def bed_to_interval(orig_bed, bam_file):
"""Add header and format BED bait and target files for Picard if necessary.
"""
with open(orig_bed) as in_handle:
line = in_handle.readline()
if line.startswith("@"):
yield orig_bed
else:
with pysam.Samfile(bam_file, "rb") as bam_handle:
header = bam_handle.text
with tmpfile(dir=os.path.dirname(orig_bed),
prefix="picardbed") as tmp_bed:
with open(tmp_bed, "w") as out_handle:
out_handle.write(header)
with open(orig_bed) as in_handle:
for i, line in enumerate(in_handle):
parts = line.rstrip().split("\t")
if len(parts) == 4:
chrom, start, end, name = parts
strand = "+"
elif len(parts) >= 3:
chrom, start, end = parts[:3]
strand = "+"
name = "r%s" % i
out = [chrom, start, end, strand, name]
out_handle.write("\t".join(out) + "\n")
yield tmp_bed
def _longest_frame(rec, work_dir):
"""Find the longest translatable frame using EMBOSS sixpack.
"""
lengths = []
with utils.tmpfile(prefix="insix", dir=work_dir) as in_file:
with utils.tmpfile(prefix="outsix", dir=work_dir) as out_file:
with open(in_file, "w") as out_handle:
SeqIO.write([rec], out_handle, "fasta")
cl = ["sixpack", "-sequence", in_file, "-outseq", out_file,
"-outfile", "/dev/null"]
with open("/dev/null", "w") as out:
subprocess.check_call(cl, stderr=out)
with open(out_file) as in_handle:
for rec in SeqIO.parse(in_handle, "fasta"):
lengths.append(len(rec.seq))
return max(lengths) * 3
def merge_bam_files(bam_files, work_dir, config, out_file=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Uses bamtools for merging, which handles large numbers of input BAMs.
"""
if len(bam_files) == 1:
return bam_files[0]
else:
if out_file is None:
out_file = os.path.join(work_dir,
os.path.basename(sorted(bam_files)[0]))
if not utils.file_exists(out_file) or not utils.file_exists(out_file +
".bai"):
bamtools = config_utils.get_program("bamtools", config)
resources = config_utils.get_resources("bamtools", config)
max_mem = resources.get("memory", "2048")
with file_transaction(out_file) as tx_out_file:
with utils.tmpfile(dir=work_dir,
prefix="bammergelist") as bam_file_list:
with open(bam_file_list, "w") as out_handle:
for f in sorted(bam_files):
out_handle.write("%s\n" % f)
cmd = ("{bamtools} merge -list {bam_file_list} | "
"{bamtools} sort -mem {max_mem} -out {tx_out_file}")
do.run(cmd.format(**locals()), "Merge bam files", None)
for b in bam_files:
utils.save_diskspace(b, "BAM merged to %s" % out_file, config)
picard = broad.runner_from_config(config)
picard.run_fn("picard_index", out_file)
return out_file
def coverage(data):
bed_file = dd.get_coverage_experimental(data)
if not bed_file:
return data
work_dir = os.path.join(dd.get_work_dir(data), "report", "coverage")
with chdir(work_dir):
in_bam = data['work_bam']
sample = os.path.splitext(os.path.basename(in_bam))[0]
logger.debug("doing coverage for %s" % sample)
region_bed = pybedtools.BedTool(bed_file)
parse_file = os.path.join(sample + "_coverage.bed")
parse_total_file = os.path.join(sample + "_cov_total.tsv")
if not file_exists(parse_file):
total_cov = cov_class(0, None, sample)
bam_api = pysam.AlignmentFile(in_bam)
with file_transaction(parse_file) as out_tx:
with open(out_tx, 'w') as out_handle:
print >>out_handle, "#chrom\tstart\tend\tregion\treads\tstrand\tsize\tsample\tmean\tsdt\tq10\tq20\tq4\tq50"
with tmpfile() as tx_tmp_file:
# tx_tmp_file = "tmpintersect"
for line in region_bed:
chrom = line.chrom
start = max(line.start, 0)
end = line.end
region_file = pybedtools.BedTool(str(line), from_string=True).saveas().fn
coords = "%s:%s-%s" % (chrom, start, end)
cmd = ("samtools view -b {in_bam} {coords} | "
"bedtools coverage -a {region_file} -b - -hist > {tx_tmp_file}")
_silence_run(cmd.format(**locals()))
total_cov = _get_exome_coverage_stats(os.path.abspath(tx_tmp_file), sample, out_tx, total_cov)
total_cov.write_coverage(parse_total_file)
data['coverage'] = os.path.abspath(parse_file)
return data
def bed_to_interval(orig_bed, bam_file):
"""Add header and format BED bait and target files for Picard if necessary.
