio/server/main.py | add_subparser | def add_subparser(subparsers):
"""Add command line arguments as server subparser.
"""
parser = subparsers.add_parser("server", help="Run a bcbio-nextgen server allowing remote job execution.")
parser.add_argument("-c", "--config", help=("Global YAML configuration file specifying system details."
... | python | def add_subparser(subparsers):
"""Add command line arguments as server subparser.
"""
parser = subparsers.add_parser("server", help="Run a bcbio-nextgen server allowing remote job execution.")
parser.add_argument("-c", "--config", help=("Global YAML configuration file specifying system details."
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bcbio/bcbio-nextgen | bcbio/provenance/data.py | write_versions | def write_versions(dirs, items):
"""Write data versioning for genomes present in the configuration.
"""
genomes = {}
for d in items:
genomes[d["genome_build"]] = d.get("reference", {}).get("versions")
out_file = _get_out_file(dirs)
found_versions = False
if genomes and out_file:
... | python | def write_versions(dirs, items):
"""Write data versioning for genomes present in the configuration.
"""
genomes = {}
for d in items:
genomes[d["genome_build"]] = d.get("reference", {}).get("versions")
out_file = _get_out_file(dirs)
found_versions = False
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bcbio/bcbio-nextgen | bcbio/variation/ensemble.py | combine_calls | def combine_calls(*args):
"""Combine multiple callsets into a final set of merged calls.
"""
if len(args) == 3:
is_cwl = False
batch_id, samples, data = args
caller_names, vrn_files = _organize_variants(samples, batch_id)
else:
is_cwl = True
samples = [utils.to_si... | python | def combine_calls(*args):
"""Combine multiple callsets into a final set of merged calls.
"""
if len(args) == 3:
is_cwl = False
batch_id, samples, data = args
caller_names, vrn_files = _organize_variants(samples, batch_id)
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is_cwl = True
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bcbio/bcbio-nextgen | bcbio/variation/ensemble.py | combine_calls_parallel | def combine_calls_parallel(samples, run_parallel):
"""Combine calls using batched Ensemble approach.
"""
batch_groups, extras = _group_by_batches(samples, _has_ensemble)
out = []
if batch_groups:
processed = run_parallel("combine_calls", ((b, xs, xs[0]) for b, xs in batch_groups.items()))
... | python | def combine_calls_parallel(samples, run_parallel):
"""Combine calls using batched Ensemble approach.
"""
batch_groups, extras = _group_by_batches(samples, _has_ensemble)
out = []
if batch_groups:
processed = run_parallel("combine_calls", ((b, xs, xs[0]) for b, xs in batch_groups.items()))
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bcbio/bcbio-nextgen | bcbio/variation/ensemble.py | _group_by_batches | def _group_by_batches(samples, check_fn):
"""Group calls by batches, processing families together during ensemble calling.
"""
batch_groups = collections.defaultdict(list)
extras = []
for data in [x[0] for x in samples]:
if check_fn(data):
batch_groups[multi.get_batch_for_key(dat... | python | def _group_by_batches(samples, check_fn):
"""Group calls by batches, processing families together during ensemble calling.
"""
batch_groups = collections.defaultdict(list)
extras = []
for data in [x[0] for x in samples]:
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bcbio/bcbio-nextgen | bcbio/variation/ensemble.py | _organize_variants | def _organize_variants(samples, batch_id):
"""Retrieve variant calls for all samples, merging batched samples into single VCF.
"""
caller_names = [x["variantcaller"] for x in samples[0]["variants"]]
calls = collections.defaultdict(list)
for data in samples:
for vrn in data["variants"]:
... | python | def _organize_variants(samples, batch_id):
"""Retrieve variant calls for all samples, merging batched samples into single VCF.
"""
caller_names = [x["variantcaller"] for x in samples[0]["variants"]]
calls = collections.defaultdict(list)
for data in samples:
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bcbio/bcbio-nextgen | bcbio/variation/ensemble.py | _handle_somatic_ensemble | def _handle_somatic_ensemble(vrn_file, data):
"""For somatic ensemble, discard normal samples and filtered variants from vcfs.
Only needed for bcbio.variation based ensemble calling.
"""
if tz.get_in(["metadata", "phenotype"], data, "").lower().startswith("tumor"):
vrn_file_temp = vrn_file.repl... | python | def _handle_somatic_ensemble(vrn_file, data):
"""For somatic ensemble, discard normal samples and filtered variants from vcfs.
