atexit.register(cleanup)
if not GUI() and len(sys.argv) == 2 and sys.argv[1] == '--GUI':
from optparse_gui.needswx import *
sys.exit(1)
if GUI() and len(sys.argv) == 1:
from optparse_gui import OptionParserGUI
parser = OptionParserGUI(version=VERSION)
error_kwargs = {'exit': False}
sys.excepthook = excepthook
else:
parser = OptionParser(version=VERSION)
error_kwargs = {}
advanced = OptionGroup(parser, "Advanced")
parser.add_option("-s",
"--snvs",
type="files",
dest="snvs",
default=None,
help="Single-Nucleotide-Variant files. Required.",
name="SNV Files",
notNone=True,
remember=True,
filetypes=[("SNV Files",
"*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-r",
"--readalignments",
type="files",
dest="alignments",
from version import VERSION
VERSION = '%s' % (VERSION, )
from os.path import join, dirname, realpath, split
try:
scriptdir = dirname(realpath(__file__))
except NameError:
scriptdir = dirname(realpath(sys.argv[0]))
sys.path.append(join(scriptdir, '..', '..', 'common', 'src'))
from optparse_gui import OptionParser, OptionGroup, ProgressText
parser = OptionParser(version=VERSION)
regexs = OptionGroup(parser, "Filename Matching")
parser.add_option("--counts",
type="file",
dest="counts",
default=None,
help="Output file from readCounts. Required.",
notNone=True,
filetypes=[("readCount Output", "*.tsv")])
parser.add_option("--cosmic",
type="file",
dest="cosmic",
default=None,
help="COSMIC Mutants.",
filetypes=[("COSMIC Annotations", "*.tsv;*.tsv.gz")])
parser.add_option("--darned",
atexit.register(cleanup)
if not GUI() and len(sys.argv) == 2 and sys.argv[1] == '--GUI':
from optparse_gui.needswx import *
sys.exit(1)
if GUI() and len(sys.argv) == 1:
from optparse_gui import OptionParserGUI
parser = OptionParserGUI(version=VERSION)
error_kwargs = {'exit': False}
sys.excepthook = excepthook
else:
parser = OptionParser(version=VERSION)
error_kwargs = {}
exfilt = OptionGroup(parser, "Filtering")
readcounts = OptionGroup(parser, "Read Counting")
regexs = OptionGroup(parser, "Filename Matching")
snvannot = OptionGroup(parser, "SNV Annotation")
parser.add_option("-s", "--snvs", type="files", dest="snvs", default=None,
help="Single-Nucleotide-Variant files. Required.", name="SNV Files",
notNone=True, remember=True,
filetypes=[("SNV Files", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-r", "--readalignments", type="files", dest="alignments", default=None,
help="Read alignment files in indexed BAM format. Required.", name="Read Alignment Files",
notNone=True, remember=True,
filetypes=[("Read Alignment Files (Indexed BAM)", "*.bam")])
exfilt.add_option("-e", "--exoncoords", type="file", dest="exoncoords", default=None,
help="Exon coordinates for SNV filtering. Optional.", name="Exon Coords.",
remember=True,
filetypes=[("Exonic Coordinates", "*.txt")])
