id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
|---|---|---|---|---|---|---|---|---|---|---|---|
223,200 | bcbio/bcbio-nextgen | bcbio/structural/purple.py | _counts_to_amber | def _counts_to_amber(t_vals, n_vals):
"""Converts a line of CollectAllelicCounts into AMBER line.
"""
t_depth = int(t_vals["REF_COUNT"]) + int(t_vals["ALT_COUNT"])
n_depth = int(n_vals["REF_COUNT"]) + int(n_vals["ALT_COUNT"])
if n_depth > 0 and t_depth > 0:
t_baf = float(t_vals["ALT_COUNT"])... | python | def _counts_to_amber(t_vals, n_vals):
"""Converts a line of CollectAllelicCounts into AMBER line.
"""
t_depth = int(t_vals["REF_COUNT"]) + int(t_vals["ALT_COUNT"])
n_depth = int(n_vals["REF_COUNT"]) + int(n_vals["ALT_COUNT"])
if n_depth > 0 and t_depth > 0:
t_baf = float(t_vals["ALT_COUNT"])... | [
"def",
"_counts_to_amber",
"(",
"t_vals",
",",
"n_vals",
")",
":",
"t_depth",
"=",
"int",
"(",
"t_vals",
"[",
"\"REF_COUNT\"",
"]",
")",
"+",
"int",
"(",
"t_vals",
"[",
"\"ALT_COUNT\"",
"]",
")",
"n_depth",
"=",
"int",
"(",
"n_vals",
"[",
"\"REF_COUNT\""... | Converts a line of CollectAllelicCounts into AMBER line. | [
"Converts",
"a",
"line",
"of",
"CollectAllelicCounts",
"into",
"AMBER",
"line",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/purple.py#L113-L122 |
223,201 | bcbio/bcbio-nextgen | bcbio/structural/purple.py | _count_files_to_amber | def _count_files_to_amber(tumor_counts, normal_counts, work_dir, data):
"""Converts tumor and normal counts from GATK CollectAllelicCounts into Amber format.
"""
amber_dir = utils.safe_makedir(os.path.join(work_dir, "amber"))
out_file = os.path.join(amber_dir, "%s.amber.baf" % dd.get_sample_name(data))
... | python | def _count_files_to_amber(tumor_counts, normal_counts, work_dir, data):
"""Converts tumor and normal counts from GATK CollectAllelicCounts into Amber format.
"""
amber_dir = utils.safe_makedir(os.path.join(work_dir, "amber"))
out_file = os.path.join(amber_dir, "%s.amber.baf" % dd.get_sample_name(data))
... | [
"def",
"_count_files_to_amber",
"(",
"tumor_counts",
",",
"normal_counts",
",",
"work_dir",
",",
"data",
")",
":",
"amber_dir",
"=",
"utils",
".",
"safe_makedir",
"(",
"os",
".",
"path",
".",
"join",
"(",
"work_dir",
",",
"\"amber\"",
")",
")",
"out_file",
... | Converts tumor and normal counts from GATK CollectAllelicCounts into Amber format. | [
"Converts",
"tumor",
"and",
"normal",
"counts",
"from",
"GATK",
"CollectAllelicCounts",
"into",
"Amber",
"format",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/purple.py#L124-L148 |
223,202 | bcbio/bcbio-nextgen | bcbio/structural/purple.py | _amber_het_file | def _amber_het_file(method, vrn_files, work_dir, paired):
"""Create file of BAFs in normal heterozygous positions compatible with AMBER.
Two available methods:
- pon -- Use panel of normals with likely heterozygous sites.
- variants -- Use pre-existing variant calls, filtered to likely heterozygote... | python | def _amber_het_file(method, vrn_files, work_dir, paired):
"""Create file of BAFs in normal heterozygous positions compatible with AMBER.
Two available methods:
- pon -- Use panel of normals with likely heterozygous sites.
- variants -- Use pre-existing variant calls, filtered to likely heterozygote... | [
"def",
"_amber_het_file",
"(",
"method",
",",
"vrn_files",
",",
"work_dir",
",",
"paired",
")",
":",
"assert",
"vrn_files",
",",
"\"Did not find compatible variant calling files for PURPLE inputs\"",
"from",
"bcbio",
".",
"heterogeneity",
"import",
"bubbletree",
"if",
"... | Create file of BAFs in normal heterozygous positions compatible with AMBER.
Two available methods:
- pon -- Use panel of normals with likely heterozygous sites.
- variants -- Use pre-existing variant calls, filtered to likely heterozygotes.
https://github.com/hartwigmedical/hmftools/tree/master/am... | [
"Create",
"file",
"of",
"BAFs",
"in",
"normal",
"heterozygous",
"positions",
"compatible",
"with",
"AMBER",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/purple.py#L166-L197 |
223,203 | bcbio/bcbio-nextgen | bcbio/structural/purple.py | _run_cobalt | def _run_cobalt(paired, work_dir):
"""Run Cobalt for counting read depth across genomic windows.
PURPLE requires even 1000bp windows so use integrated counting solution
directly rather than converting from CNVkit calculations. If this approach
is useful should be moved upstream to be available to other... | python | def _run_cobalt(paired, work_dir):
"""Run Cobalt for counting read depth across genomic windows.
PURPLE requires even 1000bp windows so use integrated counting solution
directly rather than converting from CNVkit calculations. If this approach
is useful should be moved upstream to be available to other... | [
"def",
"_run_cobalt",
"(",
"paired",
",",
"work_dir",
")",
":",
"cobalt_dir",
"=",
"utils",
".",
"safe_makedir",
"(",
"os",
".",
"path",
".",
"join",
"(",
"work_dir",
",",
"\"cobalt\"",
")",
")",
"out_file",
"=",
"os",
".",
"path",
".",
"join",
"(",
... | Run Cobalt for counting read depth across genomic windows.
PURPLE requires even 1000bp windows so use integrated counting solution
directly rather than converting from CNVkit calculations. If this approach
is useful should be moved upstream to be available to other tools as
an input comparison.
ht... | [
"Run",
"Cobalt",
"for",
"counting",
"read",
"depth",
"across",
"genomic",
"windows",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/purple.py#L259-L285 |
223,204 | bcbio/bcbio-nextgen | bcbio/structural/purple.py | _cobalt_ratio_file | def _cobalt_ratio_file(paired, work_dir):
"""Convert CNVkit binning counts into cobalt ratio output.
This contains read counts plus normalization for GC, from section 7.2
"Determine read depth ratios for tumor and reference genomes"
https://www.biorxiv.org/content/biorxiv/early/2018/09/20/415133.full.... | python | def _cobalt_ratio_file(paired, work_dir):
"""Convert CNVkit binning counts into cobalt ratio output.
This contains read counts plus normalization for GC, from section 7.2
"Determine read depth ratios for tumor and reference genomes"
https://www.biorxiv.org/content/biorxiv/early/2018/09/20/415133.full.... | [
"def",
"_cobalt_ratio_file",
"(",
"paired",
",",
"work_dir",
")",
":",
"cobalt_dir",
"=",
"utils",
".",
"safe_makedir",
"(",
"os",
".",
"path",
".",
"join",
"(",
"work_dir",
",",
"\"cobalt\"",
")",
")",
"out_file",
"=",
"os",
".",
"path",
".",
"join",
... | Convert CNVkit binning counts into cobalt ratio output.
This contains read counts plus normalization for GC, from section 7.2
"Determine read depth ratios for tumor and reference genomes"
https://www.biorxiv.org/content/biorxiv/early/2018/09/20/415133.full.pdf
Since CNVkit cnr files already have GC b... | [
"Convert",
"CNVkit",
"binning",
"counts",
"into",
"cobalt",
"ratio",
"output",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/purple.py#L287-L313 |
223,205 | bcbio/bcbio-nextgen | bcbio/structural/purple.py | _export_to_vcf | def _export_to_vcf(cur):
"""Convert PURPLE custom output into VCF.
"""
if float(cur["copyNumber"]) > 2.0:
svtype = "DUP"
elif float(cur["copyNumber"]) < 2.0:
svtype = "DEL"
else:
svtype = None
if svtype:
info = ["END=%s" % cur["end"], "SVLEN=%s" % (int(cur["end"])... | python | def _export_to_vcf(cur):
"""Convert PURPLE custom output into VCF.
"""
if float(cur["copyNumber"]) > 2.0:
svtype = "DUP"
elif float(cur["copyNumber"]) < 2.0:
svtype = "DEL"
else:
svtype = None
if svtype:
info = ["END=%s" % cur["end"], "SVLEN=%s" % (int(cur["end"])... | [
"def",
"_export_to_vcf",
"(",
"cur",
")",
":",
"if",
"float",
"(",
"cur",
"[",
"\"copyNumber\"",
"]",
")",
">",
"2.0",
":",
"svtype",
"=",
"\"DUP\"",
"elif",
"float",
"(",
"cur",
"[",
"\"copyNumber\"",
"]",
")",
"<",
"2.0",
":",
"svtype",
"=",
"\"DEL... | Convert PURPLE custom output into VCF. | [
"Convert",
"PURPLE",
"custom",
"output",
"into",
"VCF",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/purple.py#L324-L337 |
223,206 | bcbio/bcbio-nextgen | bcbio/rnaseq/pizzly.py | make_pizzly_gtf | def make_pizzly_gtf(gtf_file, out_file, data):
"""
pizzly needs the GTF to be in gene -> transcript -> exon order for each
gene. it also wants the gene biotype set as the source
"""
if file_exists(out_file):
return out_file
db = gtf.get_gtf_db(gtf_file)
with file_transaction(data, ou... | python | def make_pizzly_gtf(gtf_file, out_file, data):
"""
pizzly needs the GTF to be in gene -> transcript -> exon order for each
gene. it also wants the gene biotype set as the source
"""
if file_exists(out_file):
return out_file
db = gtf.get_gtf_db(gtf_file)
with file_transaction(data, ou... | [
"def",
"make_pizzly_gtf",
"(",
"gtf_file",
",",
"out_file",
",",
"data",
")",
":",
"if",
"file_exists",
"(",
"out_file",
")",
":",
"return",
"out_file",
"db",
"=",
"gtf",
".",
"get_gtf_db",
"(",
"gtf_file",
")",
"with",
"file_transaction",
"(",
"data",
","... | pizzly needs the GTF to be in gene -> transcript -> exon order for each
gene. it also wants the gene biotype set as the source | [
"pizzly",
"needs",
"the",
"GTF",
"to",
"be",
"in",
"gene",
"-",
">",
"transcript",
"-",
">",
"exon",
"order",
"for",
"each",
"gene",
".",
"it",
"also",
"wants",
"the",
"gene",
"biotype",
"set",
"as",
"the",
"source"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/rnaseq/pizzly.py#L82-L105 |
223,207 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | _validate_caller_vcf | def _validate_caller_vcf(call_vcf, truth_vcf, callable_bed, svcaller, work_dir, data):
"""Validate a caller VCF against truth within callable regions using SURVIVOR.
Combines files with SURIVOR merge and counts (https://github.com/fritzsedlazeck/SURVIVOR/)
"""
stats = _calculate_comparison_stats(truth_... | python | def _validate_caller_vcf(call_vcf, truth_vcf, callable_bed, svcaller, work_dir, data):
"""Validate a caller VCF against truth within callable regions using SURVIVOR.
Combines files with SURIVOR merge and counts (https://github.com/fritzsedlazeck/SURVIVOR/)
"""
stats = _calculate_comparison_stats(truth_... | [
"def",
"_validate_caller_vcf",
"(",
"call_vcf",
",",
"truth_vcf",
",",
"callable_bed",
",",
"svcaller",
",",
"work_dir",
",",
"data",
")",
":",
"stats",
"=",
"_calculate_comparison_stats",
"(",
"truth_vcf",
")",
"call_vcf",
"=",
"_prep_vcf",
"(",
"call_vcf",
","... | Validate a caller VCF against truth within callable regions using SURVIVOR.
Combines files with SURIVOR merge and counts (https://github.com/fritzsedlazeck/SURVIVOR/) | [
"Validate",
"a",
"caller",
"VCF",
"against",
"truth",
"within",
"callable",
"regions",
"using",
"SURVIVOR",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L44-L55 |
223,208 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | _survivor_merge | def _survivor_merge(call_vcf, truth_vcf, stats, work_dir, data):
"""Perform a merge of two callsets using SURVIVOR,
"""
out_file = os.path.join(work_dir, "eval-merge.vcf")
if not utils.file_uptodate(out_file, call_vcf):
in_call_vcf = call_vcf.replace(".vcf.gz", ".vcf")
if not utils.file_... | python | def _survivor_merge(call_vcf, truth_vcf, stats, work_dir, data):
"""Perform a merge of two callsets using SURVIVOR,
"""
out_file = os.path.join(work_dir, "eval-merge.vcf")
if not utils.file_uptodate(out_file, call_vcf):
in_call_vcf = call_vcf.replace(".vcf.gz", ".vcf")
if not utils.file_... | [
"def",
"_survivor_merge",
"(",
"call_vcf",
",",
"truth_vcf",
",",
"stats",
",",
"work_dir",
",",
"data",
")",
":",
"out_file",
"=",
"os",
".",
"path",
".",
"join",
"(",
"work_dir",
",",
"\"eval-merge.vcf\"",
")",
"if",
"not",
"utils",
".",
"file_uptodate",... | Perform a merge of two callsets using SURVIVOR, | [
"Perform",
"a",
"merge",
"of",
"two",
"callsets",
"using",
"SURVIVOR"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L77-L96 |
223,209 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | _calculate_comparison_stats | def _calculate_comparison_stats(truth_vcf):
"""Identify calls to validate from the input truth VCF.
"""
# Avoid very small events for average calculations
min_stat_size = 50
min_median_size = 250
sizes = []
svtypes = set([])
with utils.open_gzipsafe(truth_vcf) as in_handle:
for c... | python | def _calculate_comparison_stats(truth_vcf):
"""Identify calls to validate from the input truth VCF.
"""
# Avoid very small events for average calculations
min_stat_size = 50
min_median_size = 250
sizes = []
svtypes = set([])
with utils.open_gzipsafe(truth_vcf) as in_handle:
for c... | [
"def",
"_calculate_comparison_stats",
"(",
"truth_vcf",
")",
":",
"# Avoid very small events for average calculations",
"min_stat_size",
"=",
"50",
"min_median_size",
"=",
"250",
"sizes",
"=",
"[",
"]",
"svtypes",
"=",
"set",
"(",
"[",
"]",
")",
"with",
"utils",
"... | Identify calls to validate from the input truth VCF. | [
"Identify",
"calls",
"to",
"validate",
"from",
"the",
"input",
"truth",
"VCF",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L110-L133 |
223,210 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | _get_start_end | def _get_start_end(parts, index=7):
"""Retrieve start and end for a VCF record, skips BNDs without END coords
"""
start = parts[1]
end = [x.split("=")[-1] for x in parts[index].split(";") if x.startswith("END=")]
if end:
end = end[0]
return start, end
return None, None | python | def _get_start_end(parts, index=7):
"""Retrieve start and end for a VCF record, skips BNDs without END coords
"""
start = parts[1]
end = [x.split("=")[-1] for x in parts[index].split(";") if x.startswith("END=")]
if end:
end = end[0]
return start, end
return None, None | [
"def",
"_get_start_end",
"(",
"parts",
",",
"index",
"=",
"7",
")",
":",
"start",
"=",
"parts",
"[",
"1",
"]",
"end",
"=",
"[",
"x",
".",
"split",
"(",
"\"=\"",
")",
"[",
"-",
"1",
"]",
"for",
"x",
"in",
"parts",
"[",
"index",
"]",
".",
"spli... | Retrieve start and end for a VCF record, skips BNDs without END coords | [
"Retrieve",
"start",
"and",
"end",
"for",
"a",
"VCF",
"record",
"skips",
"BNDs",
"without",
"END",
"coords"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L135-L143 |
223,211 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | _summarize_call | def _summarize_call(parts):
"""Provide summary metrics on size and svtype for a SV call.