"""
with open(orig_bed) as in_handle:
line = in_handle.readline()
if line.startswith("@"):
yield orig_bed
else:
with pysam.Samfile(bam_file, "rb") as bam_handle:
header = bam_handle.text
with tmpfile(dir=os.path.dirname(orig_bed), prefix="picardbed") as tmp_bed:
with open(tmp_bed, "w") as out_handle:
out_handle.write(header)
with open(orig_bed) as in_handle:
for i, line in enumerate(in_handle):
parts = line.rstrip().split("\t")
if len(parts) == 4:
chrom, start, end, name = parts
strand = "+"
elif len(parts) >= 3:
chrom, start, end = parts[:3]
strand = "+"
name = "r%s" % i
out = [chrom, start, end, strand, name]
out_handle.write("\t".join(out) + "\n")
yield tmp_bed
def merge_bam_files(bam_files, work_dir, config, out_file=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Uses bamtools for merging, which handles large numbers of input BAMs.
"""
if len(bam_files) == 1:
return bam_files[0]
else:
if out_file is None:
out_file = os.path.join(work_dir, os.path.basename(sorted(bam_files)[0]))
if not utils.file_exists(out_file) or not utils.file_exists(out_file + ".bai"):
bamtools = config_utils.get_program("bamtools", config)
samtools = config_utils.get_program("samtools", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
max_mem = resources.get("memory", "1G")
with file_transaction(out_file) as tx_out_file:
tx_out_prefix = os.path.splitext(tx_out_file)[0]
with utils.tmpfile(dir=work_dir, prefix="bammergelist") as bam_file_list:
bam_file_list = "%s.list" % os.path.splitext(out_file)[0]
with open(bam_file_list, "w") as out_handle:
for f in sorted(bam_files):
out_handle.write("%s\n" % f)
cmd = (
"{bamtools} merge -list {bam_file_list} | "
"{samtools} sort -@ {num_cores} -m {max_mem} - {tx_out_prefix}"
)
do.run(cmd.format(**locals()), "Merge bam files", None)
for b in bam_files:
utils.save_diskspace(b, "BAM merged to %s" % out_file, config)
picard = broad.runner_from_config(config)
picard.run_fn("picard_index", out_file)
return out_file
def _longest_frame(rec, work_dir):
"""Find the longest translatable frame using EMBOSS sixpack.
"""
lengths = []
with utils.tmpfile(prefix="insix", dir=work_dir) as in_file:
with utils.tmpfile(prefix="outsix", dir=work_dir) as out_file:
with open(in_file, "w") as out_handle:
SeqIO.write([rec], out_handle, "fasta")
cl = [
"sixpack", "-sequence", in_file, "-outseq", out_file,
"-outfile", "/dev/null"
]
with open("/dev/null", "w") as out:
subprocess.check_call(cl, stderr=out)
with open(out_file) as in_handle:
for rec in SeqIO.parse(in_handle, "fasta"):
lengths.append(len(rec.seq))
return max(lengths) * 3
def _clean_regions(items, region):
"""Intersect region with target file if it exists"""
variant_regions = bedutils.population_variant_regions(items, merged=True)
with utils.tmpfile() as tx_out_file:
target = subset_variant_regions(variant_regions, region, tx_out_file, items)
if target:
if isinstance(target, six.string_types) and os.path.isfile(target):
target = _load_regions(target)
else:
target = [target]
return target
def _clean_regions(items, region):
"""Intersect region with target file if it exists"""
variant_regions = bedutils.merge_overlaps(bedutils.population_variant_regions(items), items[0])
with utils.tmpfile() as tx_out_file:
target = subset_variant_regions(variant_regions, region, tx_out_file, items)
if target:
if isinstance(target, basestring) and os.path.isfile(target):
target = _load_regions(target)
else:
target = [target]
return target
def _clean_regions(items, region):
"""Intersect region with target file if it exists"""
variant_regions = bedutils.population_variant_regions(items, merged=True)
with utils.tmpfile() as tx_out_file:
target = subset_variant_regions(variant_regions, region, tx_out_file,
items)
if target:
if isinstance(target, six.string_types) and os.path.isfile(target):
target = _load_regions(target)
else:
target = [target]
return target
def _clean_regions(items, region):
"""Intersect region with target file if it exists"""
config = items[0]["config"]
variant_regions = bedutils.merge_overlaps(utils.get_in(config, ("algorithm", "varaint_regions")), items[0])
with utils.tmpfile() as tx_out_file:
target = subset_variant_regions(variant_regions, region, tx_out_file, items)
if target:
if isinstance(target, basestring) and os.path.isfile(target):
target = _load_regions(target)
else:
target = [target]
return target
def merge_bam_files(bam_files, work_dir, config, out_file=None, batch=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Checks system open file limit and merges in batches if necessary to avoid
file handle limits.
