def locus(args):
"""
%prog locus bamfile
Extract selected locus from a list of TREDs for validation, and run lobSTR.
"""
from jcvi.formats.sam import get_minibam
# See `Format-lobSTR-database.ipynb` for a list of TREDs for validation
INCLUDE = [
"HD", "SBMA", "SCA1", "SCA2", "SCA8", "SCA17", "DM1", "DM2", "FXTAS"
]
db_choices = ("hg38", "hg19")
p = OptionParser(locus.__doc__)
p.add_option("--tred", choices=INCLUDE, help="TRED name")
p.add_option("--ref",
choices=db_choices,
default="hg38",
help="Reference genome")
p.set_home("lobstr")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(bamfile, ) = args
ref = opts.ref
lhome = opts.lobstr_home
tred = opts.tred
tredsfile = datafile("TREDs.meta.csv")
tf = pd.read_csv(tredsfile, index_col=0)
row = tf.ix[tred]
tag = "repeat_location"
ldb = "TREDs"
if ref == "hg19":
tag += "." + ref
ldb += "-" + ref
seqid, start_end = row[tag].split(":")
PAD = 1000
start, end = start_end.split("-")
start, end = int(start) - PAD, int(end) + PAD
region = "{}:{}-{}".format(seqid, start, end)
minibamfile = get_minibam(bamfile, region)
c = seqid.replace("chr", "")
cmd, vcf = allelotype_on_chr(minibamfile, c, lhome, ldb)
sh(cmd)
parser = LobSTRvcf(columnidsfile=None)
parser.parse(vcf, filtered=False)
items = parser.items()
if not items:
print("No entry found!", file=sys.stderr)
return
k, v = parser.items()[0]
print("{} => {}".format(tred, v.replace(",", "/")), file=sys.stderr)
def locus(args):
"""
%prog locus bamfile
Extract selected locus from a list of TREDs for validation, and run lobSTR.
"""
from jcvi.formats.sam import get_minibam
# See `Format-lobSTR-database.ipynb` for a list of TREDs for validation
INCLUDE = ["HD", "SBMA", "SCA1", "SCA2", "SCA8", "SCA17", "DM1", "DM2",
"FXTAS"]
db_choices = ("hg38", "hg19")
p = OptionParser(locus.__doc__)
p.add_option("--tred", choices=INCLUDE,
help="TRED name")
p.add_option("--ref", choices=db_choices, default="hg38",
help="Reference genome")
p.set_home("lobstr")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
bamfile, = args
ref = opts.ref
lhome = opts.lobstr_home
tred = opts.tred
tredsfile = datafile("TREDs.meta.csv")
tf = pd.read_csv(tredsfile, index_col=0)
row = tf.ix[tred]
tag = "repeat_location"
ldb = "TREDs"
if ref == "hg19":
tag += "." + ref
ldb += "-" + ref
seqid, start_end = row[tag].split(":")
PAD = 1000
start, end = start_end.split('-')
start, end = int(start) - PAD, int(end) + PAD
region = "{}:{}-{}".format(seqid, start, end)
minibamfile = get_minibam(bamfile, region)
c = seqid.replace("chr", "")
cmd, vcf = allelotype_on_chr(minibamfile, c, lhome, ldb)
sh(cmd)
parser = LobSTRvcf(columnidsfile=None)
parser.parse(vcf, filtered=False)
items = parser.items()
if not items:
print("No entry found!", file=sys.stderr)
return
k, v = parser.items()[0]
print("{} => {}".format(tred, v.replace(',', '/')), file=sys.stderr)
def locus(args):
"""
%prog locus bamfile
Extract selected locus from a list of TREDs for validation, and run lobSTR.
"""
from jcvi.formats.sam import get_minibam
# See `Format-lobSTR-database.ipynb` for a list of TREDs for validation
INCLUDE = ["HD", "SBMA", "SCA1", "SCA2", "SCA8", "SCA17", "DM1", "DM2"]
p = OptionParser(locus.__doc__)
p.add_option("--tred", choices=INCLUDE, help="TRED name")
p.set_home("lobstr")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
bamfile, = args
lhome = opts.lobstr_home
tred = opts.tred
tredsfile = op.join(datadir, "TREDs.meta.csv")
tf = pd.read_csv(tredsfile, index_col=0)
row = tf.ix[tred]
seqid, start_end = row["repeat_location"].split(":")
PAD = 1000
start, end = start_end.split('-')
start, end = int(start) - PAD, int(end) + PAD
region = "{}:{}-{}".format(seqid, start, end)
minibamfile = get_minibam(bamfile, region)
c = seqid.replace("chr", "")
cmd, vcf = allelotype_on_chr(minibamfile, c, lhome, "TREDs")
sh(cmd)
parser = LobSTRvcf(columnidsfile=None)
parser.parse(vcf, filtered=False)
k, v = parser.items()[0]
print >> sys.stderr, "{} => {}".format(tred, v.replace(',', '/'))
def htt(args):
"""
%prog htt bamfile chr4:3070000-3080000
Extract HTT region and run lobSTR.