"""
svtype = [x.split("=")[1] for x in parts[7].split(";") if x.startswith("SVTYPE=")]
svtype = svtype[0] if svtype else ""
start, end = _get_start_end(parts)
return {"svtype": svtype, "size": int(end) - int... | python | def _summarize_call(parts):
"""Provide summary metrics on size and svtype for a SV call.
"""
svtype = [x.split("=")[1] for x in parts[7].split(";") if x.startswith("SVTYPE=")]
svtype = svtype[0] if svtype else ""
start, end = _get_start_end(parts)
return {"svtype": svtype, "size": int(end) - int... | [
"def",
"_summarize_call",
"(",
"parts",
")",
":",
"svtype",
"=",
"[",
"x",
".",
"split",
"(",
"\"=\"",
")",
"[",
"1",
"]",
"for",
"x",
"in",
"parts",
"[",
"7",
"]",
".",
"split",
"(",
"\";\"",
")",
"if",
"x",
".",
"startswith",
"(",
"\"SVTYPE=\""... | Provide summary metrics on size and svtype for a SV call. | [
"Provide",
"summary",
"metrics",
"on",
"size",
"and",
"svtype",
"for",
"a",
"SV",
"call",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L145-L151 |
223,212 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | _prep_callable_bed | def _prep_callable_bed(in_file, work_dir, stats, data):
"""Sort and merge callable BED regions to prevent SV double counting
"""
out_file = os.path.join(work_dir, "%s-merge.bed.gz" % utils.splitext_plus(os.path.basename(in_file))[0])
gsort = config_utils.get_program("gsort", data)
if not utils.file_... | python | def _prep_callable_bed(in_file, work_dir, stats, data):
"""Sort and merge callable BED regions to prevent SV double counting
"""
out_file = os.path.join(work_dir, "%s-merge.bed.gz" % utils.splitext_plus(os.path.basename(in_file))[0])
gsort = config_utils.get_program("gsort", data)
if not utils.file_... | [
"def",
"_prep_callable_bed",
"(",
"in_file",
",",
"work_dir",
",",
"stats",
",",
"data",
")",
":",
"out_file",
"=",
"os",
".",
"path",
".",
"join",
"(",
"work_dir",
",",
"\"%s-merge.bed.gz\"",
"%",
"utils",
".",
"splitext_plus",
"(",
"os",
".",
"path",
"... | Sort and merge callable BED regions to prevent SV double counting | [
"Sort",
"and",
"merge",
"callable",
"BED",
"regions",
"to",
"prevent",
"SV",
"double",
"counting"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L176-L187 |
223,213 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | _get_anns_to_remove | def _get_anns_to_remove(in_file):
"""Find larger annotations, if present in VCF, that slow down processing.
"""
to_remove = ["ANN", "LOF"]
to_remove_str = tuple(["##INFO=<ID=%s" % x for x in to_remove])
cur_remove = []
with utils.open_gzipsafe(in_file) as in_handle:
for line in in_handle... | python | def _get_anns_to_remove(in_file):
"""Find larger annotations, if present in VCF, that slow down processing.
"""
to_remove = ["ANN", "LOF"]
to_remove_str = tuple(["##INFO=<ID=%s" % x for x in to_remove])
cur_remove = []
with utils.open_gzipsafe(in_file) as in_handle:
for line in in_handle... | [
"def",
"_get_anns_to_remove",
"(",
"in_file",
")",
":",
"to_remove",
"=",
"[",
"\"ANN\"",
",",
"\"LOF\"",
"]",
"to_remove_str",
"=",
"tuple",
"(",
"[",
"\"##INFO=<ID=%s\"",
"%",
"x",
"for",
"x",
"in",
"to_remove",
"]",
")",
"cur_remove",
"=",
"[",
"]",
"... | Find larger annotations, if present in VCF, that slow down processing. | [
"Find",
"larger",
"annotations",
"if",
"present",
"in",
"VCF",
"that",
"slow",
"down",
"processing",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L189-L202 |
223,214 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | cnv_to_event | def cnv_to_event(name, data):
"""Convert a CNV to an event name.
"""
cur_ploidy = ploidy.get_ploidy([data])
if name.startswith("cnv"):
num = max([int(x) for x in name.split("_")[0].replace("cnv", "").split(";")])
if num < cur_ploidy:
return "DEL"
elif num > cur_ploidy... | python | def cnv_to_event(name, data):
"""Convert a CNV to an event name.
"""
cur_ploidy = ploidy.get_ploidy([data])
if name.startswith("cnv"):
num = max([int(x) for x in name.split("_")[0].replace("cnv", "").split(";")])
if num < cur_ploidy:
return "DEL"
elif num > cur_ploidy... | [
"def",
"cnv_to_event",
"(",
"name",
",",
"data",
")",
":",
"cur_ploidy",
"=",
"ploidy",
".",
"get_ploidy",
"(",
"[",
"data",
"]",
")",
"if",
"name",
".",
"startswith",
"(",
"\"cnv\"",
")",
":",
"num",
"=",
"max",
"(",
"[",
"int",
"(",
"x",
")",
"... | Convert a CNV to an event name. | [
"Convert",
"a",
"CNV",
"to",
"an",
"event",
"name",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L216-L229 |
223,215 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | _evaluate_one | def _evaluate_one(caller, svtype, size_range, ensemble, truth, data):
"""Compare a ensemble results for a caller against a specific caller and SV type.
"""
def cnv_matches(name):
return cnv_to_event(name, data) == svtype
def is_breakend(name):
return name.startswith("BND")
def in_siz... | python | def _evaluate_one(caller, svtype, size_range, ensemble, truth, data):
"""Compare a ensemble results for a caller against a specific caller and SV type.
"""
def cnv_matches(name):
return cnv_to_event(name, data) == svtype
def is_breakend(name):
return name.startswith("BND")
def in_siz... | [
"def",
"_evaluate_one",
"(",
"caller",
",",
"svtype",
",",
"size_range",
",",
"ensemble",
",",
"truth",
",",
"data",
")",
":",
"def",
"cnv_matches",
"(",
"name",
")",
":",
"return",
"cnv_to_event",
"(",
"name",
",",
"data",
")",
"==",
"svtype",
"def",
... | Compare a ensemble results for a caller against a specific caller and SV type. | [
"Compare",
"a",
"ensemble",
"results",
"for",
"a",
"caller",
"against",
"a",
"specific",
"caller",
"and",
"SV",
"type",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L231-L258 |
223,216 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | _plot_evaluation_event | def _plot_evaluation_event(df_csv, svtype):
"""Provide plot of evaluation metrics for an SV event, stratified by event size.
"""
titles = {"INV": "Inversions", "DEL": "Deletions", "DUP": "Duplications",
"INS": "Insertions"}
out_file = "%s-%s.png" % (os.path.splitext(df_csv)[0], svtype)
... | python | def _plot_evaluation_event(df_csv, svtype):
"""Provide plot of evaluation metrics for an SV event, stratified by event size.
"""
titles = {"INV": "Inversions", "DEL": "Deletions", "DUP": "Duplications",
"INS": "Insertions"}
out_file = "%s-%s.png" % (os.path.splitext(df_csv)[0], svtype)
... | [
"def",
"_plot_evaluation_event",
"(",
"df_csv",
",",
"svtype",
")",
":",
"titles",
"=",
"{",
"\"INV\"",
":",
"\"Inversions\"",
",",
"\"DEL\"",
":",
"\"Deletions\"",
",",
"\"DUP\"",
":",
"\"Duplications\"",
",",
"\"INS\"",
":",
"\"Insertions\"",
"}",
"out_file",
... | Provide plot of evaluation metrics for an SV event, stratified by event size. | [
"Provide",
"plot",
"of",
"evaluation",
"metrics",
"for",
"an",
"SV",
"event",
"stratified",
"by",
"event",
"size",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L300-L348 |
223,217 | bcbio/bcbio-nextgen | bcbio/structural/validate.py | evaluate | def evaluate(data):
"""Provide evaluations for multiple callers split by structural variant type.
"""
work_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "structural",
dd.get_sample_name(data), "validate"))
truth_sets = tz.get_in(["config", "al... | python | def evaluate(data):
"""Provide evaluations for multiple callers split by structural variant type.
"""
work_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "structural",
dd.get_sample_name(data), "validate"))
truth_sets = tz.get_in(["config", "al... | [
"def",
"evaluate",
"(",
"data",
")",
":",
"work_dir",
"=",
"utils",
".",
"safe_makedir",
"(",
"os",
".",
"path",
".",
"join",
"(",
"data",
"[",
"\"dirs\"",
"]",
"[",
"\"work\"",
"]",
",",
"\"structural\"",
",",
"dd",
".",
"get_sample_name",
"(",
"data"... | Provide evaluations for multiple callers split by structural variant type. | [
"Provide",
"evaluations",
"for",
"multiple",
"callers",
"split",
"by",
"structural",
"variant",
"type",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/validate.py#L375-L392 |
223,218 | bcbio/bcbio-nextgen | bcbio/variation/mutect2.py | _add_region_params | def _add_region_params(region, out_file, items, gatk_type):
"""Add parameters for selecting by region to command line.
"""
params = []
variant_regions = bedutils.population_variant_regions(items)
region = subset_variant_regions(variant_regions, region, out_file, items)
if region:
if gatk... | python | def _add_region_params(region, out_file, items, gatk_type):
"""Add parameters for selecting by region to command line.
"""
params = []
variant_regions = bedutils.population_variant_regions(items)
region = subset_variant_regions(variant_regions, region, out_file, items)
if region:
if gatk... | [
"def",
"_add_region_params",
"(",
"region",
",",
"out_file",
",",
"items",
",",
"gatk_type",
")",
":",
"params",
"=",
"[",
"]",
"variant_regions",
"=",
"bedutils",
".",
"population_variant_regions",
"(",
"items",
")",
"region",
"=",
"subset_variant_regions",
"("... | Add parameters for selecting by region to command line. | [
"Add",
"parameters",
"for",
"selecting",
"by",
"region",
"to",
"command",
"line",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/variation/mutect2.py#L48-L60 |
223,219 | bcbio/bcbio-nextgen | bcbio/variation/mutect2.py | _prep_inputs | def _prep_inputs(align_bams, ref_file, items):
"""Ensure inputs to calling are indexed as expected.
"""
broad_runner = broad.runner_from_path("picard", items[0]["config"])
broad_runner.run_fn("picard_index_ref", ref_file)
for x in align_bams:
bam.index(x, items[0]["config"]) | python | def _prep_inputs(align_bams, ref_file, items):
"""Ensure inputs to calling are indexed as expected.
"""
broad_runner = broad.runner_from_path("picard", items[0]["config"])
broad_runner.run_fn("picard_index_ref", ref_file)
for x in align_bams:
bam.index(x, items[0]["config"]) | [
"def",
"_prep_inputs",
"(",
"align_bams",
",",
"ref_file",
",",
"items",
")",
":",
"broad_runner",
"=",
"broad",
".",
"runner_from_path",
"(",
"\"picard\"",
",",
"items",
"[",
"0",
"]",
"[",
"\"config\"",
"]",
")",
"broad_runner",
".",
"run_fn",
"(",
"\"pi... | Ensure inputs to calling are indexed as expected. | [
"Ensure",
"inputs",
"to",
"calling",
"are",
"indexed",
"as",
"expected",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/variation/mutect2.py#L70-L76 |
223,220 | bcbio/bcbio-nextgen | bcbio/variation/mutect2.py | mutect2_caller | def mutect2_caller(align_bams, items, ref_file, assoc_files,
region=None, out_file=None):
"""Call variation with GATK's MuTect2.
This requires the full non open-source version of GATK 3.5+.
"""
if out_file is None:
out_file = "%s-variants.vcf.gz" % utils.splitext_plus(ali... | python | def mutect2_caller(align_bams, items, ref_file, assoc_files,
region=None, out_file=None):
"""Call variation with GATK's MuTect2.
This requires the full non open-source version of GATK 3.5+.
"""
if out_file is None:
out_file = "%s-variants.vcf.gz" % utils.splitext_plus(ali... | [
"def",
"mutect2_caller",
"(",
"align_bams",
",",
"items",
",",
"ref_file",
",",
"assoc_files",
",",
"region",
"=",
"None",
",",
"out_file",
"=",
"None",
")",
":",
"if",
"out_file",
"is",
"None",
":",
"out_file",
"=",
"\"%s-variants.vcf.gz\"",
"%",
"utils",
... | Call variation with GATK's MuTect2.
This requires the full non open-source version of GATK 3.5+. | [
"Call",
"variation",
"with",
"GATK",
"s",
"MuTect2",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/variation/mutect2.py#L78-L126 |
223,221 | bcbio/bcbio-nextgen | bcbio/variation/mutect2.py | _mutect2_filter | def _mutect2_filter(broad_runner, in_file, out_file, ref_file):
"""Filter of MuTect2 calls, a separate step in GATK4.
"""
params = ["-T", "FilterMutectCalls", "--reference", ref_file, "--variant", in_file, "--output", out_file]
return broad_runner.cl_gatk(params, os.path.dirname(out_file)) | python | def _mutect2_filter(broad_runner, in_file, out_file, ref_file):
"""Filter of MuTect2 calls, a separate step in GATK4.
"""
params = ["-T", "FilterMutectCalls", "--reference", ref_file, "--variant", in_file, "--output", out_file]
return broad_runner.cl_gatk(params, os.path.dirname(out_file)) | [
"def",
"_mutect2_filter",
"(",
"broad_runner",
",",
"in_file",
",",
"out_file",
",",
"ref_file",
")",
":",
"params",
"=",
"[",
"\"-T\"",
",",
"\"FilterMutectCalls\"",
",",
"\"--reference\"",
",",
"ref_file",
",",
"\"--variant\"",
",",
"in_file",
",",
"\"--output... | Filter of MuTect2 calls, a separate step in GATK4. | [
"Filter",
"of",
"MuTect2",
"calls",
"a",
"separate",
"step",
"in",
"GATK4",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/variation/mutect2.py#L128-L132 |
223,222 | bcbio/bcbio-nextgen | bcbio/upload/irods.py | update_file | def update_file(finfo, sample_info, config):
"""
Update the file to an iRODS repository.
"""
ffinal = filesystem.update_file(finfo, sample_info, config, pass_uptodate=True)
_upload_dir_icommands_cli(config.get("dir"), config.get("folder"), config) | python | def update_file(finfo, sample_info, config):
"""
Update the file to an iRODS repository.
"""
ffinal = filesystem.update_file(finfo, sample_info, config, pass_uptodate=True)
_upload_dir_icommands_cli(config.get("dir"), config.get("folder"), config) | [
"def",
"update_file",
"(",
"finfo",
",",
"sample_info",
",",
"config",
")",
":",
"ffinal",
"=",
"filesystem",
".",
"update_file",
"(",
"finfo",
",",
"sample_info",
",",
"config",
",",
"pass_uptodate",
"=",
"True",
")",
"_upload_dir_icommands_cli",
"(",
"config... | Update the file to an iRODS repository. | [
"Update",
"the",
"file",
"to",
"an",
"iRODS",
"repository",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/upload/irods.py#L25-L31 |
223,223 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | _get_callers | def _get_callers(items, stage, special_cases=False):
"""Retrieve available callers for the provided stage.
Handles special cases like CNVkit that can be in initial or standard
depending on if fed into Lumpy analysis.
"""
callers = utils.deepish_copy(_CALLERS[stage])
if special_cases and "cnvkit... | python | def _get_callers(items, stage, special_cases=False):
"""Retrieve available callers for the provided stage.
Handles special cases like CNVkit that can be in initial or standard
depending on if fed into Lumpy analysis.
"""
callers = utils.deepish_copy(_CALLERS[stage])
if special_cases and "cnvkit... | [
"def",
"_get_callers",
"(",
"items",
",",
"stage",
",",
"special_cases",
"=",
"False",
")",
":",
"callers",
"=",
"utils",
".",
"deepish_copy",
"(",
"_CALLERS",
"[",
"stage",
"]",
")",
"if",
"special_cases",
"and",
"\"cnvkit\"",
"in",
"callers",
":",
"has_l... | Retrieve available callers for the provided stage.