"""
if len(bam_files) == 1:
return bam_files[0]
else:
if out_file is None:
out_file = os.path.join(work_dir,
os.path.basename(sorted(bam_files)[0]))
if batch is not None:
base, ext = os.path.splitext(out_file)
out_file = "%s-b%s%s" % (base, batch, ext)
if not utils.file_exists(out_file) or not utils.file_exists(out_file +
".bai"):
bamtools = config_utils.get_program("bamtools", config)
samtools = config_utils.get_program("samtools", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
max_mem = resources.get("memory", "1G")
batch_size = system.open_file_limit() - 100
if len(bam_files) > batch_size:
bam_files = [
merge_bam_files(xs, work_dir, config, out_file, i)
for i, xs in enumerate(
utils.partition_all(batch_size, bam_files))
]
with utils.curdir_tmpdir() as tmpdir:
with utils.chdir(tmpdir):
merge_cl = _bamtools_merge(bam_files)
with file_transaction(out_file) as tx_out_file:
tx_out_prefix = os.path.splitext(tx_out_file)[0]
with utils.tmpfile(
dir=work_dir,
prefix="bammergelist") as bam_file_list:
bam_file_list = "%s.list" % os.path.splitext(
out_file)[0]
with open(bam_file_list, "w") as out_handle:
for f in sorted(bam_files):
out_handle.write("%s\n" % f)
cmd = (
merge_cl + " | "
"{samtools} sort -@ {num_cores} -m {max_mem} - {tx_out_prefix}"
)
do.run(cmd.format(**locals()), "Merge bam files",
None)
for b in bam_files:
utils.save_diskspace(b, "BAM merged to %s" % out_file, config)
bam.index(out_file, config)
return out_file
def coverage(data):
AVERAGE_REGION_STRING_LENGTH = 100
bed_file = dd.get_coverage_experimental(data)
if not bed_file:
return data
work_dir = os.path.join(dd.get_work_dir(data), "report", "coverage")
batch_size = max_command_length() / AVERAGE_REGION_STRING_LENGTH
with chdir(work_dir):
in_bam = data['work_bam']
sample = dd.get_sample_name(data)
logger.debug("doing coverage for %s" % sample)
region_bed = pybedtools.BedTool(bed_file)
parse_file = os.path.join(sample + "_coverage.bed")
parse_total_file = os.path.join(sample + "_cov_total.tsv")
if not file_exists(parse_file):
total_cov = cov_class(0, None, sample)
with file_transaction(parse_file) as out_tx:
with open(out_tx, 'w') as out_handle:
HEADER = ["#chrom", "start", "end", "region", "reads",
"strand", "size", "sample", "mean", "sd", "cutoff10",
"cutoff20", "cutoff4", "cutoff50"]
out_handle.write("\t".join(HEADER) + "\n")
with tmpfile() as tx_tmp_file:
lcount = 0
for chunk in robust_partition_all(batch_size, region_bed):
coord_batch = []
line_batch = ""
for line in chunk:
lcount += 1
chrom = line.chrom
start = max(line.start, 0)
end = line.end
coords = "%s:%s-%s" % (chrom, start, end)
coord_batch.append(coords)
line_batch += str(line)
if not coord_batch:
continue
region_file = pybedtools.BedTool(line_batch,
from_string=True).saveas().fn
coord_string = " ".join(coord_batch)
cmd = ("samtools view -b {in_bam} {coord_string} | "
"bedtools coverage -a {region_file} -b - "
"-hist > {tx_tmp_file}")
_silence_run(cmd.format(**locals()))
total_cov = _get_exome_coverage_stats(os.path.abspath(tx_tmp_file), sample, out_tx, total_cov)
logger.debug("Processed %d regions." % lcount)
total_cov.write_coverage(parse_total_file)
data['coverage'] = os.path.abspath(parse_file)
return data
def _clean_regions(items, region):
"""Intersect region with target file if it exists"""
config = items[0]["config"]
variant_regions = bedutils.merge_overlaps(
utils.get_in(config, ("algorithm", "varaint_regions")), items[0])
with utils.tmpfile() as tx_out_file:
target = subset_variant_regions(variant_regions, region, tx_out_file,
items)
if target:
if isinstance(target, basestring) and os.path.isfile(target):
target = _load_regions(target)
else:
target = [target]
return target
def bcbb_demultiplex(input_file, barcodes, tmp_dir, config):
ext = ".fastq"
base_name = os.path.splitext(input_file)[0]
metrics_file = "%s_bc.metrics" % base_name
out_base = "%s_--b--_--r--%s" % (base_name, ext)
if not os.path.exists(metrics_file):
with tmpfile(dir=tmp_dir, prefix="bc") as bc_file:
_write_bcbb_bcfile(barcodes, bc_file)
cl = [config["program"]["barcode"], bc_file,
out_base, input_file,
"--mismatch=%s" % (config["algorithm"]["barcode_mismatch"]),
"--metrics=%s" % metrics_file]
subprocess.check_call(cl)
return [f for f in glob.glob("%s_*_[1-9]%s" % (base_name, ext))
if f.find("unmatched") == -1]
def assemble_clusters(in_file, wcd_out, config):
"""Provide assembled FASTA records based on wcd clustering.
