def __init__(self, in_dir, out_dir, num_procs = 1):
self.in_dir = in_dir
self.out_dir = out_dir
self.num_procs = num_procs
self.assembly, self.chroms = _common.find_genome_files(self.in_dir)
if os.path.exists(self.out_dir):
raise ValueError("Output directory %s already exists!" % (self.out_dir,))
os.mkdir(self.out_dir)
def __init__(self, in_dir, out_dir, num_procs=1):
self.in_dir = in_dir
self.out_dir = out_dir
self.num_procs = num_procs
self.assembly, self.chroms = _common.find_genome_files(self.in_dir)
if os.path.exists(self.out_dir):
raise ValueError("Output directory %s already exists!" %
(self.out_dir, ))
os.mkdir(self.out_dir)
def parse_options(arguments):
global options, args
parser = OptionParser(usage="%prog [options] <assembly> <sample1.sam> [...sampleN.sam]",
version="%prog " + str(__version__))
parser.add_option("-o",
dest="output_dir",
metavar="[./txome_out]",
default="./txome_out",
help="write output files to this directory")
parser.add_option("-p",
dest="num_threads",
type="int",
metavar="[1]",
default=1,
help="number of threads used during analysis")
parser.add_option("-L",
dest="labels",
metavar="sample1,...sampleN",
default=None,
help="comma-separated list of condition labels")
parser.add_option("-r",
dest="reference",
metavar="reference.gtf",
default=None,
help="reference annotation (i.e. refGene) GTF file")
parser.add_option("-M",
dest="mask",
metavar="mask.gtf",
default=None,
help="ignore all alignment within transcripts in this file")
parser.add_option("--prerun",
dest="prerun",
action="store_true",
default=False,
help="perform only the 'discovery' Cufflinks/Scripture runs")
parser.add_option("--pool-transcripts",
dest="pool_transcripts",
action="store_true",
default=False,
help="pool transcripts with Cuffcompare")
parser.add_option("--realrun",
dest="realrun",
action="store_true",
default=False,
help="perform only the quantitation Cufflinks runs")
options, args = parser.parse_args()
if len(args) < 2:
print "Error: Not enough arguments"
parser.print_help()
sys.exit(0)
if options.labels != None:
options.labels = options.labels.split(",")
if len(options.labels) <> len(args) - 1:
print "Error: When using -L, must specify a label for every condition"
parser.print_help()
sys.exit(0)
else:
options.labels = ["sample%s" % (x,) for x in range(len(args))]
options.genome_dir = _common.genome_fasta[args[0]]
options.assembly, options.chroms = _common.find_genome_files(options.genome_dir)
if options.assembly != args[0]:
print "Error: Specified assembly does not match assembly found"
parser.print_help()
sys.exit(0)
