def main():
usage = 'Usage: %prog [-h] [--version] --samplelist [sample list] --config [config file] [options]'
description = Rhea_Chip.__description__
author = Rhea_Chip.__author__
version = Rhea_Chip.__version__
parser = OptionParser(usage=usage, version=version, description=description, epilog=author)
expect = OptionGroup(parser, 'Expected arguments', 'Caution: These parameters are necessary for Rhea_Chip.')
expect.add_option('-s', '--samplelist', metavar='FILE', dest='samplelist',
help=r'''The sample list file
Column 1: sample name
Column 2: family name
Column 3: library
Column 4: FQ file [formact:
lane1/fq1:lane1/adapter1;lane1/fq2:lane1/adapter2|
lane2/fq1:lane2/adapter1;lane2/fq2:lane2/adapter2|...]
Column 5: case/control''')
expect.add_option('-c', '--config', metavar='FILE', dest='config',
help='The config file, contain all specific settings')
parser.add_option_group(expect)
optinal = OptionGroup(parser, 'Optional arguments', 'Caution: If you do not set these parameters in addition,'
' Rhea_Chip will select the default value.')
optinal.add_option('-o', '--outdir', dest='outdir', default=os.getcwd(),
help='The output dir [ default: %s ]' % os.getcwd())
optinal.add_option('-p', '--project_name', dest='project_name', help='set your project name', default=None)
parser.add_option_group(optinal)
options, args = parser.parse_args()
if not options.samplelist or not options.config:
parser.print_help()
return 'Expected arguments lost !!!'
samplelist = os.path.abspath(options.samplelist)
config = os.path.abspath(options.config)
outdir = os.path.abspath(options.outdir)
logger.info("Rhea_Chip Tasks initialization !")
logger.info("Parser the setting config file !")
baseconfig = ParserConfig(config)
config_stat = baseconfig.config_check()
if config_stat != "Success":
return config_stat
logger.info("Parser the Sample list file !")
samples = SampleMessageParser(samplelist)
logger.info("Total {0} sample(s) in our analysis !".format(len(samples)))
prepair_dir = FolderMaker(outdir)
logger.info("Create the whole working directory !")
prepair_dir.create_subdirectory(['alignment', 'doc', 'doc/QC', 'fq', 'fq/raw_data', 'cnv',
'fq/clean_data', 'javatmp', 'script', 'variation', 'annotation'])
baseconfig.config_save(os.path.join(outdir, 'doc', 'Rhea_Chip.conf'))
job_client = process(samples, baseconfig.handle, prepair_dir)
open(os.path.join(outdir, 'doc', 'Rhea_Chip.log'), "wb").write(open(LogFile, "rb").read())
if samplelist != os.path.join(outdir, 'doc', 'sample.list'):
open(os.path.join(outdir, 'doc', 'sample.list'), "wb").write(open(samplelist, "rb").read())
return "All scripts have been generated, Next, please run : %s" % job_client
def __init__(self, **kwargs):
self.region = os.path.abspath(kwargs["region"])
sample_f = os.path.abspath(kwargs["samplelist"])
depth_dir = os.path.abspath(
kwargs["depths"]
) if kwargs["depths"] is not None else os.path.join(
os.path.dirname(sample_f), 'QC')
self.reference = os.path.abspath(kwargs["reference"])
self.rmsk = os.path.abspath(kwargs["repeatdb"])
self.outdir = os.path.abspath(kwargs["outdir"])
self.script = os.path.join(self.outdir, 'script')
self.log = os.path.join(self.script, 'log')
self.winlen = int(kwargs["winlen"]) or 30
self.siftlen = int(kwargs["siftlen"]) or 25
self.SamplesDepth = dict()
self.contigs = set()
self.databases = os.path.abspath(kwargs["dbdir"])
self.plot = kwargs["plot"]
samples = set()
with smart_open(sample_f) as sam:
for line in sam:
if line.startswith("#"):
continue
sample_name = str(line.strip().split()[0])
samples.add(sample_name)
dep = os.path.join(
depth_dir,
"{0}/depthAnno/Flank/{0}.Rmdup.depth.tsv.gz".format(
sample_name))
self.SamplesDepth[sample_name] = dep
if len(samples) <= 5:
raise IOError('Sorry, Six or more samples are needed !!!')