"""
rec_find = FastaNumToRec(in_file)
with open(wcd_out) as wcd_handle:
for line in wcd_handle:
nums = [int(n) for n in line.rstrip()[:-1].split()]
if len(nums) == 1:
yield rec_find[nums[0]]
else:
with utils.tmpfile(prefix="incap3", dir=config["dir"]["work"]) as input_file:
with open(input_file, "w") as input_handle:
SeqIO.write((rec_find.shortname_rec(n) for n in nums),
input_handle, "fasta")
yield cap3_assemble(input_file, config)
for fname in glob.glob("%s.cap.*" % input_file):
os.remove(fname)
def sabre_demultiplex(input_file, barcodes, tmp_dir, config):
"""Do barcode de-multiplexing using sabre.
Sabre only appears to trim off the 5' side of the read so
currently not supported.
"""
raise NotImplementedError
with tmpfile(dir=tmp_dir, prefix="sabrebc") as bc_file:
out_files, unmatched_file = _write_sabre_bcfile(barcodes, input_file, bc_file)
if not os.path.exists(unmatched_file) and not os.path.exists(out_files[0]):
cl = [config["program"]["barcode"], "se",
"-m", str(config["algorithm"]["barcode_mismatch"]),
"-f", input_file,
"-b", bc_file,
"-u", unmatched_file]
subprocess.check_call(cl)
return out_files
def cap3_assemble(in_file, config):
"""Assemble a FASTA file of clustered sequences with CAP3.
"""
with utils.tmpfile(prefix="outcap3", dir=config["dir"]["work"]) as cap3_file:
with open(cap3_file, "w") as out_handle:
cl = ["cap3", in_file]
subprocess.check_call(cl, stdout=out_handle)
seqs = []
with open(cap3_file) as in_handle:
for line in in_handle:
if line.startswith("consensus"):
seqs.append(line.rstrip().split()[-1])
with open(in_file) as in_handle:
names = []
for rec in SeqIO.parse(in_handle, "fasta"):
names.append(rec.id)
return _make_seqrec("-".join(names), "".join(seqs).replace("-", ""))
def assemble_clusters(in_file, wcd_out, config):
"""Provide assembled FASTA records based on wcd clustering.
"""
rec_find = FastaNumToRec(in_file)
with open(wcd_out) as wcd_handle:
for line in wcd_handle:
nums = [int(n) for n in line.rstrip()[:-1].split()]
if len(nums) == 1:
yield rec_find[nums[0]]
else:
with utils.tmpfile(prefix="incap3",
dir=config["dir"]["work"]) as input_file:
with open(input_file, "w") as input_handle:
SeqIO.write((rec_find.shortname_rec(n) for n in nums),
input_handle, "fasta")
yield cap3_assemble(input_file, config)
for fname in glob.glob("%s.cap.*" % input_file):
os.remove(fname)
def cap3_assemble(in_file, config):
"""Assemble a FASTA file of clustered sequences with CAP3.
"""
with utils.tmpfile(prefix="outcap3",
dir=config["dir"]["work"]) as cap3_file:
with open(cap3_file, "w") as out_handle:
cl = ["cap3", in_file]
subprocess.check_call(cl, stdout=out_handle)
seqs = []
with open(cap3_file) as in_handle:
for line in in_handle:
if line.startswith("consensus"):
seqs.append(line.rstrip().split()[-1])
with open(in_file) as in_handle:
names = []
for rec in SeqIO.parse(in_handle, "fasta"):
names.append(rec.id)
return _make_seqrec("-".join(names), "".join(seqs).replace("-", ""))
def bcbb_demultiplex(input_file, barcodes, tmp_dir, config):
ext = ".fastq"
base_name = os.path.splitext(input_file)[0]
metrics_file = "%s_bc.metrics" % base_name
out_base = "%s_--b--_--r--%s" % (base_name, ext)
if not os.path.exists(metrics_file):
with tmpfile(dir=tmp_dir, prefix="bc") as bc_file:
_write_bcbb_bcfile(barcodes, bc_file)
cl = [
config["program"]["barcode"], bc_file, out_base, input_file,
"--mismatch=%s" % (config["algorithm"]["barcode_mismatch"]),
"--metrics=%s" % metrics_file
]
subprocess.check_call(cl)
return [
f for f in glob.glob("%s_*_[1-9]%s" % (base_name, ext))
if f.find("unmatched") == -1
]
def merge_bam_files(bam_files, work_dir, config, out_file=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Uses bamtools for merging, which handles large numbers of input BAMs.