Handles special cases like CNVkit that can be in initial or standard
depending on if fed into Lumpy analysis. | [
"Retrieve",
"available",
"callers",
"for",
"the",
"provided",
"stage",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L38-L54 |
223,224 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | _handle_multiple_svcallers | def _handle_multiple_svcallers(data, stage):
"""Retrieve configured structural variation caller, handling multiple.
"""
svs = get_svcallers(data)
# special cases -- prioritization
if stage == "ensemble" and dd.get_svprioritize(data):
svs.append("prioritize")
out = []
for svcaller in ... | python | def _handle_multiple_svcallers(data, stage):
"""Retrieve configured structural variation caller, handling multiple.
"""
svs = get_svcallers(data)
# special cases -- prioritization
if stage == "ensemble" and dd.get_svprioritize(data):
svs.append("prioritize")
out = []
for svcaller in ... | [
"def",
"_handle_multiple_svcallers",
"(",
"data",
",",
"stage",
")",
":",
"svs",
"=",
"get_svcallers",
"(",
"data",
")",
"# special cases -- prioritization",
"if",
"stage",
"==",
"\"ensemble\"",
"and",
"dd",
".",
"get_svprioritize",
"(",
"data",
")",
":",
"svs",... | Retrieve configured structural variation caller, handling multiple. | [
"Retrieve",
"configured",
"structural",
"variation",
"caller",
"handling",
"multiple",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L64-L85 |
223,225 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | finalize_sv | def finalize_sv(samples, config):
"""Combine results from multiple sv callers into a single ordered 'sv' key.
"""
by_bam = collections.OrderedDict()
for x in samples:
batch = dd.get_batch(x) or [dd.get_sample_name(x)]
try:
by_bam[x["align_bam"], tuple(batch)].append(x)
... | python | def finalize_sv(samples, config):
"""Combine results from multiple sv callers into a single ordered 'sv' key.
"""
by_bam = collections.OrderedDict()
for x in samples:
batch = dd.get_batch(x) or [dd.get_sample_name(x)]
try:
by_bam[x["align_bam"], tuple(batch)].append(x)
... | [
"def",
"finalize_sv",
"(",
"samples",
",",
"config",
")",
":",
"by_bam",
"=",
"collections",
".",
"OrderedDict",
"(",
")",
"for",
"x",
"in",
"samples",
":",
"batch",
"=",
"dd",
".",
"get_batch",
"(",
"x",
")",
"or",
"[",
"dd",
".",
"get_sample_name",
... | Combine results from multiple sv callers into a single ordered 'sv' key. | [
"Combine",
"results",
"from",
"multiple",
"sv",
"callers",
"into",
"a",
"single",
"ordered",
"sv",
"key",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L87-L126 |
223,226 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | batch_for_sv | def batch_for_sv(samples):
"""Prepare a set of samples for parallel structural variant calling.
CWL input target -- groups samples into batches and structural variant
callers for parallel processing.
"""
samples = cwlutils.assign_complex_to_samples(samples)
to_process, extras, background = _bat... | python | def batch_for_sv(samples):
"""Prepare a set of samples for parallel structural variant calling.
CWL input target -- groups samples into batches and structural variant
callers for parallel processing.
"""
samples = cwlutils.assign_complex_to_samples(samples)
to_process, extras, background = _bat... | [
"def",
"batch_for_sv",
"(",
"samples",
")",
":",
"samples",
"=",
"cwlutils",
".",
"assign_complex_to_samples",
"(",
"samples",
")",
"to_process",
",",
"extras",
",",
"background",
"=",
"_batch_split_by_sv",
"(",
"samples",
",",
"\"standard\"",
")",
"out",
"=",
... | Prepare a set of samples for parallel structural variant calling.
CWL input target -- groups samples into batches and structural variant
callers for parallel processing. | [
"Prepare",
"a",
"set",
"of",
"samples",
"for",
"parallel",
"structural",
"variant",
"calling",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L133-L142 |
223,227 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | run | def run(samples, run_parallel, stage):
"""Run structural variation detection.
The stage indicates which level of structural variant calling to run.
- initial, callers that can be used in subsequent structural variation steps (cnvkit -> lumpy)
- standard, regular batch calling
- ensemble, post... | python | def run(samples, run_parallel, stage):
"""Run structural variation detection.
The stage indicates which level of structural variant calling to run.
- initial, callers that can be used in subsequent structural variation steps (cnvkit -> lumpy)
- standard, regular batch calling
- ensemble, post... | [
"def",
"run",
"(",
"samples",
",",
"run_parallel",
",",
"stage",
")",
":",
"to_process",
",",
"extras",
",",
"background",
"=",
"_batch_split_by_sv",
"(",
"samples",
",",
"stage",
")",
"processed",
"=",
"run_parallel",
"(",
"\"detect_sv\"",
",",
"(",
"[",
... | Run structural variation detection.
The stage indicates which level of structural variant calling to run.
- initial, callers that can be used in subsequent structural variation steps (cnvkit -> lumpy)
- standard, regular batch calling
- ensemble, post-calling, combine other callers or prioritize ... | [
"Run",
"structural",
"variation",
"detection",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L174-L187 |
223,228 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | detect_sv | def detect_sv(items, all_items=None, stage="standard"):
"""Top level parallel target for examining structural variation.
"""
items = [utils.to_single_data(x) for x in items]
items = cwlutils.unpack_tarballs(items, items[0])
svcaller = items[0]["config"]["algorithm"].get("svcaller")
caller_fn = _... | python | def detect_sv(items, all_items=None, stage="standard"):
"""Top level parallel target for examining structural variation.
"""
items = [utils.to_single_data(x) for x in items]
items = cwlutils.unpack_tarballs(items, items[0])
svcaller = items[0]["config"]["algorithm"].get("svcaller")
caller_fn = _... | [
"def",
"detect_sv",
"(",
"items",
",",
"all_items",
"=",
"None",
",",
"stage",
"=",
"\"standard\"",
")",
":",
"items",
"=",
"[",
"utils",
".",
"to_single_data",
"(",
"x",
")",
"for",
"x",
"in",
"items",
"]",
"items",
"=",
"cwlutils",
".",
"unpack_tarba... | Top level parallel target for examining structural variation. | [
"Top",
"level",
"parallel",
"target",
"for",
"examining",
"structural",
"variation",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L189-L226 |
223,229 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | _add_supplemental | def _add_supplemental(data):
"""Add additional supplemental files to CWL sv output, give useful names.
"""
if "supplemental" not in data["sv"]:
data["sv"]["supplemental"] = []
if data["sv"].get("variantcaller"):
cur_name = _useful_basename(data)
for k in ["cns", "vrn_bed"]:
... | python | def _add_supplemental(data):
"""Add additional supplemental files to CWL sv output, give useful names.
"""
if "supplemental" not in data["sv"]:
data["sv"]["supplemental"] = []
if data["sv"].get("variantcaller"):
cur_name = _useful_basename(data)
for k in ["cns", "vrn_bed"]:
... | [
"def",
"_add_supplemental",
"(",
"data",
")",
":",
"if",
"\"supplemental\"",
"not",
"in",
"data",
"[",
"\"sv\"",
"]",
":",
"data",
"[",
"\"sv\"",
"]",
"[",
"\"supplemental\"",
"]",
"=",
"[",
"]",
"if",
"data",
"[",
"\"sv\"",
"]",
".",
"get",
"(",
"\"... | Add additional supplemental files to CWL sv output, give useful names. | [
"Add",
"additional",
"supplemental",
"files",
"to",
"CWL",
"sv",
"output",
"give",
"useful",
"names",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L228-L247 |
223,230 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | _clean_name | def _clean_name(fname, data):
"""Remove standard prefixes from a filename before renaming with useful names.
"""
for to_remove in dd.get_batches(data) + [dd.get_sample_name(data), data["sv"]["variantcaller"]]:
for ext in ("-", "_"):
if fname.startswith("%s%s" % (to_remove, ext)):
... | python | def _clean_name(fname, data):
"""Remove standard prefixes from a filename before renaming with useful names.
"""
for to_remove in dd.get_batches(data) + [dd.get_sample_name(data), data["sv"]["variantcaller"]]:
for ext in ("-", "_"):
if fname.startswith("%s%s" % (to_remove, ext)):
... | [
"def",
"_clean_name",
"(",
"fname",
",",
"data",
")",
":",
"for",
"to_remove",
"in",
"dd",
".",
"get_batches",
"(",
"data",
")",
"+",
"[",
"dd",
".",
"get_sample_name",
"(",
"data",
")",
",",
"data",
"[",
"\"sv\"",
"]",
"[",
"\"variantcaller\"",
"]",
... | Remove standard prefixes from a filename before renaming with useful names. | [
"Remove",
"standard",
"prefixes",
"from",
"a",
"filename",
"before",
"renaming",
"with",
"useful",
"names",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L249-L258 |
223,231 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | _group_by_sample | def _group_by_sample(items):
"""Group a set of items by sample names + multiple callers for prioritization
"""
by_sample = collections.defaultdict(list)
for d in items:
by_sample[dd.get_sample_name(d)].append(d)
out = []
for sample_group in by_sample.values():
cur = utils.deepish... | python | def _group_by_sample(items):
"""Group a set of items by sample names + multiple callers for prioritization
"""
by_sample = collections.defaultdict(list)
for d in items:
by_sample[dd.get_sample_name(d)].append(d)
out = []
for sample_group in by_sample.values():
cur = utils.deepish... | [
"def",
"_group_by_sample",
"(",
"items",
")",
":",
"by_sample",
"=",
"collections",
".",
"defaultdict",
"(",
"list",
")",
"for",
"d",
"in",
"items",
":",
"by_sample",
"[",
"dd",
".",
"get_sample_name",
"(",
"d",
")",
"]",
".",
"append",
"(",
"d",
")",
... | Group a set of items by sample names + multiple callers for prioritization | [
"Group",
"a",
"set",
"of",
"items",
"by",
"sample",
"names",
"+",
"multiple",
"callers",
"for",
"prioritization"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L269-L283 |
223,232 | bcbio/bcbio-nextgen | bcbio/structural/__init__.py | standardize_cnv_reference | def standardize_cnv_reference(data):
"""Standardize cnv_reference background to support multiple callers.
"""
out = tz.get_in(["config", "algorithm", "background", "cnv_reference"], data, {})
cur_callers = set(data["config"]["algorithm"].get("svcaller")) & _CNV_REFERENCE
if isinstance(out, six.strin... | python | def standardize_cnv_reference(data):
"""Standardize cnv_reference background to support multiple callers.
"""
out = tz.get_in(["config", "algorithm", "background", "cnv_reference"], data, {})
cur_callers = set(data["config"]["algorithm"].get("svcaller")) & _CNV_REFERENCE
if isinstance(out, six.strin... | [
"def",
"standardize_cnv_reference",
"(",
"data",
")",
":",
"out",
"=",
"tz",
".",
"get_in",
"(",
"[",
"\"config\"",
",",
"\"algorithm\"",
",",
"\"background\"",
",",
"\"cnv_reference\"",
"]",
",",
"data",
",",
"{",
"}",
")",
"cur_callers",
"=",
"set",
"(",... | Standardize cnv_reference background to support multiple callers. | [
"Standardize",
"cnv_reference",
"background",
"to",
"support",
"multiple",
"callers",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/__init__.py#L324-L335 |
223,233 | bcbio/bcbio-nextgen | bcbio/ngsalign/bowtie2.py | _bowtie2_args_from_config | def _bowtie2_args_from_config(config, curcl):
"""Configurable high level options for bowtie2.
"""
qual_format = config["algorithm"].get("quality_format", "")
if qual_format.lower() == "illumina":
qual_flags = ["--phred64-quals"]
else:
qual_flags = []
num_cores = config["algorithm... | python | def _bowtie2_args_from_config(config, curcl):
"""Configurable high level options for bowtie2.
"""
qual_format = config["algorithm"].get("quality_format", "")
if qual_format.lower() == "illumina":
qual_flags = ["--phred64-quals"]
else:
qual_flags = []
num_cores = config["algorithm... | [
"def",
"_bowtie2_args_from_config",
"(",
"config",
",",
"curcl",
")",
":",
"qual_format",
"=",
"config",
"[",
"\"algorithm\"",
"]",
".",
"get",
"(",
"\"quality_format\"",
",",
"\"\"",
")",
"if",
"qual_format",
".",
"lower",
"(",
")",
"==",
"\"illumina\"",
":... | Configurable high level options for bowtie2. | [
"Configurable",
"high",
"level",
"options",
"for",
"bowtie2",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/ngsalign/bowtie2.py#L15-L30 |
223,234 | bcbio/bcbio-nextgen | bcbio/ngsalign/bowtie2.py | align | def align(fastq_file, pair_file, ref_file, names, align_dir, data,
extra_args=None):
"""Alignment with bowtie2.
"""
config = data["config"]
analysis_config = ANALYSIS.get(data["analysis"].lower())
assert analysis_config, "Analysis %s is not supported by bowtie2" % (data["analysis"])
ou... | python | def align(fastq_file, pair_file, ref_file, names, align_dir, data,
extra_args=None):
"""Alignment with bowtie2.
"""
config = data["config"]
analysis_config = ANALYSIS.get(data["analysis"].lower())
assert analysis_config, "Analysis %s is not supported by bowtie2" % (data["analysis"])
ou... | [
"def",
"align",
"(",
"fastq_file",
",",
"pair_file",
",",
"ref_file",
",",
"names",
",",
"align_dir",
",",
"data",
",",
"extra_args",
"=",
"None",
")",
":",
"config",
"=",
"data",
"[",
"\"config\"",
"]",
"analysis_config",
"=",
"ANALYSIS",
".",
"get",
"(... | Alignment with bowtie2. | [
"Alignment",
"with",
"bowtie2",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/ngsalign/bowtie2.py#L32-L66 |
223,235 | bcbio/bcbio-nextgen | bcbio/cwl/hpc.py | create_cromwell_config | def create_cromwell_config(args, work_dir, sample_file):
"""Prepare a cromwell configuration within the current working directory.
"""
docker_attrs = ["String? docker", "String? docker_user"]
cwl_attrs = ["Int? cpuMin", "Int? cpuMax", "Int? memoryMin", "Int? memoryMax", "String? outDirMin",
... | python | def create_cromwell_config(args, work_dir, sample_file):
"""Prepare a cromwell configuration within the current working directory.
"""
docker_attrs = ["String? docker", "String? docker_user"]
cwl_attrs = ["Int? cpuMin", "Int? cpuMax", "Int? memoryMin", "Int? memoryMax", "String? outDirMin",
... | [
"def",
"create_cromwell_config",
"(",
"args",
",",
"work_dir",
",",
"sample_file",
")",
":",
"docker_attrs",
"=",
"[",
"\"String? docker\"",
",",
"\"String? docker_user\"",
"]",
"cwl_attrs",
"=",
"[",
"\"Int? cpuMin\"",
",",
"\"Int? cpuMax\"",
",",
"\"Int? memoryMin\"... | Prepare a cromwell configuration within the current working directory. | [
"Prepare",
"a",
"cromwell",
"configuration",
"within",
"the",
"current",
"working",
"directory",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/cwl/hpc.py#L8-L40 |
223,236 | bcbio/bcbio-nextgen | bcbio/cwl/hpc.py | _get_file_paths | def _get_file_paths(cur):
"""Retrieve a list of file paths, recursively traversing the
"""
out = []
if isinstance(cur, (list, tuple)):
for x in cur:
new = _get_file_paths(x)
if new:
out.extend(new)
elif isinstance(cur, dict):
if "class" in cur:... | python | def _get_file_paths(cur):
"""Retrieve a list of file paths, recursively traversing the
"""
out = []
if isinstance(cur, (list, tuple)):
for x in cur:
new = _get_file_paths(x)
if new:
out.extend(new)
elif isinstance(cur, dict):
if "class" in cur:... | [
"def",
"_get_file_paths",
"(",
"cur",
")",
":",
"out",
"=",
"[",
"]",
"if",
"isinstance",
"(",
"cur",
",",
"(",
"list",
",",
"tuple",
")",
")",
":",
"for",
"x",
"in",
"cur",
":",
"new",
"=",
"_get_file_paths",
"(",
"x",
")",
"if",
"new",
":",
"... | Retrieve a list of file paths, recursively traversing the | [
"Retrieve",
"a",
"list",
"of",
"file",
"paths",
"recursively",
"traversing",
"the"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/cwl/hpc.py#L42-L59 |
223,237 | bcbio/bcbio-nextgen | bcbio/cwl/hpc.py | _load_custom_config | def _load_custom_config(run_config):
"""Load custom configuration input HOCON file for cromwell.