self.samples = sorted(samples)
with smart_open(self.region) as bed:
for line in bed:
if line.startswith("#"):
continue
chrom_name = str(line.strip().split()[0])
self.contigs.add(chrom_name)
prepair_dir = FolderMaker(self.outdir)
prepair_dir.create_subdirectory(self.samples)
if not os.path.isdir(self.script):
os.makedirs(self.script)
def __init__(self, **kwargs):
self.region = os.path.abspath(kwargs["region"])
sample_f = os.path.abspath(kwargs["samplelist"])
depth_dir = os.path.abspath(kwargs["depths"]) if kwargs["depths"] is not None else os.path.join(
os.path.dirname(sample_f), 'QC')
self.reference = os.path.abspath(kwargs["reference"])
self.rmsk = os.path.abspath(kwargs["repeatdb"])
self.outdir = os.path.abspath(kwargs["outdir"])
self.script = os.path.join(self.outdir, 'script')
self.log = os.path.join(self.script, 'log')
self.winlen = int(kwargs["winlen"]) or 30
self.siftlen = int(kwargs["siftlen"]) or 25
self.SamplesDepth = dict()
self.contigs = set()
self.databases = os.path.abspath(kwargs["dbdir"])
self.plot = kwargs["plot"]
samples = set()
with smart_open(sample_f) as sam:
for line in sam:
if line.startswith("#"):
continue
sample_name = str(line.strip().split()[0])
samples.add(sample_name)
dep = os.path.join(depth_dir, "{0}/depthAnno/Flank/{0}.Rmdup.depth.tsv.gz".format(sample_name))
self.SamplesDepth[sample_name] = dep
if len(samples) <= 5:
raise IOError('Sorry, Six or more samples are needed !!!')
self.samples = sorted(samples)
with smart_open(self.region) as bed:
for line in bed:
if line.startswith("#"):
continue
chrom_name = str(line.strip().split()[0])
self.contigs.add(chrom_name)
prepair_dir = FolderMaker(self.outdir)
prepair_dir.create_subdirectory(self.samples)
if not os.path.isdir(self.script):
os.makedirs(self.script)
def main():
usage = 'Usage: %prog [-h] [--version] --target [target bed] -b [bam file] -r [ref seq] [options]'
description = Rhea_Chip.__description__
author = Rhea_Chip.__author__
version = Rhea_Chip.__version__
parser = OptionParser(usage=usage, version=version, description=description, epilog=author)
expect = OptionGroup(parser, 'Expected arguments', 'Caution: These parameters are necessary for depthQC.')
expect.add_option('-b', '--bam', metavar='FILE', dest='bam', help='bam file')
expect.add_option('-r', '--reference', metavar='FILE', dest='reference', help='humman reference')
expect.add_option('--target', metavar='FILE', dest='target', help='target bed region file')
parser.add_option_group(expect)
optinal = OptionGroup(parser, 'Optional arguments', 'Caution: If you do not set these parameters in addition,'
' depthQC will select the default value.')
optinal.add_option('-o', '--outdir', dest='outdir', default=os.getcwd(),
help='The output dir [ default: %s ]' % os.getcwd())
optinal.add_option('-t', '--threads', dest='threads', default=0,
help='The max threads [ default: <cpus> ], only use in plot exon graph')
optinal.add_option('--flank', dest='flank', default=None, help='Flank bed region file [ default: None ]')
optinal.add_option('--trans', dest='trans', default=None, help='Trans list file [ default: None ]')
optinal.add_option('--genes', dest='genes', default=None, help='Genes list file [ default: None ]')
optinal.add_option('-p', '--plot', help='Plot exon depth graph', dest='plot', default=False, action="store_true")
parser.add_option_group(optinal)
(options, args) = parser.parse_args()
if not options.bam or not options.reference or not options.target:
parser.print_help()
return 'Expected arguments lost !!!'