"""
if len(bam_files) == 1:
return bam_files[0]
else:
if out_file is None:
out_file = os.path.join(work_dir,
os.path.basename(sorted(bam_files)[0]))
if not utils.file_exists(out_file) or not utils.file_exists(out_file +
".bai"):
bamtools = config_utils.get_program("bamtools", config)
samtools = config_utils.get_program("samtools", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
max_mem = resources.get("memory", "1G")
if len(bam_files) > system.open_file_limit():
raise IOError(
"More files to merge (%s) then available open file descriptors (%s)\n"
"See documentation on tips for changing file limits:\n"
"https://bcbio-nextgen.readthedocs.org/en/latest/contents/"
"parallel.html#tuning-systems-for-scale" %
(len(bam_files), system.open_file_limit()))
with file_transaction(out_file) as tx_out_file:
tx_out_prefix = os.path.splitext(tx_out_file)[0]
with utils.tmpfile(dir=work_dir,
prefix="bammergelist") as bam_file_list:
bam_file_list = "%s.list" % os.path.splitext(out_file)[0]
with open(bam_file_list, "w") as out_handle:
for f in sorted(bam_files):
out_handle.write("%s\n" % f)
cmd = (
"{bamtools} merge -list {bam_file_list} | "
"{samtools} sort -@ {num_cores} -m {max_mem} - {tx_out_prefix}"
)
do.run(cmd.format(**locals()), "Merge bam files", None)
for b in bam_files:
utils.save_diskspace(b, "BAM merged to %s" % out_file, config)
picard = broad.runner_from_config(config)
picard.run_fn("picard_index", out_file)
return out_file
def sabre_demultiplex(input_file, barcodes, tmp_dir, config):
"""Do barcode de-multiplexing using sabre.
Sabre only appears to trim off the 5' side of the read so
currently not supported.
"""
raise NotImplementedError
with tmpfile(dir=tmp_dir, prefix="sabrebc") as bc_file:
out_files, unmatched_file = _write_sabre_bcfile(
barcodes, input_file, bc_file)
if not os.path.exists(unmatched_file) and not os.path.exists(
out_files[0]):
cl = [
config["program"]["barcode"], "se", "-m",
str(config["algorithm"]["barcode_mismatch"]), "-f", input_file,
"-b", bc_file, "-u", unmatched_file
]
subprocess.check_call(cl)
return out_files
def merge_bam_files(bam_files, work_dir, config, out_file=None, batch=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Checks system open file limit and merges in batches if necessary to avoid
file handle limits.
"""
if len(bam_files) == 1:
return bam_files[0]
else:
if out_file is None:
out_file = os.path.join(work_dir, os.path.basename(sorted(bam_files)[0]))
if batch is not None:
base, ext = os.path.splitext(out_file)
out_file = "%s-b%s%s" % (base, batch, ext)
if not utils.file_exists(out_file) or not utils.file_exists(out_file + ".bai"):
bamtools = config_utils.get_program("bamtools", config)
samtools = config_utils.get_program("samtools", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
max_mem = resources.get("memory", "1G")
batch_size = system.open_file_limit() - 100
if len(bam_files) > batch_size:
bam_files = [merge_bam_files(xs, work_dir, config, out_file, i)
for i, xs in enumerate(utils.partition_all(batch_size, bam_files))]
with utils.curdir_tmpdir() as tmpdir:
with utils.chdir(tmpdir):
merge_cl = _bamtools_merge(bam_files)
with file_transaction(out_file) as tx_out_file:
tx_out_prefix = os.path.splitext(tx_out_file)[0]
with utils.tmpfile(dir=work_dir, prefix="bammergelist") as bam_file_list:
bam_file_list = "%s.list" % os.path.splitext(out_file)[0]
with open(bam_file_list, "w") as out_handle:
for f in sorted(bam_files):
out_handle.write("%s\n" % f)
cmd = (merge_cl + " | "
"{samtools} sort -@ {num_cores} -m {max_mem} - {tx_out_prefix}")
do.run(cmd.format(**locals()), "Merge bam files", None)
for b in bam_files:
utils.save_diskspace(b, "BAM merged to %s" % out_file, config)
bam.index(out_file, config)
return out_file
def bed_to_interval(orig_bed, bam_file):
"""Add header and format BED bait and target files for Picard if necessary.