"""
from jcvi.formats.sam import get_minibam
p = OptionParser(htt.__doc__)
p.set_home("lobstr")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
bamfile, region = args
lhome = opts.lobstr_home
minibamfile = get_minibam(bamfile, region)
c = region.split(":")[0].replace("chr", "")
cmd, vcf = allelotype_on_chr(minibamfile, c, lhome, "hg38")
sh(cmd)
def htt(args):
"""
%prog htt bamfile chr4:3070000-3080000
Extract HTT region and run lobSTR.
"""
from jcvi.formats.sam import get_minibam
p = OptionParser(htt.__doc__)
p.set_home("lobstr")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
bamfile, region = args
lhome = opts.lobstr_home
minibamfile = get_minibam(bamfile, region)
c = region.split(":")[0].replace("chr", "")
cmd, vcf = allelotype_on_chr(minibamfile, c, lhome, "hg38")
sh(cmd)
def run_mito(
chrMfa, bamfile, opts, realignonly=False, svonly=False, store=None, cleanup=False
):
from jcvi.formats.sam import get_minibam
region = "chrM"
minibam = op.basename(bamfile).replace(".bam", ".{}.bam".format(region))
if not op.exists(minibam):
get_minibam(bamfile, region)
else:
logging.debug("{} found. Skipped.".format(minibam))
speedseq_bin = op.join(opts.speedseq_home, "speedseq")
realign = minibam.rsplit(".", 1)[0] + ".realign"
realignbam = realign + ".bam"
margs = " -v -t {} -o {}".format(opts.cpus, realign)
if need_update(minibam, realign + ".bam"):
cmd = speedseq_bin + " realign"
cmd += margs
cmd += " {} {}".format(chrMfa, minibam)
sh(cmd)
else:
logging.debug("{} found. Skipped.".format(realignbam))
if realignonly:
return
depthfile = realign + ".depth"
if need_update(realignbam, depthfile):
coverage(
[
chrMfa,
realignbam,
"--nosort",
"--format=coverage",
"--outfile={}".format(depthfile),
]
)
if store:
push_to_s3(store, depthfile)
vcffile = realign + ".sv.vcf.gz"
if need_update(realignbam, vcffile):
cmd = speedseq_bin + " sv"
cmd += margs
cmd += " -R {}".format(chrMfa)
cmd += " -m {}".format(opts.support)
cmd += " -B {} -D {} -S {}".format(
realignbam, realign + ".discordants.bam", realign + ".splitters.bam"
)
sh(cmd)
else:
logging.debug("{} found. Skipped.".format(vcffile))
if store:
push_to_s3(store, vcffile)
if svonly:
if cleanup:
do_cleanup(minibam, realignbam)
return
piledriver = realign + ".piledriver"
if need_update(realignbam, piledriver):
cmd = "bamtools piledriver -fasta {}".format(chrMfa)
cmd += " -in {}".format(realignbam)
sh(cmd, outfile=piledriver)
if store:
push_to_s3(store, piledriver)
if cleanup:
do_cleanup(minibam, realignbam)
def run_mito(chrMfa, bamfile, opts, realignonly=False, svonly=False,
store=None, cleanup=False):
from jcvi.formats.sam import get_minibam
region = "chrM"
minibam = op.basename(bamfile).replace(".bam", ".{}.bam".format(region))
if not op.exists(minibam):
get_minibam(bamfile, region)
else:
logging.debug("{} found. Skipped.".format(minibam))
speedseq_bin = op.join(opts.speedseq_home, "speedseq")
realign = minibam.rsplit(".", 1)[0] + ".realign"
realignbam = realign + ".bam"
margs = " -v -t {} -o {}".format(opts.cpus, realign)
if need_update(minibam, realign + ".bam"):
cmd = speedseq_bin + " realign"
cmd += margs
cmd += " {} {}".format(chrMfa, minibam)
sh(cmd)
else:
logging.debug("{} found. Skipped.".format(realignbam))
if realignonly:
return
depthfile = realign + ".depth"
if need_update(realignbam, depthfile):
coverage([chrMfa, realignbam, "--nosort", "--format=coverage",
"--outfile={}".format(depthfile)])
if store:
push_to_s3(store, depthfile)
vcffile = realign + ".sv.vcf.gz"
if need_update(realignbam, vcffile):
cmd = speedseq_bin + " sv"
cmd += margs
cmd += " -R {}".format(chrMfa)
cmd += " -m {}".format(opts.support)
cmd += " -B {} -D {} -S {}".format(realignbam,
realign + ".discordants.bam", realign + ".splitters.bam")
sh(cmd)
else:
logging.debug("{} found. Skipped.".format(vcffile))
if store:
push_to_s3(store, vcffile)
if svonly:
if cleanup:
do_cleanup(minibam, realignbam)
return
piledriver = realign + ".piledriver"
if need_update(realignbam, piledriver):
cmd = "bamtools piledriver -fasta {}".format(chrMfa)
cmd += " -in {}".format(realignbam)
sh(cmd, outfile=piledriver)
if store:
push_to_s3(store, piledriver)
if cleanup:
do_cleanup(minibam, realignbam)