Only needed for bcbio.variation based ensemble calling.
"""
if tz.get_in(["metadata", "phenotype"], data, "").lower().startswith("tumor"):
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bcbio/bcbio-nextgen | bcbio/variation/ensemble.py | _run_ensemble | def _run_ensemble(batch_id, vrn_files, config_file, base_dir, ref_file, data):
"""Run an ensemble call using merging and SVM-based approach in bcbio.variation
"""
out_vcf_file = os.path.join(base_dir, "{0}-ensemble.vcf".format(batch_id))
out_bed_file = os.path.join(base_dir, "{0}-callregions.bed".format... | python | def _run_ensemble(batch_id, vrn_files, config_file, base_dir, ref_file, data):
"""Run an ensemble call using merging and SVM-based approach in bcbio.variation
"""
out_vcf_file = os.path.join(base_dir, "{0}-ensemble.vcf".format(batch_id))
out_bed_file = os.path.join(base_dir, "{0}-callregions.bed".format... | [
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bcbio/bcbio-nextgen | bcbio/variation/ensemble.py | _write_config_file | def _write_config_file(batch_id, caller_names, base_dir, data):
"""Write YAML configuration to generate an ensemble set of combined calls.
"""
config_dir = utils.safe_makedir(os.path.join(base_dir, "config"))
config_file = os.path.join(config_dir, "{0}-ensemble.yaml".format(batch_id))
algorithm = da... | python | def _write_config_file(batch_id, caller_names, base_dir, data):
"""Write YAML configuration to generate an ensemble set of combined calls.
"""
config_dir = utils.safe_makedir(os.path.join(base_dir, "config"))
config_file = os.path.join(config_dir, "{0}-ensemble.yaml".format(batch_id))
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bcbio/bcbio-nextgen | bcbio/variation/ensemble.py | _get_num_pass | def _get_num_pass(data, n):
"""Calculate the number of samples needed to pass ensemble calling.
"""
numpass = tz.get_in(["config", "algorithm", "ensemble", "numpass"], data)
if numpass:
return int(numpass)
trusted_pct = tz.get_in(["config", "algorithm", "ensemble", "trusted_pct"], data)
... | python | def _get_num_pass(data, n):
"""Calculate the number of samples needed to pass ensemble calling.
"""
numpass = tz.get_in(["config", "algorithm", "ensemble", "numpass"], data)
if numpass:
return int(numpass)
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bcbio/bcbio-nextgen | bcbio/variation/ensemble.py | _run_ensemble_intersection | def _run_ensemble_intersection(batch_id, vrn_files, callers, base_dir, edata):
"""Run intersection n out of x based ensemble method using bcbio.variation.recall.
"""
out_vcf_file = os.path.join(base_dir, "{0}-ensemble.vcf.gz".format(batch_id))
if not utils.file_exists(out_vcf_file):
num_pass = _... | python | def _run_ensemble_intersection(batch_id, vrn_files, callers, base_dir, edata):
"""Run intersection n out of x based ensemble method using bcbio.variation.recall.
"""
out_vcf_file = os.path.join(base_dir, "{0}-ensemble.vcf.gz".format(batch_id))
if not utils.file_exists(out_vcf_file):
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bcbio/bcbio-nextgen | bcbio/variation/joint.py | _get_callable_regions | def _get_callable_regions(data):
"""Retrieve regions to parallelize by from callable regions or chromosomes.
"""
import pybedtools
callable_files = data.get("callable_regions")
if callable_files:
assert len(callable_files) == 1
regions = [(r.chrom, int(r.start), int(r.stop)) for r in... | python | def _get_callable_regions(data):
"""Retrieve regions to parallelize by from callable regions or chromosomes.
"""
import pybedtools
callable_files = data.get("callable_regions")
if callable_files:
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bcbio/bcbio-nextgen | bcbio/variation/joint.py | _split_by_callable_region | def _split_by_callable_region(data):
"""Split by callable or variant regions.
We expect joint calling to be deep in numbers of samples per region, so prefer
splitting aggressively by regions.
"""
batch = tz.get_in(("metadata", "batch"), data)
jointcaller = tz.get_in(("config", "algorithm", "joi... | python | def _split_by_callable_region(data):
"""Split by callable or variant regions.
We expect joint calling to be deep in numbers of samples per region, so prefer
splitting aggressively by regions.