"""
with open(orig_bed) as in_handle:
line = in_handle.readline()
if line.startswith("@"):
yield orig_bed
else:
with pysam.Samfile(bam_file, "rb") as bam_handle:
header = bam_handle.text
with tmpfile(dir=os.path.dirname(orig_bed), prefix="picardbed") as tmp_bed:
with open(tmp_bed, "w") as out_handle:
out_handle.write(header)
with open(orig_bed) as in_handle:
for line in in_handle:
parts = line.rstrip().split("\t")
if len(parts) == 3:
parts.append("+")
parts.append("a")
out_handle.write("\t".join(parts) + "\n")
yield tmp_bed
def make_refflat(genome_dir):
"""
makes a refflat file for use with Picard from a GTF file
"""
gtf_file = get_transcript_gtf(genome_dir)
base, _ = os.path.splitext(gtf_file)
refflat_file = base + ".refFlat"
print "Making %s into a refFlat file named %s." % (gtf_file, refflat_file)
if file_exists(refflat_file):
print "%s already exists, skipping." % refflat_file
return refflat_file
with tmpfile(dir=os.getcwd(), prefix="genepred") as tmp_file:
cmd = "gtfToGenePred {gtf_file} {tmp_file}".format(**locals())
subprocess.check_call(cmd, shell=True)
with open(tmp_file) as tmp_handle, open(refflat_file, "w") as out_handle:
for line in tmp_handle:
l = line.split("\t")
l = [l[0]] + l
out_handle.write("\t".join(l) + "\n")
return refflat_file
def make_refflat(genome_dir):
"""
makes a refflat file for use with Picard from a GTF file
"""
gtf_file = get_transcript_gtf(genome_dir)
base, _ = os.path.splitext(gtf_file)
refflat_file = base + ".refFlat"
print "Making %s into a refFlat file named %s." % (gtf_file, refflat_file)
if file_exists(refflat_file):
print "%s already exists, skipping." % refflat_file
return refflat_file
with tmpfile(dir=os.getcwd(), prefix="genepred") as tmp_file:
cmd = "gtfToGenePred {gtf_file} {tmp_file}".format(**locals())
subprocess.check_call(cmd, shell=True)
with open(tmp_file) as tmp_handle, open(refflat_file,
"w") as out_handle:
for line in tmp_handle:
l = line.split("\t")
l = [l[0]] + l
out_handle.write("\t".join(l) + "\n")
return refflat_file
def bed_to_interval(orig_bed, bam_file):
"""Add header and format BED bait and target files for Picard if necessary.
"""
with open(orig_bed) as in_handle:
line = in_handle.readline()
if line.startswith("@"):
yield orig_bed
else:
bam_handle = pysam.Samfile(bam_file, "rb")
with contextlib.closing(bam_handle):
header = bam_handle.text
with tmpfile(dir=os.getcwd(), prefix="picardbed") as tmp_bed:
with open(tmp_bed, "w") as out_handle:
out_handle.write(header)
with open(orig_bed) as in_handle:
for line in in_handle:
parts = line.rstrip().split("\t")
if len(parts) == 3:
parts.append("+")
parts.append("a")
out_handle.write("\t".join(parts) + "\n")
yield tmp_bed
def coverage(data):
bed_file = dd.get_coverage_experimental(data)
if not bed_file:
return data
work_dir = os.path.join(dd.get_work_dir(data), "report", "coverage")
with chdir(work_dir):
in_bam = data['work_bam']
sample = os.path.splitext(os.path.basename(in_bam))[0]
logger.debug("doing coverage for %s" % sample)
region_bed = pybedtools.BedTool(bed_file)
parse_file = os.path.join(sample + "_coverage.bed")
parse_total_file = os.path.join(sample + "_cov_total.tsv")
if not file_exists(parse_file):
total_cov = cov_class(0, None, sample)
bam_api = pysam.AlignmentFile(in_bam)
with file_transaction(parse_file) as out_tx:
with open(out_tx, 'w') as out_handle:
print >> out_handle, "#chrom\tstart\tend\tregion\treads\tstrand\tsize\tsample\tmean\tsdt\tq10\tq20\tq4\tq50"
with tmpfile() as tx_tmp_file:
# tx_tmp_file = "tmpintersect"
for line in region_bed:
chrom = line.chrom
start = max(line.start, 0)
end = line.end
region_file = pybedtools.BedTool(
str(line), from_string=True).saveas().fn
coords = "%s:%s-%s" % (chrom, start, end)
cmd = (
"samtools view -b {in_bam} {coords} | "
"bedtools coverage -a {region_file} -b - -hist > {tx_tmp_file}"
)
_silence_run(cmd.format(**locals()))
total_cov = _get_exome_coverage_stats(
os.path.abspath(tx_tmp_file), sample, out_tx,
total_cov)
total_cov.write_coverage(parse_total_file)
data['coverage'] = os.path.abspath(parse_file)
return data
def merge_bam_files(bam_files, work_dir, config, out_file=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Uses samtools or bamtools for merging, both of which have some cavaets.
