Esempio n. 1
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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",
Esempio n. 2
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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", 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")])
advanced.add_option("-m", "--minreads", type="int", dest="minreads", default=10, remember=True,
                    help="Minimum number of good reads at SNV locus per alignment file. Default=10.", name="Min. Reads")
advanced.add_option("-M", "--maxreads", type="float", dest="maxreads", default=None, remember=True,
                    help="Scale read counts at high-coverage loci to ensure at most this many good reads at SNV locus per alignment file. Values greater than 1 indicate absolute read counts, otherwise the value indicates the coverage distribution percentile. Default=No maximum.", name="Max. Reads")
advanced.add_option("-F", "--full", action="store_true", dest="full", default=False, remember=True,
                    help="Output extra diagnostic read count fields. Default=False.", name="All Fields")
advanced.add_option("-f", "--alignmentfilter", action="store_false", dest="filter", default=True, remember=True,
Esempio n. 3
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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",
Esempio n. 4
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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",
Esempio n. 5
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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}
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="SNVs",
                  notNone=True,
                  remember=True,
                  filetypes=[("SNVs", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-r",
                  "--readalignments",
                  type="files",
                  dest="alignments",
                  default=None,
Esempio n. 6
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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")])
Esempio n. 7
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        shutil.rmtree(d, ignore_errors=True)
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}
else:
    parser = OptionParser(version=VERSION)
    error_kwargs = {}

advanced = OptionGroup(parser, "Advanced")
parser.add_option("-s", "--snps", type="files", dest="snps", default=None,
                  help="Single-Nucleotide-Polymophisms. Required.", name="SNPs",
                  notNone=True, remember=True,
                  filetypes=[("SNPs", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-j", "--junctions", type="files", dest="junctions", default=None,
                  help="Splice junctions. Required.", name="Splice Junctions",
                  notNone=True, remember=True,
                  filetypes=[("Splice Junctions (BED Format)", "*.bed")])
parser.add_option("-r", "--readalignments", type="files", dest="alignments", default=None,
                  help="Read alignments in BAM/SAM format. Required.", name="Read Alignments",
                  notNone=True, remember=True,
                  filetypes=[("Read Alignments (BAM/SAM Format)", "*.bam;*.sam")])
advanced.add_option("-d", "--distance", type="int", dest="dist", default=50, remember=True,
                    help="Upper bound on the distance between SNP locus and splice junction. Default: 50.",
                    name="Distance Bound")
Esempio n. 8
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import re
from collections import defaultdict

from version import VERSION
VERSION = '1.0.6 (%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", type="file", dest="darned", default=None,
                  help="DARNED annotations.",
                  filetypes=[("DARNED Annotations", "*.txt")])
regexs.add_option("--normaldnare", type="str", dest="normaldnare", default=r'GDNA',
                  help="Germline/Normal DNA filename regular expression. Default: GDNA.",
                  remember=True, name="Germline DNA RE")
regexs.add_option("--normaltransre", type="str", dest="normaltransre", default=r'NRNA',
                  help="Normal transcriptome filename regular expression. Default: NRNA.",
Esempio n. 9
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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}
else:
    parser = OptionParser(version=VERSION)
    error_kwargs = {}

advanced = OptionGroup(parser, "Advanced")
parser.add_option("-s",
                  "--snps",
                  type="files",
                  dest="snps",
                  default=None,
                  help="Single-Nucleotide-Polymophisms. Required.",
                  name="SNPs",
                  notNone=True,
                  remember=True,
                  filetypes=[("SNPs", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-j",
                  "--junctions",
                  type="files",
                  dest="junctions",
                  default=None,
Esempio n. 10
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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}
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="SNVs",
    notNone=True,
    remember=True,
    filetypes=[("SNVs", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")],
)
parser.add_option(
    "-r",
    "--readalignments",
Esempio n. 11
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    parser = OptionParser(version=VERSION)
    error_kwargs = {}

filterFactory = ReadFilterFactory()
filterOptions = [t[0] for t in filterFactory.list()]

groupFactory = ReadGroupFactory()
groupOptions = [""] + [t[0] for t in groupFactory.list()]

minreads_default = 5
maxreads_default = None
tpb_default = 0
filter_default = "Basic"
readgroup_default = "UMI-tools"

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",
Esempio n. 12
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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")])