"""
from pyhocon import ConfigFactory, HOCONConverter, ConfigTree
conf = ConfigFactory.parse_file(run_config)
out = {}
if "database" in conf:
out["database"] = HOCONConverter.to_hocon(ConfigT... | python | def _load_custom_config(run_config):
"""Load custom configuration input HOCON file for cromwell.
"""
from pyhocon import ConfigFactory, HOCONConverter, ConfigTree
conf = ConfigFactory.parse_file(run_config)
out = {}
if "database" in conf:
out["database"] = HOCONConverter.to_hocon(ConfigT... | [
"def",
"_load_custom_config",
"(",
"run_config",
")",
":",
"from",
"pyhocon",
"import",
"ConfigFactory",
",",
"HOCONConverter",
",",
"ConfigTree",
"conf",
"=",
"ConfigFactory",
".",
"parse_file",
"(",
"run_config",
")",
"out",
"=",
"{",
"}",
"if",
"\"database\""... | Load custom configuration input HOCON file for cromwell. | [
"Load",
"custom",
"configuration",
"input",
"HOCON",
"file",
"for",
"cromwell",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/cwl/hpc.py#L61-L69 |
223,238 | bcbio/bcbio-nextgen | bcbio/cwl/hpc.py | _args_to_cromwell | def _args_to_cromwell(args):
"""Convert input arguments into cromwell inputs for config and command line.
"""
default_config = {"slurm": {"timelimit": "1-00:00", "account": ""},
"sge": {"memtype": "mem_free", "pename": "smp"},
"lsf": {"walltime": "24:00", "account... | python | def _args_to_cromwell(args):
"""Convert input arguments into cromwell inputs for config and command line.
"""
default_config = {"slurm": {"timelimit": "1-00:00", "account": ""},
"sge": {"memtype": "mem_free", "pename": "smp"},
"lsf": {"walltime": "24:00", "account... | [
"def",
"_args_to_cromwell",
"(",
"args",
")",
":",
"default_config",
"=",
"{",
"\"slurm\"",
":",
"{",
"\"timelimit\"",
":",
"\"1-00:00\"",
",",
"\"account\"",
":",
"\"\"",
"}",
",",
"\"sge\"",
":",
"{",
"\"memtype\"",
":",
"\"mem_free\"",
",",
"\"pename\"",
... | Convert input arguments into cromwell inputs for config and command line. | [
"Convert",
"input",
"arguments",
"into",
"cromwell",
"inputs",
"for",
"config",
"and",
"command",
"line",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/cwl/hpc.py#L77-L128 |
223,239 | bcbio/bcbio-nextgen | bcbio/cwl/hpc.py | _get_filesystem_types | def _get_filesystem_types(args, sample_file):
"""Retrieve the types of inputs and staging based on sample JSON and arguments.
"""
out = set([])
ext = "" if args.no_container else "_container"
with open(sample_file) as in_handle:
for f in _get_file_paths(json.load(in_handle)):
if ... | python | def _get_filesystem_types(args, sample_file):
"""Retrieve the types of inputs and staging based on sample JSON and arguments.
"""
out = set([])
ext = "" if args.no_container else "_container"
with open(sample_file) as in_handle:
for f in _get_file_paths(json.load(in_handle)):
if ... | [
"def",
"_get_filesystem_types",
"(",
"args",
",",
"sample_file",
")",
":",
"out",
"=",
"set",
"(",
"[",
"]",
")",
"ext",
"=",
"\"\"",
"if",
"args",
".",
"no_container",
"else",
"\"_container\"",
"with",
"open",
"(",
"sample_file",
")",
"as",
"in_handle",
... | Retrieve the types of inputs and staging based on sample JSON and arguments. | [
"Retrieve",
"the",
"types",
"of",
"inputs",
"and",
"staging",
"based",
"on",
"sample",
"JSON",
"and",
"arguments",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/cwl/hpc.py#L130-L145 |
223,240 | bcbio/bcbio-nextgen | bcbio/cwl/hpc.py | _get_filesystem_config | def _get_filesystem_config(file_types):
"""Retrieve filesystem configuration, including support for specified file types.
"""
out = " filesystems {\n"
for file_type in sorted(list(file_types)):
if file_type in _FILESYSTEM_CONFIG:
out += _FILESYSTEM_CONFIG[file_type]
out += " ... | python | def _get_filesystem_config(file_types):
"""Retrieve filesystem configuration, including support for specified file types.
"""
out = " filesystems {\n"
for file_type in sorted(list(file_types)):
if file_type in _FILESYSTEM_CONFIG:
out += _FILESYSTEM_CONFIG[file_type]
out += " ... | [
"def",
"_get_filesystem_config",
"(",
"file_types",
")",
":",
"out",
"=",
"\" filesystems {\\n\"",
"for",
"file_type",
"in",
"sorted",
"(",
"list",
"(",
"file_types",
")",
")",
":",
"if",
"file_type",
"in",
"_FILESYSTEM_CONFIG",
":",
"out",
"+=",
"_FILESYSTE... | Retrieve filesystem configuration, including support for specified file types. | [
"Retrieve",
"filesystem",
"configuration",
"including",
"support",
"for",
"specified",
"file",
"types",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/cwl/hpc.py#L147-L155 |
223,241 | bcbio/bcbio-nextgen | bcbio/cwl/hpc.py | _get_engine_filesystem_config | def _get_engine_filesystem_config(file_types, args, conf_args):
"""Retriever authorization and engine filesystem configuration.
"""
file_types = [x.replace("_container", "") for x in list(file_types)]
out = ""
if "gcp" in file_types:
out += _AUTH_CONFIG_GOOGLE
if "s3" in file_types:
... | python | def _get_engine_filesystem_config(file_types, args, conf_args):
"""Retriever authorization and engine filesystem configuration.
"""
file_types = [x.replace("_container", "") for x in list(file_types)]
out = ""
if "gcp" in file_types:
out += _AUTH_CONFIG_GOOGLE
if "s3" in file_types:
... | [
"def",
"_get_engine_filesystem_config",
"(",
"file_types",
",",
"args",
",",
"conf_args",
")",
":",
"file_types",
"=",
"[",
"x",
".",
"replace",
"(",
"\"_container\"",
",",
"\"\"",
")",
"for",
"x",
"in",
"list",
"(",
"file_types",
")",
"]",
"out",
"=",
"... | Retriever authorization and engine filesystem configuration. | [
"Retriever",
"authorization",
"and",
"engine",
"filesystem",
"configuration",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/cwl/hpc.py#L212-L237 |
223,242 | bcbio/bcbio-nextgen | bcbio/variation/normalize.py | normalize | def normalize(in_file, data, passonly=False, normalize_indels=True, split_biallelic=True,
rerun_effects=True, remove_oldeffects=False, nonrefonly=False, work_dir=None):
"""Normalizes variants and reruns SnpEFF for resulting VCF
"""
if remove_oldeffects:
out_file = "%s-noeff-nomultialle... | python | def normalize(in_file, data, passonly=False, normalize_indels=True, split_biallelic=True,
rerun_effects=True, remove_oldeffects=False, nonrefonly=False, work_dir=None):
"""Normalizes variants and reruns SnpEFF for resulting VCF
"""
if remove_oldeffects:
out_file = "%s-noeff-nomultialle... | [
"def",
"normalize",
"(",
"in_file",
",",
"data",
",",
"passonly",
"=",
"False",
",",
"normalize_indels",
"=",
"True",
",",
"split_biallelic",
"=",
"True",
",",
"rerun_effects",
"=",
"True",
",",
"remove_oldeffects",
"=",
"False",
",",
"nonrefonly",
"=",
"Fal... | Normalizes variants and reruns SnpEFF for resulting VCF | [
"Normalizes",
"variants",
"and",
"reruns",
"SnpEFF",
"for",
"resulting",
"VCF"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/variation/normalize.py#L59-L84 |
223,243 | bcbio/bcbio-nextgen | bcbio/variation/normalize.py | _normalize | def _normalize(in_file, data, passonly=False, normalize_indels=True, split_biallelic=True,
remove_oldeffects=False, nonrefonly=False, work_dir=None):
"""Convert multi-allelic variants into single allelic.
`vt normalize` has the -n flag passed (skipping reference checks) because
of errors whe... | python | def _normalize(in_file, data, passonly=False, normalize_indels=True, split_biallelic=True,
remove_oldeffects=False, nonrefonly=False, work_dir=None):
"""Convert multi-allelic variants into single allelic.
`vt normalize` has the -n flag passed (skipping reference checks) because
of errors whe... | [
"def",
"_normalize",
"(",
"in_file",
",",
"data",
",",
"passonly",
"=",
"False",
",",
"normalize_indels",
"=",
"True",
",",
"split_biallelic",
"=",
"True",
",",
"remove_oldeffects",
"=",
"False",
",",
"nonrefonly",
"=",
"False",
",",
"work_dir",
"=",
"None",... | Convert multi-allelic variants into single allelic.
`vt normalize` has the -n flag passed (skipping reference checks) because
of errors where the reference genome has non GATCN ambiguous bases. These
are not supported in VCF, so you'll have a mismatch of N in VCF versus R
(or other ambiguous bases) in ... | [
"Convert",
"multi",
"-",
"allelic",
"variants",
"into",
"single",
"allelic",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/variation/normalize.py#L86-L130 |
223,244 | bcbio/bcbio-nextgen | bcbio/rnaseq/sailfish.py | sleuthify_sailfish | def sleuthify_sailfish(sailfish_dir):
"""
if installed, use wasabi to create abundance.h5 output for use with
sleuth
"""
if not R_package_path("wasabi"):
return None
else:
rscript = Rscript_cmd()
cmd = """{rscript} --no-environ -e 'library("wasabi"); prepare_fish_for_sleu... | python | def sleuthify_sailfish(sailfish_dir):
"""
if installed, use wasabi to create abundance.h5 output for use with
sleuth
"""
if not R_package_path("wasabi"):
return None
else:
rscript = Rscript_cmd()
cmd = """{rscript} --no-environ -e 'library("wasabi"); prepare_fish_for_sleu... | [
"def",
"sleuthify_sailfish",
"(",
"sailfish_dir",
")",
":",
"if",
"not",
"R_package_path",
"(",
"\"wasabi\"",
")",
":",
"return",
"None",
"else",
":",
"rscript",
"=",
"Rscript_cmd",
"(",
")",
"cmd",
"=",
"\"\"\"{rscript} --no-environ -e 'library(\"wasabi\"); prepare_f... | if installed, use wasabi to create abundance.h5 output for use with
sleuth | [
"if",
"installed",
"use",
"wasabi",
"to",
"create",
"abundance",
".",
"h5",
"output",
"for",
"use",
"with",
"sleuth"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/rnaseq/sailfish.py#L66-L77 |
223,245 | bcbio/bcbio-nextgen | bcbio/rnaseq/sailfish.py | create_combined_fasta | def create_combined_fasta(data):
"""
if there are genomes to be disambiguated, create a FASTA file of
all of the transcripts for all genomes
"""
out_dir = os.path.join(dd.get_work_dir(data), "inputs", "transcriptome")
items = disambiguate.split([data])
fasta_files = []
for i in items:
... | python | def create_combined_fasta(data):
"""
if there are genomes to be disambiguated, create a FASTA file of
all of the transcripts for all genomes
"""
out_dir = os.path.join(dd.get_work_dir(data), "inputs", "transcriptome")
items = disambiguate.split([data])
fasta_files = []
for i in items:
... | [
"def",
"create_combined_fasta",
"(",
"data",
")",
":",
"out_dir",
"=",
"os",
".",
"path",
".",
"join",
"(",
"dd",
".",
"get_work_dir",
"(",
"data",
")",
",",
"\"inputs\"",
",",
"\"transcriptome\"",
")",
"items",
"=",
"disambiguate",
".",
"split",
"(",
"[... | if there are genomes to be disambiguated, create a FASTA file of
all of the transcripts for all genomes | [
"if",
"there",
"are",
"genomes",
"to",
"be",
"disambiguated",
"create",
"a",
"FASTA",
"file",
"of",
"all",
"of",
"the",
"transcripts",
"for",
"all",
"genomes"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/rnaseq/sailfish.py#L79-L108 |
223,246 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | prep_samples_and_config | def prep_samples_and_config(run_folder, ldetails, fastq_dir, config):
"""Prepare sample fastq files and provide global sample configuration for the flowcell.
Handles merging of fastq files split by lane and also by the bcl2fastq
preparation process.
"""
fastq_final_dir = utils.safe_makedir(os.path.... | python | def prep_samples_and_config(run_folder, ldetails, fastq_dir, config):
"""Prepare sample fastq files and provide global sample configuration for the flowcell.
Handles merging of fastq files split by lane and also by the bcl2fastq
preparation process.
"""
fastq_final_dir = utils.safe_makedir(os.path.... | [
"def",
"prep_samples_and_config",
"(",
"run_folder",
",",
"ldetails",
",",
"fastq_dir",
",",
"config",
")",
":",
"fastq_final_dir",
"=",
"utils",
".",
"safe_makedir",
"(",
"os",
".",
"path",
".",
"join",
"(",
"fastq_dir",
",",
"\"merged\"",
")",
")",
"cores"... | Prepare sample fastq files and provide global sample configuration for the flowcell.
Handles merging of fastq files split by lane and also by the bcl2fastq
preparation process. | [
"Prepare",
"sample",
"fastq",
"files",
"and",
"provide",
"global",
"sample",
"configuration",
"for",
"the",
"flowcell",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L23-L34 |
223,247 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | _prep_sample_and_config | def _prep_sample_and_config(ldetail_group, fastq_dir, fastq_final_dir):
"""Prepare output fastq file and configuration for a single sample.
Only passes non-empty files through for processing.
"""
files = []
print("->", ldetail_group[0]["name"], len(ldetail_group))
for read in ["R1", "R2"]:
... | python | def _prep_sample_and_config(ldetail_group, fastq_dir, fastq_final_dir):
"""Prepare output fastq file and configuration for a single sample.
Only passes non-empty files through for processing.
"""
files = []
print("->", ldetail_group[0]["name"], len(ldetail_group))
for read in ["R1", "R2"]:
... | [
"def",
"_prep_sample_and_config",
"(",
"ldetail_group",
",",
"fastq_dir",
",",
"fastq_final_dir",
")",
":",
"files",
"=",
"[",
"]",
"print",
"(",
"\"->\"",
",",
"ldetail_group",
"[",
"0",
"]",
"[",
"\"name\"",
"]",
",",
"len",
"(",
"ldetail_group",
")",
")... | Prepare output fastq file and configuration for a single sample.
Only passes non-empty files through for processing. | [
"Prepare",
"output",
"fastq",
"file",
"and",
"configuration",
"for",
"a",
"single",
"sample",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L36-L52 |
223,248 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | _write_sample_config | def _write_sample_config(run_folder, ldetails):
"""Generate a bcbio-nextgen YAML configuration file for processing a sample.
"""
out_file = os.path.join(run_folder, "%s.yaml" % os.path.basename(run_folder))
with open(out_file, "w") as out_handle:
fc_name, fc_date = flowcell.parse_dirname(run_fol... | python | def _write_sample_config(run_folder, ldetails):
"""Generate a bcbio-nextgen YAML configuration file for processing a sample.