samtools can run into file system limits on command line length, while
bamtools runs into open file handle issues.
"""
if len(bam_files) == 1:
return bam_files[0]
else:
if out_file is None:
out_file = os.path.join(work_dir, os.path.basename(sorted(bam_files)[0]))
if not utils.file_exists(out_file) or not utils.file_exists(out_file + ".bai"):
bamtools = config_utils.get_program("bamtools", config)
samtools = config_utils.get_program("samtools", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
max_mem = resources.get("memory", "1G")
with utils.curdir_tmpdir() as tmpdir:
with utils.chdir(tmpdir):
if len(bam_files) < 4096:
merge_cl = _samtools_cat(bam_files, tmpdir)
else:
merge_cl = _bamtools_merge(bam_files)
with file_transaction(out_file) as tx_out_file:
tx_out_prefix = os.path.splitext(tx_out_file)[0]
with utils.tmpfile(dir=work_dir, prefix="bammergelist") as bam_file_list:
bam_file_list = "%s.list" % os.path.splitext(out_file)[0]
with open(bam_file_list, "w") as out_handle:
for f in sorted(bam_files):
out_handle.write("%s\n" % f)
cmd = (merge_cl + " | "
"{samtools} sort -@ {num_cores} -m {max_mem} - {tx_out_prefix}")
do.run(cmd.format(**locals()), "Merge bam files", None)
for b in bam_files:
utils.save_diskspace(b, "BAM merged to %s" % out_file, config)
bam.index(out_file, config)
return out_file
def merge_bam_files(bam_files, work_dir, config, out_file=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Uses bamtools for merging, which handles large numbers of input BAMs.
"""
if len(bam_files) == 1:
return bam_files[0]
else:
if out_file is None:
out_file = os.path.join(work_dir, os.path.basename(sorted(bam_files)[0]))
if not utils.file_exists(out_file) or not utils.file_exists(out_file + ".bai"):
bamtools = config_utils.get_program("bamtools", config)
samtools = config_utils.get_program("samtools", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
max_mem = resources.get("memory", "1G")
if len(bam_files) > system.open_file_limit():
raise IOError("More files to merge (%s) then available open file descriptors (%s)\n"
"See documentation on tips for changing file limits:\n"
"https://bcbio-nextgen.readthedocs.org/en/latest/contents/"
"parallel.html#tuning-systems-for-scale"
% (len(bam_files), system.open_file_limit()))
with file_transaction(out_file) as tx_out_file:
tx_out_prefix = os.path.splitext(tx_out_file)[0]
with utils.tmpfile(dir=work_dir, prefix="bammergelist") as bam_file_list:
bam_file_list = "%s.list" % os.path.splitext(out_file)[0]
with open(bam_file_list, "w") as out_handle:
for f in sorted(bam_files):
out_handle.write("%s\n" % f)
cmd = ("{bamtools} merge -list {bam_file_list} | "
"{samtools} sort -@ {num_cores} -m {max_mem} - {tx_out_prefix}")
do.run(cmd.format(**locals()), "Merge bam files", None)
for b in bam_files:
utils.save_diskspace(b, "BAM merged to %s" % out_file, config)
picard = broad.runner_from_config(config)
picard.run_fn("picard_index", out_file)
return out_file
def merge_bam_files(bam_files, work_dir, config, out_file=None):
"""Merge multiple BAM files from a sample into a single BAM for processing.
Uses bamtools for merging, which handles large numbers of input BAMs.