"""
batch = tz.get_in(("metadata", "batch"), data)
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bcbio/bcbio-nextgen | bcbio/variation/joint.py | _is_jointcaller_compatible | def _is_jointcaller_compatible(data):
"""Match variant caller inputs to compatible joint callers.
"""
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), data)
variantcaller = tz.get_in(("config", "algorithm", "variantcaller"), data)
if isinstance(variantcaller, (list, tuple)) and len(va... | python | def _is_jointcaller_compatible(data):
"""Match variant caller inputs to compatible joint callers.
"""
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), data)
variantcaller = tz.get_in(("config", "algorithm", "variantcaller"), data)
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bcbio/bcbio-nextgen | bcbio/variation/joint.py | square_off | def square_off(samples, run_parallel):
"""Perform joint calling at all variants within a batch.
"""
to_process = []
extras = []
for data in [utils.to_single_data(x) for x in samples]:
added = False
if tz.get_in(("metadata", "batch"), data):
for add in genotype.handle_mult... | python | def square_off(samples, run_parallel):
"""Perform joint calling at all variants within a batch.
"""
to_process = []
extras = []
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added = False
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bcbio/bcbio-nextgen | bcbio/variation/joint.py | _combine_to_jointcaller | def _combine_to_jointcaller(processed):
"""Add joint calling information to variants, while collapsing independent regions.
"""
by_vrn_file = collections.OrderedDict()
for data in (x[0] for x in processed):
key = (tz.get_in(("config", "algorithm", "jointcaller"), data), data["vrn_file"])
... | python | def _combine_to_jointcaller(processed):
"""Add joint calling information to variants, while collapsing independent regions.
"""
by_vrn_file = collections.OrderedDict()
for data in (x[0] for x in processed):
key = (tz.get_in(("config", "algorithm", "jointcaller"), data), data["vrn_file"])
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bcbio/bcbio-nextgen | bcbio/variation/joint.py | square_batch_region | def square_batch_region(data, region, bam_files, vrn_files, out_file):
"""Perform squaring of a batch in a supplied region, with input BAMs
"""
from bcbio.variation import sentieon, strelka2
if not utils.file_exists(out_file):
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), data)... | python | def square_batch_region(data, region, bam_files, vrn_files, out_file):
"""Perform squaring of a batch in a supplied region, with input BAMs
"""
from bcbio.variation import sentieon, strelka2
if not utils.file_exists(out_file):
jointcaller = tz.get_in(("config", "algorithm", "jointcaller"), data)... | [
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bcbio/bcbio-nextgen | bcbio/variation/joint.py | _fix_orig_vcf_refs | def _fix_orig_vcf_refs(data):
"""Supply references to initial variantcalls if run in addition to batching.
"""
variantcaller = tz.get_in(("config", "algorithm", "variantcaller"), data)
if variantcaller:
data["vrn_file_orig"] = data["vrn_file"]
for i, sub in enumerate(data.get("group_orig", [... | python | def _fix_orig_vcf_refs(data):
"""Supply references to initial variantcalls if run in addition to batching.
"""
variantcaller = tz.get_in(("config", "algorithm", "variantcaller"), data)
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data["vrn_file_orig"] = data["vrn_file"]
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bcbio/bcbio-nextgen | bcbio/variation/joint.py | _square_batch_bcbio_variation | def _square_batch_bcbio_variation(data, region, bam_files, vrn_files, out_file,
todo="square"):
"""Run squaring or merging analysis using bcbio.variation.recall.
"""
ref_file = tz.get_in(("reference", "fasta", "base"), data)
cores = tz.get_in(("config", "algorithm", "nu... | python | def _square_batch_bcbio_variation(data, region, bam_files, vrn_files, out_file,
todo="square"):
"""Run squaring or merging analysis using bcbio.variation.recall.
"""
ref_file = tz.get_in(("reference", "fasta", "base"), data)
cores = tz.get_in(("config", "algorithm", "nu... | [
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bcbio/bcbio-nextgen | bcbio/structural/seq2c.py | run | def run(items):
"""Normalization and log2 ratio calculation plus CNV calling for full cohort.
- Combine coverage of each region for each sample
- Prepare read counts for each sample
- Normalize coverages in cohort by gene and sample, and calculate log2 ratios
- Call amplifications and deletions
... | python | def run(items):
"""Normalization and log2 ratio calculation plus CNV calling for full cohort.