"""
out_file = os.path.join(run_folder, "%s.yaml" % os.path.basename(run_folder))
with open(out_file, "w") as out_handle:
fc_name, fc_date = flowcell.parse_dirname(run_fol... | [
"def",
"_write_sample_config",
"(",
"run_folder",
",",
"ldetails",
")",
":",
"out_file",
"=",
"os",
".",
"path",
".",
"join",
"(",
"run_folder",
",",
"\"%s.yaml\"",
"%",
"os",
".",
"path",
".",
"basename",
"(",
"run_folder",
")",
")",
"with",
"open",
"("... | Generate a bcbio-nextgen YAML configuration file for processing a sample. | [
"Generate",
"a",
"bcbio",
"-",
"nextgen",
"YAML",
"configuration",
"file",
"for",
"processing",
"a",
"sample",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L60-L71 |
223,249 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | _prepare_sample | def _prepare_sample(data, run_folder):
"""Extract passed keywords from input LIMS information.
"""
want = set(["description", "files", "genome_build", "name", "analysis", "upload", "algorithm"])
out = {}
for k, v in data.items():
if k in want:
out[k] = _relative_paths(v, run_fold... | python | def _prepare_sample(data, run_folder):
"""Extract passed keywords from input LIMS information.
"""
want = set(["description", "files", "genome_build", "name", "analysis", "upload", "algorithm"])
out = {}
for k, v in data.items():
if k in want:
out[k] = _relative_paths(v, run_fold... | [
"def",
"_prepare_sample",
"(",
"data",
",",
"run_folder",
")",
":",
"want",
"=",
"set",
"(",
"[",
"\"description\"",
",",
"\"files\"",
",",
"\"genome_build\"",
",",
"\"name\"",
",",
"\"analysis\"",
",",
"\"upload\"",
",",
"\"algorithm\"",
"]",
")",
"out",
"=... | Extract passed keywords from input LIMS information. | [
"Extract",
"passed",
"keywords",
"from",
"input",
"LIMS",
"information",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L73-L88 |
223,250 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | _select_default_algorithm | def _select_default_algorithm(analysis):
"""Provide default algorithm sections from templates or standard
"""
if not analysis or analysis == "Standard":
return "Standard", {"aligner": "bwa", "platform": "illumina", "quality_format": "Standard",
"recalibrate": False, "real... | python | def _select_default_algorithm(analysis):
"""Provide default algorithm sections from templates or standard
"""
if not analysis or analysis == "Standard":
return "Standard", {"aligner": "bwa", "platform": "illumina", "quality_format": "Standard",
"recalibrate": False, "real... | [
"def",
"_select_default_algorithm",
"(",
"analysis",
")",
":",
"if",
"not",
"analysis",
"or",
"analysis",
"==",
"\"Standard\"",
":",
"return",
"\"Standard\"",
",",
"{",
"\"aligner\"",
":",
"\"bwa\"",
",",
"\"platform\"",
":",
"\"illumina\"",
",",
"\"quality_format... | Provide default algorithm sections from templates or standard | [
"Provide",
"default",
"algorithm",
"sections",
"from",
"templates",
"or",
"standard"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L90-L104 |
223,251 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | _relative_paths | def _relative_paths(xs, base_path):
"""Adjust paths to be relative to the provided base path.
"""
if isinstance(xs, six.string_types):
if xs.startswith(base_path):
return xs.replace(base_path + "/", "", 1)
else:
return xs
elif isinstance(xs, (list, tuple)):
... | python | def _relative_paths(xs, base_path):
"""Adjust paths to be relative to the provided base path.
"""
if isinstance(xs, six.string_types):
if xs.startswith(base_path):
return xs.replace(base_path + "/", "", 1)
else:
return xs
elif isinstance(xs, (list, tuple)):
... | [
"def",
"_relative_paths",
"(",
"xs",
",",
"base_path",
")",
":",
"if",
"isinstance",
"(",
"xs",
",",
"six",
".",
"string_types",
")",
":",
"if",
"xs",
".",
"startswith",
"(",
"base_path",
")",
":",
"return",
"xs",
".",
"replace",
"(",
"base_path",
"+",... | Adjust paths to be relative to the provided base path. | [
"Adjust",
"paths",
"to",
"be",
"relative",
"to",
"the",
"provided",
"base",
"path",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L106-L122 |
223,252 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | _get_fastq_files | def _get_fastq_files(ldetail, read, fastq_dir):
"""Retrieve fastq files corresponding to the sample and read number.
"""
return glob.glob(os.path.join(fastq_dir, "Project_%s" % ldetail["project_name"],
"Sample_%s" % ldetail["name"],
"%s_*_%... | python | def _get_fastq_files(ldetail, read, fastq_dir):
"""Retrieve fastq files corresponding to the sample and read number.
"""
return glob.glob(os.path.join(fastq_dir, "Project_%s" % ldetail["project_name"],
"Sample_%s" % ldetail["name"],
"%s_*_%... | [
"def",
"_get_fastq_files",
"(",
"ldetail",
",",
"read",
",",
"fastq_dir",
")",
":",
"return",
"glob",
".",
"glob",
"(",
"os",
".",
"path",
".",
"join",
"(",
"fastq_dir",
",",
"\"Project_%s\"",
"%",
"ldetail",
"[",
"\"project_name\"",
"]",
",",
"\"Sample_%s... | Retrieve fastq files corresponding to the sample and read number. | [
"Retrieve",
"fastq",
"files",
"corresponding",
"to",
"the",
"sample",
"and",
"read",
"number",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L124-L129 |
223,253 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | _concat_bgzip_fastq | def _concat_bgzip_fastq(finputs, out_dir, read, ldetail):
"""Concatenate multiple input fastq files, preparing a bgzipped output file.
"""
out_file = os.path.join(out_dir, "%s_%s.fastq.gz" % (ldetail["name"], read))
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_fi... | python | def _concat_bgzip_fastq(finputs, out_dir, read, ldetail):
"""Concatenate multiple input fastq files, preparing a bgzipped output file.
"""
out_file = os.path.join(out_dir, "%s_%s.fastq.gz" % (ldetail["name"], read))
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_fi... | [
"def",
"_concat_bgzip_fastq",
"(",
"finputs",
",",
"out_dir",
",",
"read",
",",
"ldetail",
")",
":",
"out_file",
"=",
"os",
".",
"path",
".",
"join",
"(",
"out_dir",
",",
"\"%s_%s.fastq.gz\"",
"%",
"(",
"ldetail",
"[",
"\"name\"",
"]",
",",
"read",
")",
... | Concatenate multiple input fastq files, preparing a bgzipped output file. | [
"Concatenate",
"multiple",
"input",
"fastq",
"files",
"preparing",
"a",
"bgzipped",
"output",
"file",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L131-L138 |
223,254 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | get_runinfo | def get_runinfo(galaxy_url, galaxy_apikey, run_folder, storedir):
"""Retrieve flattened run information for a processed directory from Galaxy nglims API.
"""
galaxy_api = GalaxyApiAccess(galaxy_url, galaxy_apikey)
fc_name, fc_date = flowcell.parse_dirname(run_folder)
galaxy_info = galaxy_api.run_det... | python | def get_runinfo(galaxy_url, galaxy_apikey, run_folder, storedir):
"""Retrieve flattened run information for a processed directory from Galaxy nglims API.
"""
galaxy_api = GalaxyApiAccess(galaxy_url, galaxy_apikey)
fc_name, fc_date = flowcell.parse_dirname(run_folder)
galaxy_info = galaxy_api.run_det... | [
"def",
"get_runinfo",
"(",
"galaxy_url",
",",
"galaxy_apikey",
",",
"run_folder",
",",
"storedir",
")",
":",
"galaxy_api",
"=",
"GalaxyApiAccess",
"(",
"galaxy_url",
",",
"galaxy_apikey",
")",
"fc_name",
",",
"fc_date",
"=",
"flowcell",
".",
"parse_dirname",
"("... | Retrieve flattened run information for a processed directory from Galaxy nglims API. | [
"Retrieve",
"flattened",
"run",
"information",
"for",
"a",
"processed",
"directory",
"from",
"Galaxy",
"nglims",
"API",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L148-L172 |
223,255 | bcbio/bcbio-nextgen | bcbio/galaxy/nglims.py | _flatten_lane_details | def _flatten_lane_details(runinfo):
"""Provide flattened lane information with multiplexed barcodes separated.
"""
out = []
for ldetail in runinfo["details"]:
# handle controls
if "project_name" not in ldetail and ldetail["description"] == "control":
ldetail["project_name"] =... | python | def _flatten_lane_details(runinfo):
"""Provide flattened lane information with multiplexed barcodes separated.
"""
out = []
for ldetail in runinfo["details"]:
# handle controls
if "project_name" not in ldetail and ldetail["description"] == "control":
ldetail["project_name"] =... | [
"def",
"_flatten_lane_details",
"(",
"runinfo",
")",
":",
"out",
"=",
"[",
"]",
"for",
"ldetail",
"in",
"runinfo",
"[",
"\"details\"",
"]",
":",
"# handle controls",
"if",
"\"project_name\"",
"not",
"in",
"ldetail",
"and",
"ldetail",
"[",
"\"description\"",
"]... | Provide flattened lane information with multiplexed barcodes separated. | [
"Provide",
"flattened",
"lane",
"information",
"with",
"multiplexed",
"barcodes",
"separated",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/galaxy/nglims.py#L174-L189 |
223,256 | bcbio/bcbio-nextgen | bcbio/distributed/split.py | grouped_parallel_split_combine | def grouped_parallel_split_combine(args, split_fn, group_fn, parallel_fn,
parallel_name, combine_name,
file_key, combine_arg_keys,
split_outfile_i=-1):
"""Parallel split runner that allows grouping of samples du... | python | def grouped_parallel_split_combine(args, split_fn, group_fn, parallel_fn,
parallel_name, combine_name,
file_key, combine_arg_keys,
split_outfile_i=-1):
"""Parallel split runner that allows grouping of samples du... | [
"def",
"grouped_parallel_split_combine",
"(",
"args",
",",
"split_fn",
",",
"group_fn",
",",
"parallel_fn",
",",
"parallel_name",
",",
"combine_name",
",",
"file_key",
",",
"combine_arg_keys",
",",
"split_outfile_i",
"=",
"-",
"1",
")",
":",
"grouped_args",
"=",
... | Parallel split runner that allows grouping of samples during processing.
This builds on parallel_split_combine to provide the additional ability to
group samples and subsequently split them back apart. This allows analysis
of related samples together. In addition to the arguments documented in
parallel... | [
"Parallel",
"split",
"runner",
"that",
"allows",
"grouping",
"of",
"samples",
"during",
"processing",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/distributed/split.py#L18-L39 |
223,257 | bcbio/bcbio-nextgen | bcbio/distributed/split.py | parallel_split_combine | def parallel_split_combine(args, split_fn, parallel_fn,
parallel_name, combiner,
file_key, combine_arg_keys, split_outfile_i=-1):
"""Split, run split items in parallel then combine to output file.
split_fn: Split an input file into parts for processing. Ret... | python | def parallel_split_combine(args, split_fn, parallel_fn,
parallel_name, combiner,
file_key, combine_arg_keys, split_outfile_i=-1):
"""Split, run split items in parallel then combine to output file.
split_fn: Split an input file into parts for processing. Ret... | [
"def",
"parallel_split_combine",
"(",
"args",
",",
"split_fn",
",",
"parallel_fn",
",",
"parallel_name",
",",
"combiner",
",",
"file_key",
",",
"combine_arg_keys",
",",
"split_outfile_i",
"=",
"-",
"1",
")",
":",
"args",
"=",
"[",
"x",
"[",
"0",
"]",
"for"... | Split, run split items in parallel then combine to output file.
split_fn: Split an input file into parts for processing. Returns
the name of the combined output file along with the individual
split output names and arguments for the parallel function.
parallel_fn: Reference to run_parallel function... | [
"Split",
"run",
"split",
"items",
"in",
"parallel",
"then",
"combine",
"to",
"output",
"file",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/distributed/split.py#L41-L69 |
223,258 | bcbio/bcbio-nextgen | bcbio/distributed/split.py | _get_extra_args | def _get_extra_args(extra_args, arg_keys):
"""Retrieve extra arguments to pass along to combine function.
Special cases like reference files and configuration information
are passed as single items, the rest as lists mapping to each data
item combined.
"""
# XXX back compatible hack -- should h... | python | def _get_extra_args(extra_args, arg_keys):
"""Retrieve extra arguments to pass along to combine function.
Special cases like reference files and configuration information
are passed as single items, the rest as lists mapping to each data
item combined.
"""
# XXX back compatible hack -- should h... | [
"def",
"_get_extra_args",
"(",
"extra_args",
",",
"arg_keys",
")",
":",
"# XXX back compatible hack -- should have a way to specify these.",
"single_keys",
"=",
"set",
"(",
"[",
"\"sam_ref\"",
",",
"\"config\"",
"]",
")",
"out",
"=",
"[",
"]",
"for",
"i",
",",
"ar... | Retrieve extra arguments to pass along to combine function.
Special cases like reference files and configuration information
are passed as single items, the rest as lists mapping to each data
item combined. | [
"Retrieve",
"extra",
"arguments",
"to",
"pass",
"along",
"to",
"combine",
"function",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/distributed/split.py#L71-L87 |
223,259 | bcbio/bcbio-nextgen | bcbio/distributed/split.py | _organize_output | def _organize_output(output, combine_map, file_key, combine_arg_keys):
"""Combine output details for parallelization.
file_key is the key name of the output file used in merging. We extract
this file from the output data.
combine_arg_keys are extra items to pass along to the combine function.
"""
... | python | def _organize_output(output, combine_map, file_key, combine_arg_keys):
"""Combine output details for parallelization.
file_key is the key name of the output file used in merging. We extract
this file from the output data.
combine_arg_keys are extra items to pass along to the combine function.
"""
... | [
"def",
"_organize_output",
"(",
"output",
",",
"combine_map",
",",
"file_key",
",",
"combine_arg_keys",
")",
":",
"out_map",
"=",
"collections",
".",
"defaultdict",
"(",
"list",
")",
"extra_args",
"=",
"collections",
".",
"defaultdict",
"(",
"list",
")",
"fina... | Combine output details for parallelization.
file_key is the key name of the output file used in merging. We extract
this file from the output data.
combine_arg_keys are extra items to pass along to the combine function. | [
"Combine",
"output",
"details",
"for",
"parallelization",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/distributed/split.py#L89-L116 |
223,260 | bcbio/bcbio-nextgen | bcbio/distributed/split.py | _get_split_tasks | def _get_split_tasks(args, split_fn, file_key, outfile_i=-1):
"""Split up input files and arguments, returning arguments for parallel processing.
outfile_i specifies the location of the output file in the arguments to
the processing function. Defaults to the last item in the list.
"""
split_args = ... | python | def _get_split_tasks(args, split_fn, file_key, outfile_i=-1):
"""Split up input files and arguments, returning arguments for parallel processing.
outfile_i specifies the location of the output file in the arguments to
the processing function. Defaults to the last item in the list.
"""
split_args = ... | [
"def",
"_get_split_tasks",
"(",
"args",
",",
"split_fn",
",",
"file_key",
",",
"outfile_i",
"=",
"-",
"1",
")",
":",
"split_args",
"=",
"[",
"]",
"combine_map",
"=",
"{",
"}",
"finished_map",
"=",
"collections",
".",
"OrderedDict",
"(",
")",
"extras",
"=... | Split up input files and arguments, returning arguments for parallel processing.
outfile_i specifies the location of the output file in the arguments to
the processing function. Defaults to the last item in the list. | [
"Split",
"up",
"input",
"files",
"and",
"arguments",
"returning",
"arguments",
"for",
"parallel",
"processing",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/distributed/split.py#L118-L143 |
223,261 | bcbio/bcbio-nextgen | bcbio/ngsalign/snap.py | remap_index_fn | def remap_index_fn(ref_file):
"""Map sequence references to snap reference directory, using standard layout.
"""
snap_dir = os.path.join(os.path.dirname(ref_file), os.pardir, "snap")
assert os.path.exists(snap_dir) and os.path.isdir(snap_dir), snap_dir
return snap_dir | python | def remap_index_fn(ref_file):
"""Map sequence references to snap reference directory, using standard layout.