bam = os.path.abspath(options.bam)
reference = os.path.abspath(options.reference)
target = os.path.abspath(options.target)
outdir = os.path.abspath(options.outdir)
threads = int(options.threads)
flank = os.path.abspath(options.flank) if options.flank else None
trans = os.path.abspath(options.trans) if options.trans else None
genes = os.path.abspath(options.genes) if options.genes else None
plot = options.plot
assert trans or genes, "Genes and Trans must set one ~"
prepair_dir = FolderMaker(outdir)
subdir = ["depthAnno", "depthAnno/Target"]
if flank:
subdir.append("depthAnno/Flank")
if plot:
prepair_dir.create_subdirectory(["graph_exon"])
prepair_dir.create_subdirectory(subdir)
depths = BamDepth(bam, reference)
sample = depths.name
depths.depths(target, prefix=os.path.join(outdir, "depthAnno/Target", sample + '.Rmdup'))
depths.depths(target, prefix=os.path.join(outdir, "depthAnno/Target", sample + '.Raw'), read_filter="nofilter")
if flank:
depths.depths(flank, prefix=os.path.join(outdir, "depthAnno/Flank", sample + '.Rmdup'))
depths.depths(target, prefix=os.path.join(outdir, "depthAnno/Flank", sample + '.Raw'), read_filter="nofilter")
depths.__del__()
uncovers = glob(os.path.join(outdir, 'depthAnno', "*", sample + ".Rmdup.uncover.bed"))
bedanno = BedAnno(reference=reference, trans=trans, genes=genes)
for bed in uncovers:
file_out = re.sub("\.bed$", ".anno", bed)
bedanno.bedanno(bed, fileout=file_out)
if plot:
depth_f = os.path.join(outdir, "depthAnno/Target", sample + '.Rmdup.depth.tsv.gz')
exon_graph(depth=depth_f, refseq=bedanno.refdb, prefix=sample,
outdir=os.path.join(outdir, "graph_exon"), trans=trans,
genes=genes, threads=threads)
bedanno.__del__()
def main():
usage = 'Usage: %prog [-h] [--version] --samplelist [sample list] --config [config file] [options]'
description = Rhea_Chip.__description__
author = Rhea_Chip.__author__
version = Rhea_Chip.__version__
parser = OptionParser(usage=usage,
version=version,
description=description,
epilog=author)
expect = OptionGroup(
parser, 'Expected arguments',
'Caution: These parameters are necessary for Rhea_Chip.')
expect.add_option('-s',
'--samplelist',
metavar='FILE',
dest='samplelist',
help=r'''The sample list file
Column 1: sample name
Column 2: family name
Column 3: library
Column 4: FQ file [formact:
lane1/fq1:lane1/adapter1;lane1/fq2:lane1/adapter2|
lane2/fq1:lane2/adapter1;lane2/fq2:lane2/adapter2|...]
Column 5: case/control''')
expect.add_option('-c',
'--config',
metavar='FILE',
dest='config',
help='The config file, contain all specific settings')
parser.add_option_group(expect)
optinal = OptionGroup(
parser, 'Optional arguments',
'Caution: If you do not set these parameters in addition,'
' Rhea_Chip will select the default value.')
optinal.add_option('-o',
'--outdir',
dest='outdir',
default=os.getcwd(),
help='The output dir [ default: %s ]' % os.getcwd())
optinal.add_option('-p',
'--project_name',
dest='project_name',
help='set your project name',
default=None)
parser.add_option_group(optinal)
options, args = parser.parse_args()
if not options.samplelist or not options.config:
parser.print_help()
return 'Expected arguments lost !!!'
samplelist = os.path.abspath(options.samplelist)
config = os.path.abspath(options.config)
outdir = os.path.abspath(options.outdir)
logger.info("Rhea_Chip Tasks initialization !")
logger.info("Parser the setting config file !")
baseconfig = ParserConfig(config)
config_stat = baseconfig.config_check()
if config_stat != "Success":
return config_stat
logger.info("Parser the Sample list file !")
samples = SampleMessageParser(samplelist)
logger.info("Total {0} sample(s) in our analysis !".format(len(samples)))
prepair_dir = FolderMaker(outdir)
logger.info("Create the whole working directory !")