- Combine coverage of each region for each sample
- Prepare read counts for each sample
- Normalize coverages in cohort by gene and sample, and calculate log2 ratios
- Call amplifications and deletions
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bcbio/bcbio-nextgen | bcbio/structural/seq2c.py | prep_seq2c_bed | def prep_seq2c_bed(data):
"""Selecting the bed file, cleaning, and properly annotating for Seq2C
"""
if dd.get_background_cnv_reference(data, "seq2c"):
bed_file = _background_to_bed(dd.get_background_cnv_reference(data, "seq2c"), data)
else:
bed_file = regions.get_sv_bed(data)
if bed... | python | def prep_seq2c_bed(data):
"""Selecting the bed file, cleaning, and properly annotating for Seq2C
"""
if dd.get_background_cnv_reference(data, "seq2c"):
bed_file = _background_to_bed(dd.get_background_cnv_reference(data, "seq2c"), data)
else:
bed_file = regions.get_sv_bed(data)
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bcbio/bcbio-nextgen | bcbio/structural/seq2c.py | _background_to_bed | def _background_to_bed(back_file, data):
"""Convert a seq2c background file with calls into BED regions for coverage.
seq2c background files are a concatenation of mapping and sample_coverages from
potentially multiple samples. We use the coverage information from the first
sample to translate into BED... | python | def _background_to_bed(back_file, data):
"""Convert a seq2c background file with calls into BED regions for coverage.
seq2c background files are a concatenation of mapping and sample_coverages from
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bcbio/bcbio-nextgen | bcbio/structural/seq2c.py | _get_seq2c_options | def _get_seq2c_options(data):
"""Get adjustable, through resources, or default options for seq2c.
"""
cov2lr_possible_opts = ["-F"]
defaults = {}
ropts = config_utils.get_resources("seq2c", data["config"]).get("options", [])
assert len(ropts) % 2 == 0, "Expect even number of options for seq2c" %... | python | def _get_seq2c_options(data):
"""Get adjustable, through resources, or default options for seq2c.
"""
cov2lr_possible_opts = ["-F"]
defaults = {}
ropts = config_utils.get_resources("seq2c", data["config"]).get("options", [])
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bcbio/bcbio-nextgen | bcbio/structural/seq2c.py | to_vcf | def to_vcf(in_tsv, data):
"""Convert seq2c output file into BED output.
"""
call_convert = {"Amp": "DUP", "Del": "DEL"}
out_file = "%s.vcf" % utils.splitext_plus(in_tsv)[0]
if not utils.file_uptodate(out_file, in_tsv):
with file_transaction(data, out_file) as tx_out_file:
with op... | python | def to_vcf(in_tsv, data):
"""Convert seq2c output file into BED output.
"""
call_convert = {"Amp": "DUP", "Del": "DEL"}
out_file = "%s.vcf" % utils.splitext_plus(in_tsv)[0]
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bcbio/bcbio-nextgen | bcbio/structural/seq2c.py | _combine_coverages | def _combine_coverages(items, work_dir, input_backs=None):
"""Combine coverage cnns calculated for individual inputs into single file.
Optionally moves over pre-calculated coverage samples from a background file.
"""
out_file = os.path.join(work_dir, "sample_coverages.txt")
if not utils.file_exists... | python | def _combine_coverages(items, work_dir, input_backs=None):
"""Combine coverage cnns calculated for individual inputs into single file.
Optionally moves over pre-calculated coverage samples from a background file.
"""
out_file = os.path.join(work_dir, "sample_coverages.txt")
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bcbio/bcbio-nextgen | bcbio/structural/seq2c.py | _calculate_mapping_reads | def _calculate_mapping_reads(items, work_dir, input_backs=None):
"""Calculate read counts from samtools idxstats for each sample.
Optionally moves over pre-calculated mapping counts from a background file.
"""
out_file = os.path.join(work_dir, "mapping_reads.txt")
if not utils.file_exists(out_file)... | python | def _calculate_mapping_reads(items, work_dir, input_backs=None):
"""Calculate read counts from samtools idxstats for each sample.
Optionally moves over pre-calculated mapping counts from a background file.
"""
out_file = os.path.join(work_dir, "mapping_reads.txt")
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Optionally moves over pre-calculated mapping counts from a background file. | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/seq2c.py#L311-L335 | train |
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