"""
snap_dir = os.path.join(os.path.dirname(ref_file), os.pardir, "snap")
assert os.path.exists(snap_dir) and os.path.isdir(snap_dir), snap_dir
return snap_dir | [
"def",
"remap_index_fn",
"(",
"ref_file",
")",
":",
"snap_dir",
"=",
"os",
".",
"path",
".",
"join",
"(",
"os",
".",
"path",
".",
"dirname",
"(",
"ref_file",
")",
",",
"os",
".",
"pardir",
",",
"\"snap\"",
")",
"assert",
"os",
".",
"path",
".",
"ex... | Map sequence references to snap reference directory, using standard layout. | [
"Map",
"sequence",
"references",
"to",
"snap",
"reference",
"directory",
"using",
"standard",
"layout",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/ngsalign/snap.py#L81-L86 |
223,262 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | use_general_sv_bins | def use_general_sv_bins(data):
"""Check if we should use a general binning approach for a sample.
Checks if CNVkit is enabled and we haven't already run CNVkit.
"""
if any([c in dd.get_svcaller(data) for c in ["cnvkit", "titancna", "purecn", "gatk-cnv"]]):
if not _get_original_coverage(data):
... | python | def use_general_sv_bins(data):
"""Check if we should use a general binning approach for a sample.
Checks if CNVkit is enabled and we haven't already run CNVkit.
"""
if any([c in dd.get_svcaller(data) for c in ["cnvkit", "titancna", "purecn", "gatk-cnv"]]):
if not _get_original_coverage(data):
... | [
"def",
"use_general_sv_bins",
"(",
"data",
")",
":",
"if",
"any",
"(",
"[",
"c",
"in",
"dd",
".",
"get_svcaller",
"(",
"data",
")",
"for",
"c",
"in",
"[",
"\"cnvkit\"",
",",
"\"titancna\"",
",",
"\"purecn\"",
",",
"\"gatk-cnv\"",
"]",
"]",
")",
":",
... | Check if we should use a general binning approach for a sample.
Checks if CNVkit is enabled and we haven't already run CNVkit. | [
"Check",
"if",
"we",
"should",
"use",
"a",
"general",
"binning",
"approach",
"for",
"a",
"sample",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L31-L39 |
223,263 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | bin_approach | def bin_approach(data):
"""Check for binning approach from configuration or normalized file.
"""
for approach in ["cnvkit", "gatk-cnv"]:
if approach in dd.get_svcaller(data):
return approach
norm_file = tz.get_in(["depth", "bins", "normalized"], data)
if norm_file.endswith(("-crs... | python | def bin_approach(data):
"""Check for binning approach from configuration or normalized file.
"""
for approach in ["cnvkit", "gatk-cnv"]:
if approach in dd.get_svcaller(data):
return approach
norm_file = tz.get_in(["depth", "bins", "normalized"], data)
if norm_file.endswith(("-crs... | [
"def",
"bin_approach",
"(",
"data",
")",
":",
"for",
"approach",
"in",
"[",
"\"cnvkit\"",
",",
"\"gatk-cnv\"",
"]",
":",
"if",
"approach",
"in",
"dd",
".",
"get_svcaller",
"(",
"data",
")",
":",
"return",
"approach",
"norm_file",
"=",
"tz",
".",
"get_in"... | Check for binning approach from configuration or normalized file. | [
"Check",
"for",
"binning",
"approach",
"from",
"configuration",
"or",
"normalized",
"file",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L41-L51 |
223,264 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _cnvkit_by_type | def _cnvkit_by_type(items, background):
"""Dispatch to specific CNVkit functionality based on input type.
"""
if len(items + background) == 1:
return _run_cnvkit_single(items[0])
elif vcfutils.get_paired_phenotype(items[0]):
return _run_cnvkit_cancer(items, background)
else:
... | python | def _cnvkit_by_type(items, background):
"""Dispatch to specific CNVkit functionality based on input type.
"""
if len(items + background) == 1:
return _run_cnvkit_single(items[0])
elif vcfutils.get_paired_phenotype(items[0]):
return _run_cnvkit_cancer(items, background)
else:
... | [
"def",
"_cnvkit_by_type",
"(",
"items",
",",
"background",
")",
":",
"if",
"len",
"(",
"items",
"+",
"background",
")",
"==",
"1",
":",
"return",
"_run_cnvkit_single",
"(",
"items",
"[",
"0",
"]",
")",
"elif",
"vcfutils",
".",
"get_paired_phenotype",
"(",
... | Dispatch to specific CNVkit functionality based on input type. | [
"Dispatch",
"to",
"specific",
"CNVkit",
"functionality",
"based",
"on",
"input",
"type",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L63-L71 |
223,265 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _associate_cnvkit_out | def _associate_cnvkit_out(ckouts, items, is_somatic=False):
"""Associate cnvkit output with individual items.
"""
assert len(ckouts) == len(items)
out = []
upload_counts = collections.defaultdict(int)
for ckout, data in zip(ckouts, items):
ckout = copy.deepcopy(ckout)
ckout["vari... | python | def _associate_cnvkit_out(ckouts, items, is_somatic=False):
"""Associate cnvkit output with individual items.
"""
assert len(ckouts) == len(items)
out = []
upload_counts = collections.defaultdict(int)
for ckout, data in zip(ckouts, items):
ckout = copy.deepcopy(ckout)
ckout["vari... | [
"def",
"_associate_cnvkit_out",
"(",
"ckouts",
",",
"items",
",",
"is_somatic",
"=",
"False",
")",
":",
"assert",
"len",
"(",
"ckouts",
")",
"==",
"len",
"(",
"items",
")",
"out",
"=",
"[",
"]",
"upload_counts",
"=",
"collections",
".",
"defaultdict",
"(... | Associate cnvkit output with individual items. | [
"Associate",
"cnvkit",
"output",
"with",
"individual",
"items",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L73-L98 |
223,266 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _run_cnvkit_single | def _run_cnvkit_single(data, background=None):
"""Process a single input file with BAM or uniform background.
"""
if not background:
background = []
ckouts = _run_cnvkit_shared([data], background)
if not ckouts:
return [data]
else:
assert len(ckouts) == 1
return _... | python | def _run_cnvkit_single(data, background=None):
"""Process a single input file with BAM or uniform background.
"""
if not background:
background = []
ckouts = _run_cnvkit_shared([data], background)
if not ckouts:
return [data]
else:
assert len(ckouts) == 1
return _... | [
"def",
"_run_cnvkit_single",
"(",
"data",
",",
"background",
"=",
"None",
")",
":",
"if",
"not",
"background",
":",
"background",
"=",
"[",
"]",
"ckouts",
"=",
"_run_cnvkit_shared",
"(",
"[",
"data",
"]",
",",
"background",
")",
"if",
"not",
"ckouts",
":... | Process a single input file with BAM or uniform background. | [
"Process",
"a",
"single",
"input",
"file",
"with",
"BAM",
"or",
"uniform",
"background",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L100-L110 |
223,267 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _run_cnvkit_population | def _run_cnvkit_population(items, background):
"""Run CNVkit on a population of samples.
Tries to calculate background based on case/controls, otherwise
uses samples from the same batch as background.
"""
if background and len(background) > 0:
inputs = items
else:
inputs, backgr... | python | def _run_cnvkit_population(items, background):
"""Run CNVkit on a population of samples.
Tries to calculate background based on case/controls, otherwise
uses samples from the same batch as background.
"""
if background and len(background) > 0:
inputs = items
else:
inputs, backgr... | [
"def",
"_run_cnvkit_population",
"(",
"items",
",",
"background",
")",
":",
"if",
"background",
"and",
"len",
"(",
"background",
")",
">",
"0",
":",
"inputs",
"=",
"items",
"else",
":",
"inputs",
",",
"background",
"=",
"shared",
".",
"find_case_control",
... | Run CNVkit on a population of samples.
Tries to calculate background based on case/controls, otherwise
uses samples from the same batch as background. | [
"Run",
"CNVkit",
"on",
"a",
"population",
"of",
"samples",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L141-L163 |
223,268 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _prep_cmd | def _prep_cmd(cmd, tx_out_file):
"""Wrap CNVkit commands ensuring we use local temporary directories.
"""
cmd = " ".join(cmd) if isinstance(cmd, (list, tuple)) else cmd
return "export TMPDIR=%s && %s" % (os.path.dirname(tx_out_file), cmd) | python | def _prep_cmd(cmd, tx_out_file):
"""Wrap CNVkit commands ensuring we use local temporary directories.
"""
cmd = " ".join(cmd) if isinstance(cmd, (list, tuple)) else cmd
return "export TMPDIR=%s && %s" % (os.path.dirname(tx_out_file), cmd) | [
"def",
"_prep_cmd",
"(",
"cmd",
",",
"tx_out_file",
")",
":",
"cmd",
"=",
"\" \"",
".",
"join",
"(",
"cmd",
")",
"if",
"isinstance",
"(",
"cmd",
",",
"(",
"list",
",",
"tuple",
")",
")",
"else",
"cmd",
"return",
"\"export TMPDIR=%s && %s\"",
"%",
"(",
... | Wrap CNVkit commands ensuring we use local temporary directories. | [
"Wrap",
"CNVkit",
"commands",
"ensuring",
"we",
"use",
"local",
"temporary",
"directories",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L168-L172 |
223,269 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _bam_to_outbase | def _bam_to_outbase(bam_file, work_dir, data):
"""Convert an input BAM file into CNVkit expected output.
Handles previous non-batch cases to avoid re-calculating,
returning both new and old values:
"""
batch = dd.get_batch(data) or dd.get_sample_name(data)
out_base = os.path.splitext(os.path.ba... | python | def _bam_to_outbase(bam_file, work_dir, data):
"""Convert an input BAM file into CNVkit expected output.
Handles previous non-batch cases to avoid re-calculating,
returning both new and old values:
"""
batch = dd.get_batch(data) or dd.get_sample_name(data)
out_base = os.path.splitext(os.path.ba... | [
"def",
"_bam_to_outbase",
"(",
"bam_file",
",",
"work_dir",
",",
"data",
")",
":",
"batch",
"=",
"dd",
".",
"get_batch",
"(",
"data",
")",
"or",
"dd",
".",
"get_sample_name",
"(",
"data",
")",
"out_base",
"=",
"os",
".",
"path",
".",
"splitext",
"(",
... | Convert an input BAM file into CNVkit expected output.
Handles previous non-batch cases to avoid re-calculating,
returning both new and old values: | [
"Convert",
"an",
"input",
"BAM",
"file",
"into",
"CNVkit",
"expected",
"output",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L174-L183 |
223,270 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _run_cnvkit_shared | def _run_cnvkit_shared(inputs, backgrounds):
"""Shared functionality to run CNVkit, parallelizing over multiple BAM files.
Handles new style cases where we have pre-normalized inputs and
old cases where we run CNVkit individually.
"""
if tz.get_in(["depth", "bins", "normalized"], inputs[0]):
... | python | def _run_cnvkit_shared(inputs, backgrounds):
"""Shared functionality to run CNVkit, parallelizing over multiple BAM files.
Handles new style cases where we have pre-normalized inputs and
old cases where we run CNVkit individually.
"""
if tz.get_in(["depth", "bins", "normalized"], inputs[0]):
... | [
"def",
"_run_cnvkit_shared",
"(",
"inputs",
",",
"backgrounds",
")",
":",
"if",
"tz",
".",
"get_in",
"(",
"[",
"\"depth\"",
",",
"\"bins\"",
",",
"\"normalized\"",
"]",
",",
"inputs",
"[",
"0",
"]",
")",
":",
"ckouts",
"=",
"[",
"]",
"for",
"data",
"... | Shared functionality to run CNVkit, parallelizing over multiple BAM files.
Handles new style cases where we have pre-normalized inputs and
old cases where we run CNVkit individually. | [
"Shared",
"functionality",
"to",
"run",
"CNVkit",
"parallelizing",
"over",
"multiple",
"BAM",
"files",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L201-L218 |
223,271 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _get_general_coverage | def _get_general_coverage(data, itype):
"""Retrieve coverage information from new shared SV bins.
"""
work_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
return [{"bam": work_bam, "file": tz.get_in(["depth", "bins", "target"], data),
"cnntype": "target", "itype": itype, "sample": dd.... | python | def _get_general_coverage(data, itype):
"""Retrieve coverage information from new shared SV bins.
"""
work_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
return [{"bam": work_bam, "file": tz.get_in(["depth", "bins", "target"], data),
"cnntype": "target", "itype": itype, "sample": dd.... | [
"def",
"_get_general_coverage",
"(",
"data",
",",
"itype",
")",
":",
"work_bam",
"=",
"dd",
".",
"get_align_bam",
"(",
"data",
")",
"or",
"dd",
".",
"get_work_bam",
"(",
"data",
")",
"return",
"[",
"{",
"\"bam\"",
":",
"work_bam",
",",
"\"file\"",
":",
... | Retrieve coverage information from new shared SV bins. | [
"Retrieve",
"coverage",
"information",
"from",
"new",
"shared",
"SV",
"bins",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L228-L235 |
223,272 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _cnvkit_segment | def _cnvkit_segment(cnr_file, cov_interval, data, items, out_file=None, detailed=False):
"""Perform segmentation and copy number calling on normalized inputs
"""
if not out_file:
out_file = "%s.cns" % os.path.splitext(cnr_file)[0]
if not utils.file_uptodate(out_file, cnr_file):
with file... | python | def _cnvkit_segment(cnr_file, cov_interval, data, items, out_file=None, detailed=False):
"""Perform segmentation and copy number calling on normalized inputs
"""
if not out_file:
out_file = "%s.cns" % os.path.splitext(cnr_file)[0]
if not utils.file_uptodate(out_file, cnr_file):
with file... | [
"def",
"_cnvkit_segment",
"(",
"cnr_file",
",",
"cov_interval",
",",
"data",
",",
"items",
",",
"out_file",
"=",
"None",
",",
"detailed",
"=",
"False",
")",
":",
"if",
"not",
"out_file",
":",
"out_file",
"=",
"\"%s.cns\"",
"%",
"os",
".",
"path",
".",
... | Perform segmentation and copy number calling on normalized inputs | [
"Perform",
"segmentation",
"and",
"copy",
"number",
"calling",
"on",
"normalized",
"inputs"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L297-L338 |
223,273 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _cnvkit_metrics | def _cnvkit_metrics(cnns, target_bed, antitarget_bed, cov_interval, items):
"""Estimate noise of a sample using a flat background.
Only used for panel/targeted data due to memory issues with whole genome
samples.
"""
if cov_interval == "genome":
return cnns
target_cnn = [x["file"] for ... | python | def _cnvkit_metrics(cnns, target_bed, antitarget_bed, cov_interval, items):
"""Estimate noise of a sample using a flat background.
Only used for panel/targeted data due to memory issues with whole genome
samples.
"""
if cov_interval == "genome":
return cnns
target_cnn = [x["file"] for ... | [
"def",
"_cnvkit_metrics",
"(",
"cnns",
",",
"target_bed",
",",
"antitarget_bed",
",",
"cov_interval",
",",
"items",
")",
":",
"if",
"cov_interval",
"==",
"\"genome\"",
":",
"return",
"cnns",
"target_cnn",
"=",
"[",
"x",
"[",
"\"file\"",
"]",
"for",
"x",
"i... | Estimate noise of a sample using a flat background.
Only used for panel/targeted data due to memory issues with whole genome
samples. | [
"Estimate",
"noise",
"of",
"a",
"sample",
"using",
"a",
"flat",
"background",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L340-L364 |
223,274 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _cnvkit_fix | def _cnvkit_fix(cnns, background_cnn, items, ckouts):
"""Normalize samples, correcting sources of bias.
"""
return [_cnvkit_fix_base(cnns, background_cnn, items, ckouts)] | python | def _cnvkit_fix(cnns, background_cnn, items, ckouts):
"""Normalize samples, correcting sources of bias.
"""
return [_cnvkit_fix_base(cnns, background_cnn, items, ckouts)] | [
"def",
"_cnvkit_fix",
"(",
"cnns",
",",
"background_cnn",
",",
"items",
",",
"ckouts",
")",
":",
"return",
"[",
"_cnvkit_fix_base",
"(",
"cnns",
",",
"background_cnn",
",",
"items",
",",
"ckouts",
")",
"]"
] | Normalize samples, correcting sources of bias. | [
"Normalize",
"samples",
"correcting",
"sources",
"of",
"bias",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L374-L377 |
223,275 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _select_background_cnns | def _select_background_cnns(cnns):
"""Select cnns to use for background calculations.