"""
if len(bam_files) == 1:
return bam_files[0]
else:
if out_file is None:
out_file = os.path.join(work_dir, os.path.basename(sorted(bam_files)[0]))
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_file:
with utils.tmpfile(dir=work_dir, prefix="bammergelist") as bam_file_list:
with open(bam_file_list, "w") as out_handle:
for f in bam_files:
out_handle.write("%s\n" % f)
cmd = [config_utils.get_program("bamtools", config),
"merge", "-list", bam_file_list, "-out", tx_out_file]
do.run(cmd, "Merge bam files", None)
for b in bam_files:
utils.save_diskspace(b, "BAM merged to %s" % out_file, config)
picard = broad.runner_from_config(config)
picard.run_fn("picard_index", out_file)
return out_file
def consensus(peakfiles, consensusfile, data, pad=250):
"""call consensus peaks from a set of narrow/broad peakfiles
we use this method:
https://bedops.readthedocs.io/en/latest/content/usage-examples/master-list.html
"""
if utils.file_exists(consensusfile):
return consensusfile
try:
bedops = config_utils.get_program("bedops", data)
except config_utils.CmdNotFound:
logger.info("bedops not found, skipping consensus peak calling. do a "
"--tools update to install bedops.")
return None
try:
sortbed = config_utils.get_program("sort-bed", data)
except config_utils.CmdNotFound:
logger.info("sort-bed not found, skipping consensus peak calling. do "
"--tools update to install sort-bed.")
return None
try:
bedmap = config_utils.get_program("bedmap", data)
except config_utils.CmdNotFound:
logger.info("bedmap not found, skipping consensus peak calling. do a "
"--tools update to install bedmap.")
return None
logger.info(f"Calling consensus peaks on {','.join(peakfiles)}")
logger.info(f"Removing low quality peaks from {','.join(peakfiles)}")
filteredsummits = []
for fn in peakfiles:
filteredpeak = NamedTemporaryFile(suffix=".bed", delete=False).name
df = remove_low_quality_peaks(fn, qval=0.05)
df.to_csv(filteredpeak, index=False, header=False, sep="\t")
filteredsummit = peakfile_to_summitfile(filteredpeak)
filteredsummits.append(filteredsummit)
peakfiles = filteredsummits
with file_transaction(consensusfile) as tx_consensus_file:
message = (f"Combining summits of {' '.join(peakfiles)} and "
f"expanding {pad} bases.")
with utils.tmpfile(suffix=".bed") as tmpbed:
slopcommand = f"{bedops} --range {pad} -u {' '.join(peakfiles)} > {tmpbed}"
do.run(slopcommand, message)
iteration = 0
while os.path.getsize(tmpbed):
iteration = iteration + 1
iterationbed = NamedTemporaryFile(suffix=".bed",
delete=False).name
with utils.tmpfile(suffix="bed") as mergedbed, \
utils.tmpfile(suffix="bed") as intermediatebed, \
utils.tmpfile(suffix="bed") as leftoverbed, \
utils.tmpfile(suffix="bed") as tmpsolutionbed:
mergecmd = (f"{bedops} -m --range 0:-1 {tmpbed} | "
f"{bedops} -u --range 0:1 - > "
f"{mergedbed}")
message = f"Merging non-overlapping peaks, iteration {iteration}."
do.run(mergecmd, message)
nitems = len(open(mergedbed).readlines())
message = f"Considering {nitems} peaks, choosing the highest score for overlapping peaks."
highscorecmd = (
f"{bedmap} --max-element {mergedbed} {tmpbed} |"
f"{sortbed} - > "
f"{iterationbed}")
do.run(highscorecmd, message)
message = f"Checking if there are peaks left to merge."
anyleftcmd = (
f"{bedops} -n 1 {tmpbed} {iterationbed} > {intermediatebed}"
)
do.run(anyleftcmd, message)
shutil.move(intermediatebed, tmpbed)
nitems = len(open(iterationbed).readlines())
message = f"Adding {nitems} peaks to consensus peaks."
if utils.file_exists(tx_consensus_file):
consensuscmd = (
f"{bedops} -u {tx_consensus_file} {iterationbed} > {tmpsolutionbed}"
)
do.run(consensuscmd, message)
shutil.move(tmpsolutionbed, tx_consensus_file)
else:
shutil.move(iterationbed, tx_consensus_file)
return consensusfile
def blat_search(rec, db, tmp_dir):
with utils.tmpfile(prefix="inblat", dir=tmp_dir) as in_file:
with open(in_file, "w") as out_handle:
SeqIO.write([rec], out_handle, "fasta")
with utils.tmpfile(prefix="outblat", dir=tmp_dir) as blat_out:
return _do_blat(in_file, db, blat_out)
def blat_search(rec, db, tmp_dir):
with utils.tmpfile(prefix="inblat", dir=tmp_dir) as in_file:
with open(in_file, "w") as out_handle:
SeqIO.write([rec], out_handle, "fasta")
with utils.tmpfile(prefix="outblat", dir=tmp_dir) as blat_out:
return _do_blat(in_file, db, blat_out)