prepair_dir.create_subdirectory([
'alignment', 'doc', 'doc/QC', 'fq', 'fq/raw_data', 'cnv',
'fq/clean_data', 'javatmp', 'script', 'variation', 'annotation'
])
baseconfig.config_save(os.path.join(outdir, 'doc', 'Rhea_Chip.conf'))
job_client = process(samples, baseconfig.handle, prepair_dir)
open(os.path.join(outdir, 'doc', 'Rhea_Chip.log'),
"wb").write(open(LogFile, "rb").read())
if samplelist != os.path.join(outdir, 'doc', 'sample.list'):
open(os.path.join(outdir, 'doc', 'sample.list'),
"wb").write(open(samplelist, "rb").read())
return "All scripts have been generated, Next, please run : %s" % job_client
def main():
usage = 'Usage: %prog [-h] [--version] --target [target bed] -b [bam file] -r [ref seq] [options]'
description = Rhea_Chip.__description__
author = Rhea_Chip.__author__
version = Rhea_Chip.__version__
parser = OptionParser(usage=usage,
version=version,
description=description,
epilog=author)
expect = OptionGroup(
parser, 'Expected arguments',
'Caution: These parameters are necessary for depthQC.')
expect.add_option('-b',
'--bam',
metavar='FILE',
dest='bam',
help='bam file')
expect.add_option('-r',
'--reference',
metavar='FILE',
dest='reference',
help='humman reference')
expect.add_option('--target',
metavar='FILE',
dest='target',
help='target bed region file')
parser.add_option_group(expect)
optinal = OptionGroup(
parser, 'Optional arguments',
'Caution: If you do not set these parameters in addition,'
' depthQC will select the default value.')
optinal.add_option('-o',
'--outdir',
dest='outdir',
default=os.getcwd(),
help='The output dir [ default: %s ]' % os.getcwd())
optinal.add_option(
'-t',
'--threads',
dest='threads',
default=0,
help='The max threads [ default: <cpus> ], only use in plot exon graph'
)
optinal.add_option('--flank',
dest='flank',
default=None,
help='Flank bed region file [ default: None ]')
optinal.add_option('--trans',
dest='trans',
default=None,
help='Trans list file [ default: None ]')
optinal.add_option('--genes',
dest='genes',
default=None,
help='Genes list file [ default: None ]')
optinal.add_option('-p',
'--plot',
help='Plot exon depth graph',
dest='plot',
default=False,
action="store_true")
parser.add_option_group(optinal)
(options, args) = parser.parse_args()
if not options.bam or not options.reference or not options.target:
parser.print_help()
return 'Expected arguments lost !!!'
bam = os.path.abspath(options.bam)
reference = os.path.abspath(options.reference)
target = os.path.abspath(options.target)
outdir = os.path.abspath(options.outdir)
threads = int(options.threads)
flank = os.path.abspath(options.flank) if options.flank else None
trans = os.path.abspath(options.trans) if options.trans else None
genes = os.path.abspath(options.genes) if options.genes else None
plot = options.plot
assert trans or genes, "Genes and Trans must set one ~"
prepair_dir = FolderMaker(outdir)
subdir = ["depthAnno", "depthAnno/Target"]
if flank:
subdir.append("depthAnno/Flank")
if plot:
prepair_dir.create_subdirectory(["graph_exon"])
prepair_dir.create_subdirectory(subdir)
depths = BamDepth(bam, reference)
sample = depths.name
depths.depths(target,
prefix=os.path.join(outdir, "depthAnno/Target",
sample + '.Rmdup'))
depths.depths(target,
prefix=os.path.join(outdir, "depthAnno/Target",
sample + '.Raw'),
read_filter="nofilter")
if flank:
depths.depths(flank,
prefix=os.path.join(outdir, "depthAnno/Flank",
sample + '.Rmdup'))
depths.depths(target,
prefix=os.path.join(outdir, "depthAnno/Flank",
sample + '.Raw'),
read_filter="nofilter")
depths.__del__()
uncovers = glob(
os.path.join(outdir, 'depthAnno', "*", sample + ".Rmdup.uncover.bed"))
bedanno = BedAnno(reference=reference, trans=trans, genes=genes)
for bed in uncovers:
file_out = re.sub("\.bed$", ".anno", bed)
bedanno.bedanno(bed, fileout=file_out)
if plot:
depth_f = os.path.join(outdir, "depthAnno/Target",
sample + '.Rmdup.depth.tsv.gz')
exon_graph(depth=depth_f,
refseq=bedanno.refdb,
prefix=sample,
outdir=os.path.join(outdir, "graph_exon"),
trans=trans,
genes=genes,
threads=threads)
bedanno.__del__()