Uses background samples in cohort, and will remove CNNs with high
on target variability. Uses (number of segments * biweight midvariance) as metric
for variability with higher numbers being more unreliable.
"""
... | python | def _select_background_cnns(cnns):
"""Select cnns to use for background calculations.
Uses background samples in cohort, and will remove CNNs with high
on target variability. Uses (number of segments * biweight midvariance) as metric
for variability with higher numbers being more unreliable.
"""
... | [
"def",
"_select_background_cnns",
"(",
"cnns",
")",
":",
"min_for_variability_analysis",
"=",
"20",
"pct_keep",
"=",
"0.10",
"b_cnns",
"=",
"[",
"x",
"for",
"x",
"in",
"cnns",
"if",
"x",
"[",
"\"itype\"",
"]",
"==",
"\"background\"",
"and",
"x",
".",
"get"... | Select cnns to use for background calculations.
Uses background samples in cohort, and will remove CNNs with high
on target variability. Uses (number of segments * biweight midvariance) as metric
for variability with higher numbers being more unreliable. | [
"Select",
"cnns",
"to",
"use",
"for",
"background",
"calculations",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L400-L420 |
223,276 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | cnvkit_background | def cnvkit_background(background_cnns, out_file, items, target_bed=None, antitarget_bed=None):
"""Calculate background reference, handling flat case with no normal sample.
"""
if not utils.file_exists(out_file):
with file_transaction(items[0], out_file) as tx_out_file:
cmd = [_get_cmd(),... | python | def cnvkit_background(background_cnns, out_file, items, target_bed=None, antitarget_bed=None):
"""Calculate background reference, handling flat case with no normal sample.
"""
if not utils.file_exists(out_file):
with file_transaction(items[0], out_file) as tx_out_file:
cmd = [_get_cmd(),... | [
"def",
"cnvkit_background",
"(",
"background_cnns",
",",
"out_file",
",",
"items",
",",
"target_bed",
"=",
"None",
",",
"antitarget_bed",
"=",
"None",
")",
":",
"if",
"not",
"utils",
".",
"file_exists",
"(",
"out_file",
")",
":",
"with",
"file_transaction",
... | Calculate background reference, handling flat case with no normal sample. | [
"Calculate",
"background",
"reference",
"handling",
"flat",
"case",
"with",
"no",
"normal",
"sample",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L422-L437 |
223,277 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _get_batch_gender | def _get_batch_gender(items):
"""Retrieve gender for a batch of items if consistent.
Better not to specify for mixed populations, CNVkit will work
it out
https://github.com/bcbio/bcbio-nextgen/commit/1a0e217c8a4d3cee10fa890fb3cfd4db5034281d#r26279752
"""
genders = set([population.get_gender(x) ... | python | def _get_batch_gender(items):
"""Retrieve gender for a batch of items if consistent.
Better not to specify for mixed populations, CNVkit will work
it out
https://github.com/bcbio/bcbio-nextgen/commit/1a0e217c8a4d3cee10fa890fb3cfd4db5034281d#r26279752
"""
genders = set([population.get_gender(x) ... | [
"def",
"_get_batch_gender",
"(",
"items",
")",
":",
"genders",
"=",
"set",
"(",
"[",
"population",
".",
"get_gender",
"(",
"x",
")",
"for",
"x",
"in",
"items",
"]",
")",
"if",
"len",
"(",
"genders",
")",
"==",
"1",
":",
"gender",
"=",
"genders",
".... | Retrieve gender for a batch of items if consistent.
Better not to specify for mixed populations, CNVkit will work
it out
https://github.com/bcbio/bcbio-nextgen/commit/1a0e217c8a4d3cee10fa890fb3cfd4db5034281d#r26279752 | [
"Retrieve",
"gender",
"for",
"a",
"batch",
"of",
"items",
"if",
"consistent",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L440-L451 |
223,278 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | targets_w_bins | def targets_w_bins(cnv_file, access_file, target_anti_fn, work_dir, data):
"""Calculate target and anti-target files with pre-determined bins.
"""
target_file = os.path.join(work_dir, "%s-target.bed" % dd.get_sample_name(data))
anti_file = os.path.join(work_dir, "%s-antitarget.bed" % dd.get_sample_name(... | python | def targets_w_bins(cnv_file, access_file, target_anti_fn, work_dir, data):
"""Calculate target and anti-target files with pre-determined bins.
"""
target_file = os.path.join(work_dir, "%s-target.bed" % dd.get_sample_name(data))
anti_file = os.path.join(work_dir, "%s-antitarget.bed" % dd.get_sample_name(... | [
"def",
"targets_w_bins",
"(",
"cnv_file",
",",
"access_file",
",",
"target_anti_fn",
",",
"work_dir",
",",
"data",
")",
":",
"target_file",
"=",
"os",
".",
"path",
".",
"join",
"(",
"work_dir",
",",
"\"%s-target.bed\"",
"%",
"dd",
".",
"get_sample_name",
"("... | Calculate target and anti-target files with pre-determined bins. | [
"Calculate",
"target",
"and",
"anti",
"-",
"target",
"files",
"with",
"pre",
"-",
"determined",
"bins",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L453-L475 |
223,279 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | targets_from_background | def targets_from_background(back_cnn, work_dir, data):
"""Retrieve target and antitarget BEDs from background CNN file.
"""
target_file = os.path.join(work_dir, "%s.target.bed" % dd.get_sample_name(data))
anti_file = os.path.join(work_dir, "%s.antitarget.bed" % dd.get_sample_name(data))
if not utils... | python | def targets_from_background(back_cnn, work_dir, data):
"""Retrieve target and antitarget BEDs from background CNN file.
"""
target_file = os.path.join(work_dir, "%s.target.bed" % dd.get_sample_name(data))
anti_file = os.path.join(work_dir, "%s.antitarget.bed" % dd.get_sample_name(data))
if not utils... | [
"def",
"targets_from_background",
"(",
"back_cnn",
",",
"work_dir",
",",
"data",
")",
":",
"target_file",
"=",
"os",
".",
"path",
".",
"join",
"(",
"work_dir",
",",
"\"%s.target.bed\"",
"%",
"dd",
".",
"get_sample_name",
"(",
"data",
")",
")",
"anti_file",
... | Retrieve target and antitarget BEDs from background CNN file. | [
"Retrieve",
"target",
"and",
"antitarget",
"BEDs",
"from",
"background",
"CNN",
"file",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L477-L488 |
223,280 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _add_seg_to_output | def _add_seg_to_output(out, data, enumerate_chroms=False):
"""Export outputs to 'seg' format compatible with IGV and GenePattern.
"""
out_file = "%s.seg" % os.path.splitext(out["cns"])[0]
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = ... | python | def _add_seg_to_output(out, data, enumerate_chroms=False):
"""Export outputs to 'seg' format compatible with IGV and GenePattern.
"""
out_file = "%s.seg" % os.path.splitext(out["cns"])[0]
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = ... | [
"def",
"_add_seg_to_output",
"(",
"out",
",",
"data",
",",
"enumerate_chroms",
"=",
"False",
")",
":",
"out_file",
"=",
"\"%s.seg\"",
"%",
"os",
".",
"path",
".",
"splitext",
"(",
"out",
"[",
"\"cns\"",
"]",
")",
"[",
"0",
"]",
"if",
"not",
"utils",
... | Export outputs to 'seg' format compatible with IGV and GenePattern. | [
"Export",
"outputs",
"to",
"seg",
"format",
"compatible",
"with",
"IGV",
"and",
"GenePattern",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L490-L503 |
223,281 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _add_variantcalls_to_output | def _add_variantcalls_to_output(out, data, items, is_somatic=False):
"""Call ploidy and convert into VCF and BED representations.
"""
call_file = "%s-call%s" % os.path.splitext(out["cns"])
if not utils.file_exists(call_file):
with file_transaction(data, call_file) as tx_call_file:
fi... | python | def _add_variantcalls_to_output(out, data, items, is_somatic=False):
"""Call ploidy and convert into VCF and BED representations.
"""
call_file = "%s-call%s" % os.path.splitext(out["cns"])
if not utils.file_exists(call_file):
with file_transaction(data, call_file) as tx_call_file:
fi... | [
"def",
"_add_variantcalls_to_output",
"(",
"out",
",",
"data",
",",
"items",
",",
"is_somatic",
"=",
"False",
")",
":",
"call_file",
"=",
"\"%s-call%s\"",
"%",
"os",
".",
"path",
".",
"splitext",
"(",
"out",
"[",
"\"cns\"",
"]",
")",
"if",
"not",
"utils"... | Call ploidy and convert into VCF and BED representations. | [
"Call",
"ploidy",
"and",
"convert",
"into",
"VCF",
"and",
"BED",
"representations",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L538-L576 |
223,282 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _add_segmetrics_to_output | def _add_segmetrics_to_output(out, data):
"""Add metrics for measuring reliability of CNV estimates.
"""
out_file = "%s-segmetrics.txt" % os.path.splitext(out["cns"])[0]
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = [os.path.join(os.p... | python | def _add_segmetrics_to_output(out, data):
"""Add metrics for measuring reliability of CNV estimates.
"""
out_file = "%s-segmetrics.txt" % os.path.splitext(out["cns"])[0]
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd = [os.path.join(os.p... | [
"def",
"_add_segmetrics_to_output",
"(",
"out",
",",
"data",
")",
":",
"out_file",
"=",
"\"%s-segmetrics.txt\"",
"%",
"os",
".",
"path",
".",
"splitext",
"(",
"out",
"[",
"\"cns\"",
"]",
")",
"[",
"0",
"]",
"if",
"not",
"utils",
".",
"file_exists",
"(",
... | Add metrics for measuring reliability of CNV estimates. | [
"Add",
"metrics",
"for",
"measuring",
"reliability",
"of",
"CNV",
"estimates",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L578-L594 |
223,283 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _add_gainloss_to_output | def _add_gainloss_to_output(out, data):
"""Add gainloss based on genes, helpful for identifying changes in smaller genes.
"""
out_file = "%s-gainloss.txt" % os.path.splitext(out["cns"])[0]
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd =... | python | def _add_gainloss_to_output(out, data):
"""Add gainloss based on genes, helpful for identifying changes in smaller genes.
"""
out_file = "%s-gainloss.txt" % os.path.splitext(out["cns"])[0]
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
cmd =... | [
"def",
"_add_gainloss_to_output",
"(",
"out",
",",
"data",
")",
":",
"out_file",
"=",
"\"%s-gainloss.txt\"",
"%",
"os",
".",
"path",
".",
"splitext",
"(",
"out",
"[",
"\"cns\"",
"]",
")",
"[",
"0",
"]",
"if",
"not",
"utils",
".",
"file_exists",
"(",
"o... | Add gainloss based on genes, helpful for identifying changes in smaller genes. | [
"Add",
"gainloss",
"based",
"on",
"genes",
"helpful",
"for",
"identifying",
"changes",
"in",
"smaller",
"genes",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L596-L609 |
223,284 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _add_coverage_bedgraph_to_output | def _add_coverage_bedgraph_to_output(out, data):
"""Add BedGraph representation of coverage to the output
"""
out_file = "%s.coverage.bedgraph" % os.path.splitext(out["cns"])[0]
if utils.file_exists(out_file):
out["bedgraph"] = out_file
return out
bam_file = dd.get_align_bam(data)
... | python | def _add_coverage_bedgraph_to_output(out, data):
"""Add BedGraph representation of coverage to the output
"""
out_file = "%s.coverage.bedgraph" % os.path.splitext(out["cns"])[0]
if utils.file_exists(out_file):
out["bedgraph"] = out_file
return out
bam_file = dd.get_align_bam(data)
... | [
"def",
"_add_coverage_bedgraph_to_output",
"(",
"out",
",",
"data",
")",
":",
"out_file",
"=",
"\"%s.coverage.bedgraph\"",
"%",
"os",
".",
"path",
".",
"splitext",
"(",
"out",
"[",
"\"cns\"",
"]",
")",
"[",
"0",
"]",
"if",
"utils",
".",
"file_exists",
"(",... | Add BedGraph representation of coverage to the output | [
"Add",
"BedGraph",
"representation",
"of",
"coverage",
"to",
"the",
"output"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L611-L631 |
223,285 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _add_plots_to_output | def _add_plots_to_output(out, data):
"""Add CNVkit plots summarizing called copy number values.
"""
out["plot"] = {}
diagram_plot = _add_diagram_plot(out, data)
if diagram_plot:
out["plot"]["diagram"] = diagram_plot
scatter = _add_scatter_plot(out, data)
if scatter:
out["plot... | python | def _add_plots_to_output(out, data):
"""Add CNVkit plots summarizing called copy number values.
"""
out["plot"] = {}
diagram_plot = _add_diagram_plot(out, data)
if diagram_plot:
out["plot"]["diagram"] = diagram_plot
scatter = _add_scatter_plot(out, data)
if scatter:
out["plot... | [
"def",
"_add_plots_to_output",
"(",
"out",
",",
"data",
")",
":",
"out",
"[",
"\"plot\"",
"]",
"=",
"{",
"}",
"diagram_plot",
"=",
"_add_diagram_plot",
"(",
"out",
",",
"data",
")",
"if",
"diagram_plot",
":",
"out",
"[",
"\"plot\"",
"]",
"[",
"\"diagram\... | Add CNVkit plots summarizing called copy number values. | [
"Add",
"CNVkit",
"plots",
"summarizing",
"called",
"copy",
"number",
"values",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L633-L646 |
223,286 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | _get_larger_chroms | def _get_larger_chroms(ref_file):
"""Retrieve larger chromosomes, avoiding the smaller ones for plotting.
"""
from scipy.cluster.vq import kmeans, vq
all_sizes = []
for c in ref.file_contigs(ref_file):
all_sizes.append(float(c.size))
all_sizes.sort()
if len(all_sizes) > 5:
# ... | python | def _get_larger_chroms(ref_file):
"""Retrieve larger chromosomes, avoiding the smaller ones for plotting.
"""
from scipy.cluster.vq import kmeans, vq
all_sizes = []
for c in ref.file_contigs(ref_file):
all_sizes.append(float(c.size))
all_sizes.sort()
if len(all_sizes) > 5:
# ... | [
"def",
"_get_larger_chroms",
"(",
"ref_file",
")",
":",
"from",
"scipy",
".",
"cluster",
".",
"vq",
"import",
"kmeans",
",",
"vq",
"all_sizes",
"=",
"[",
"]",
"for",
"c",
"in",
"ref",
".",
"file_contigs",
"(",
"ref_file",
")",
":",
"all_sizes",
".",
"a... | Retrieve larger chromosomes, avoiding the smaller ones for plotting. | [
"Retrieve",
"larger",
"chromosomes",
"avoiding",
"the",
"smaller",
"ones",
"for",
"plotting",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L648-L675 |
223,287 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | segment_from_cnr | def segment_from_cnr(cnr_file, data, out_base):
"""Provide segmentation on a cnr file, used in external PureCN integration.
"""
cns_file = _cnvkit_segment(cnr_file, dd.get_coverage_interval(data),
data, [data], out_file="%s.cns" % out_base, detailed=True)
out = _add_seg_to... | python | def segment_from_cnr(cnr_file, data, out_base):
"""Provide segmentation on a cnr file, used in external PureCN integration.
"""
cns_file = _cnvkit_segment(cnr_file, dd.get_coverage_interval(data),
data, [data], out_file="%s.cns" % out_base, detailed=True)
out = _add_seg_to... | [
"def",
"segment_from_cnr",
"(",
"cnr_file",
",",
"data",
",",
"out_base",
")",
":",
"cns_file",
"=",
"_cnvkit_segment",
"(",
"cnr_file",
",",
"dd",
".",
"get_coverage_interval",
"(",
"data",
")",
",",
"data",
",",
"[",
"data",
"]",
",",
"out_file",
"=",
... | Provide segmentation on a cnr file, used in external PureCN integration. | [
"Provide",
"segmentation",
"on",
"a",
"cnr",
"file",
"used",
"in",
"external",
"PureCN",
"integration",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L747-L753 |
223,288 | bcbio/bcbio-nextgen | bcbio/structural/cnvkit.py | export_theta | def export_theta(ckout, data):
"""Provide updated set of data with export information for TheTA2 input.
