Ejemplo n.º 1
0
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
Ejemplo n.º 2
0
 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)
Ejemplo n.º 3
0
	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)
Ejemplo n.º 4
0
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__()
Ejemplo n.º 5
0
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
Ejemplo n.º 6
0
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__()