"""
cns_file = chromhacks.bed_to_standardonly(ckout["cns"], data, headers="chromosome")
cnr_file = chromhacks.bed_to_standardonly(ckout["cnr"], data, headers="chromosome")
out_file = "%s-theta.inp... | python | def export_theta(ckout, data):
"""Provide updated set of data with export information for TheTA2 input.
"""
cns_file = chromhacks.bed_to_standardonly(ckout["cns"], data, headers="chromosome")
cnr_file = chromhacks.bed_to_standardonly(ckout["cnr"], data, headers="chromosome")
out_file = "%s-theta.inp... | [
"def",
"export_theta",
"(",
"ckout",
",",
"data",
")",
":",
"cns_file",
"=",
"chromhacks",
".",
"bed_to_standardonly",
"(",
"ckout",
"[",
"\"cns\"",
"]",
",",
"data",
",",
"headers",
"=",
"\"chromosome\"",
")",
"cnr_file",
"=",
"chromhacks",
".",
"bed_to_sta... | Provide updated set of data with export information for TheTA2 input. | [
"Provide",
"updated",
"set",
"of",
"data",
"with",
"export",
"information",
"for",
"TheTA2",
"input",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/cnvkit.py#L757-L768 |
223,289 | bcbio/bcbio-nextgen | bcbio/rnaseq/stringtie.py | _stringtie_expression | def _stringtie_expression(bam, data, out_dir="."):
"""
only estimate expression the Stringtie, do not assemble new transcripts
"""
gtf_file = dd.get_gtf_file(data)
num_cores = dd.get_num_cores(data)
error_message = "The %s file for %s is missing. StringTie has an error."
stringtie = config_u... | python | def _stringtie_expression(bam, data, out_dir="."):
"""
only estimate expression the Stringtie, do not assemble new transcripts
"""
gtf_file = dd.get_gtf_file(data)
num_cores = dd.get_num_cores(data)
error_message = "The %s file for %s is missing. StringTie has an error."
stringtie = config_u... | [
"def",
"_stringtie_expression",
"(",
"bam",
",",
"data",
",",
"out_dir",
"=",
"\".\"",
")",
":",
"gtf_file",
"=",
"dd",
".",
"get_gtf_file",
"(",
"data",
")",
"num_cores",
"=",
"dd",
".",
"get_num_cores",
"(",
"data",
")",
"error_message",
"=",
"\"The %s f... | only estimate expression the Stringtie, do not assemble new transcripts | [
"only",
"estimate",
"expression",
"the",
"Stringtie",
"do",
"not",
"assemble",
"new",
"transcripts"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/rnaseq/stringtie.py#L21-L43 |
223,290 | bcbio/bcbio-nextgen | bcbio/rnaseq/stringtie.py | run_stringtie_expression | def run_stringtie_expression(data):
"""
estimate expression from Stringtie, using the bcbio datadict
does not do transcriptome assembly
"""
bam = dd.get_work_bam(data)
sample_name = dd.get_sample_name(data)
out_dir = os.path.join("stringtie", sample_name)
isoform_fpkm = os.path.join(out_... | python | def run_stringtie_expression(data):
"""
estimate expression from Stringtie, using the bcbio datadict
does not do transcriptome assembly
"""
bam = dd.get_work_bam(data)
sample_name = dd.get_sample_name(data)
out_dir = os.path.join("stringtie", sample_name)
isoform_fpkm = os.path.join(out_... | [
"def",
"run_stringtie_expression",
"(",
"data",
")",
":",
"bam",
"=",
"dd",
".",
"get_work_bam",
"(",
"data",
")",
"sample_name",
"=",
"dd",
".",
"get_sample_name",
"(",
"data",
")",
"out_dir",
"=",
"os",
".",
"path",
".",
"join",
"(",
"\"stringtie\"",
"... | estimate expression from Stringtie, using the bcbio datadict
does not do transcriptome assembly | [
"estimate",
"expression",
"from",
"Stringtie",
"using",
"the",
"bcbio",
"datadict",
"does",
"not",
"do",
"transcriptome",
"assembly"
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/rnaseq/stringtie.py#L45-L76 |
223,291 | bcbio/bcbio-nextgen | bcbio/upload/filesystem.py | update_file | def update_file(finfo, sample_info, config, pass_uptodate=False):
"""Update the file in local filesystem storage.
"""
storage_dir = utils.safe_makedir(_get_storage_dir(finfo, config))
if finfo.get("type") == "directory":
return _copy_finfo_directory(finfo, storage_dir)
else:
return _... | python | def update_file(finfo, sample_info, config, pass_uptodate=False):
"""Update the file in local filesystem storage.
"""
storage_dir = utils.safe_makedir(_get_storage_dir(finfo, config))
if finfo.get("type") == "directory":
return _copy_finfo_directory(finfo, storage_dir)
else:
return _... | [
"def",
"update_file",
"(",
"finfo",
",",
"sample_info",
",",
"config",
",",
"pass_uptodate",
"=",
"False",
")",
":",
"storage_dir",
"=",
"utils",
".",
"safe_makedir",
"(",
"_get_storage_dir",
"(",
"finfo",
",",
"config",
")",
")",
"if",
"finfo",
".",
"get"... | Update the file in local filesystem storage. | [
"Update",
"the",
"file",
"in",
"local",
"filesystem",
"storage",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/upload/filesystem.py#L10-L17 |
223,292 | bcbio/bcbio-nextgen | bcbio/upload/filesystem.py | _copy_finfo | def _copy_finfo(finfo, storage_dir, pass_uptodate=False):
"""Copy a file into the output storage directory.
"""
out_file = _get_file_upload_path(finfo, storage_dir)
if not shared.up_to_date(out_file, finfo):
logger.info("Storing in local filesystem: %s" % out_file)
shutil.copy(finfo["pat... | python | def _copy_finfo(finfo, storage_dir, pass_uptodate=False):
"""Copy a file into the output storage directory.
"""
out_file = _get_file_upload_path(finfo, storage_dir)
if not shared.up_to_date(out_file, finfo):
logger.info("Storing in local filesystem: %s" % out_file)
shutil.copy(finfo["pat... | [
"def",
"_copy_finfo",
"(",
"finfo",
",",
"storage_dir",
",",
"pass_uptodate",
"=",
"False",
")",
":",
"out_file",
"=",
"_get_file_upload_path",
"(",
"finfo",
",",
"storage_dir",
")",
"if",
"not",
"shared",
".",
"up_to_date",
"(",
"out_file",
",",
"finfo",
")... | Copy a file into the output storage directory. | [
"Copy",
"a",
"file",
"into",
"the",
"output",
"storage",
"directory",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/upload/filesystem.py#L63-L72 |
223,293 | bcbio/bcbio-nextgen | bcbio/upload/filesystem.py | _copy_finfo_directory | def _copy_finfo_directory(finfo, out_dir):
"""Copy a directory into the final output directory.
"""
out_dir = _get_dir_upload_path(finfo, out_dir)
if not shared.up_to_date(out_dir, finfo):
logger.info("Storing directory in local filesystem: %s" % out_dir)
if os.path.exists(out_dir):
... | python | def _copy_finfo_directory(finfo, out_dir):
"""Copy a directory into the final output directory.
"""
out_dir = _get_dir_upload_path(finfo, out_dir)
if not shared.up_to_date(out_dir, finfo):
logger.info("Storing directory in local filesystem: %s" % out_dir)
if os.path.exists(out_dir):
... | [
"def",
"_copy_finfo_directory",
"(",
"finfo",
",",
"out_dir",
")",
":",
"out_dir",
"=",
"_get_dir_upload_path",
"(",
"finfo",
",",
"out_dir",
")",
"if",
"not",
"shared",
".",
"up_to_date",
"(",
"out_dir",
",",
"finfo",
")",
":",
"logger",
".",
"info",
"(",... | Copy a directory into the final output directory. | [
"Copy",
"a",
"directory",
"into",
"the",
"final",
"output",
"directory",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/upload/filesystem.py#L74-L87 |
223,294 | bcbio/bcbio-nextgen | bcbio/variation/naming.py | handle_synonyms | def handle_synonyms(in_file, ref_file, genome_build, work_dir, data):
"""Potentially handle remapping synonymous chromosome names between builds.
Handles tab delimited file formats like BED and VCF where the contig
is in the first column.
"""
if genome_build in GMAP and ref_file:
mappings =... | python | def handle_synonyms(in_file, ref_file, genome_build, work_dir, data):
"""Potentially handle remapping synonymous chromosome names between builds.
Handles tab delimited file formats like BED and VCF where the contig
is in the first column.
"""
if genome_build in GMAP and ref_file:
mappings =... | [
"def",
"handle_synonyms",
"(",
"in_file",
",",
"ref_file",
",",
"genome_build",
",",
"work_dir",
",",
"data",
")",
":",
"if",
"genome_build",
"in",
"GMAP",
"and",
"ref_file",
":",
"mappings",
"=",
"GMAP",
"[",
"genome_build",
"]",
"contigs",
"=",
"set",
"(... | Potentially handle remapping synonymous chromosome names between builds.
Handles tab delimited file formats like BED and VCF where the contig
is in the first column. | [
"Potentially",
"handle",
"remapping",
"synonymous",
"chromosome",
"names",
"between",
"builds",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/variation/naming.py#L101-L124 |
223,295 | bcbio/bcbio-nextgen | bcbio/variation/naming.py | _write_newname_file | def _write_newname_file(in_file, out_file, mappings):
"""Re-write an input file with contigs matching the correct reference.
"""
with utils.open_gzipsafe(in_file) as in_handle:
with open(out_file, "w") as out_handle:
for line in in_handle:
if line.startswith("#"):
... | python | def _write_newname_file(in_file, out_file, mappings):
"""Re-write an input file with contigs matching the correct reference.
"""
with utils.open_gzipsafe(in_file) as in_handle:
with open(out_file, "w") as out_handle:
for line in in_handle:
if line.startswith("#"):
... | [
"def",
"_write_newname_file",
"(",
"in_file",
",",
"out_file",
",",
"mappings",
")",
":",
"with",
"utils",
".",
"open_gzipsafe",
"(",
"in_file",
")",
"as",
"in_handle",
":",
"with",
"open",
"(",
"out_file",
",",
"\"w\"",
")",
"as",
"out_handle",
":",
"for"... | Re-write an input file with contigs matching the correct reference. | [
"Re",
"-",
"write",
"an",
"input",
"file",
"with",
"contigs",
"matching",
"the",
"correct",
"reference",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/variation/naming.py#L126-L139 |
223,296 | bcbio/bcbio-nextgen | bcbio/variation/naming.py | _matches_contigs | def _matches_contigs(in_file, contigs, checked_file):
"""Check if the contigs in the input file match the defined contigs in the reference genome.
"""
tocheck_contigs = 2
if utils.file_exists(checked_file):
with open(checked_file) as in_handle:
return in_handle.read().strip() == "mat... | python | def _matches_contigs(in_file, contigs, checked_file):
"""Check if the contigs in the input file match the defined contigs in the reference genome.
"""
tocheck_contigs = 2
if utils.file_exists(checked_file):
with open(checked_file) as in_handle:
return in_handle.read().strip() == "mat... | [
"def",
"_matches_contigs",
"(",
"in_file",
",",
"contigs",
",",
"checked_file",
")",
":",
"tocheck_contigs",
"=",
"2",
"if",
"utils",
".",
"file_exists",
"(",
"checked_file",
")",
":",
"with",
"open",
"(",
"checked_file",
")",
"as",
"in_handle",
":",
"return... | Check if the contigs in the input file match the defined contigs in the reference genome. | [
"Check",
"if",
"the",
"contigs",
"in",
"the",
"input",
"file",
"match",
"the",
"defined",
"contigs",
"in",
"the",
"reference",
"genome",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/variation/naming.py#L141-L162 |
223,297 | bcbio/bcbio-nextgen | bcbio/ngsalign/novoalign.py | align_bam | def align_bam(in_bam, ref_file, names, align_dir, data):
"""Perform realignment of input BAM file; uses unix pipes for avoid IO.
"""
config = data["config"]
out_file = os.path.join(align_dir, "{0}-sort.bam".format(names["lane"]))
novoalign = config_utils.get_program("novoalign", config)
samtools... | python | def align_bam(in_bam, ref_file, names, align_dir, data):
"""Perform realignment of input BAM file; uses unix pipes for avoid IO.
"""
config = data["config"]
out_file = os.path.join(align_dir, "{0}-sort.bam".format(names["lane"]))
novoalign = config_utils.get_program("novoalign", config)
samtools... | [
"def",
"align_bam",
"(",
"in_bam",
",",
"ref_file",
",",
"names",
",",
"align_dir",
",",
"data",
")",
":",
"config",
"=",
"data",
"[",
"\"config\"",
"]",
"out_file",
"=",
"os",
".",
"path",
".",
"join",
"(",
"align_dir",
",",
"\"{0}-sort.bam\"",
".",
"... | Perform realignment of input BAM file; uses unix pipes for avoid IO. | [
"Perform",
"realignment",
"of",
"input",
"BAM",
"file",
";",
"uses",
"unix",
"pipes",
"for",
"avoid",
"IO",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/ngsalign/novoalign.py#L29-L54 |
223,298 | bcbio/bcbio-nextgen | bcbio/ngsalign/novoalign.py | _novoalign_args_from_config | def _novoalign_args_from_config(config, need_quality=True):
"""Select novoalign options based on configuration parameters.
"""
if need_quality:
qual_format = config["algorithm"].get("quality_format", "").lower()
qual_flags = ["-F", "ILMFQ" if qual_format == "illumina" else "STDFQ"]
else:... | python | def _novoalign_args_from_config(config, need_quality=True):
"""Select novoalign options based on configuration parameters.
"""
if need_quality:
qual_format = config["algorithm"].get("quality_format", "").lower()
qual_flags = ["-F", "ILMFQ" if qual_format == "illumina" else "STDFQ"]
else:... | [
"def",
"_novoalign_args_from_config",
"(",
"config",
",",
"need_quality",
"=",
"True",
")",
":",
"if",
"need_quality",
":",
"qual_format",
"=",
"config",
"[",
"\"algorithm\"",
"]",
".",
"get",
"(",
"\"quality_format\"",
",",
"\"\"",
")",
".",
"lower",
"(",
"... | Select novoalign options based on configuration parameters. | [
"Select",
"novoalign",
"options",
"based",
"on",
"configuration",
"parameters",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/ngsalign/novoalign.py#L92-L115 |
223,299 | bcbio/bcbio-nextgen | bcbio/ngsalign/novoalign.py | remap_index_fn | def remap_index_fn(ref_file):
"""Map sequence references to equivalent novoalign indexes.
"""
checks = [os.path.splitext(ref_file)[0].replace("/seq/", "/novoalign/"),
os.path.splitext(ref_file)[0] + ".ndx",
ref_file + ".bs.ndx",
ref_file + ".ndx"]
for check in c... | python | def remap_index_fn(ref_file):
"""Map sequence references to equivalent novoalign indexes.
"""
checks = [os.path.splitext(ref_file)[0].replace("/seq/", "/novoalign/"),
os.path.splitext(ref_file)[0] + ".ndx",
ref_file + ".bs.ndx",
ref_file + ".ndx"]
for check in c... | [
"def",
"remap_index_fn",
"(",
"ref_file",
")",
":",
"checks",
"=",
"[",
"os",
".",
"path",
".",
"splitext",
"(",
"ref_file",
")",
"[",
"0",
"]",
".",
"replace",
"(",
"\"/seq/\"",
",",
"\"/novoalign/\"",
")",
",",
"os",
".",
"path",
".",
"splitext",
"... | Map sequence references to equivalent novoalign indexes. | [
"Map",
"sequence",
"references",
"to",
"equivalent",
"novoalign",
"indexes",
"."
] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/ngsalign/novoalign.py#L138-L148 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.