Python OptionParserGUI.add_optionの例

コード例 #1

ファイル: readCounts.py プロジェクト: grahnavard/NGS

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")])

コード例 #2

ファイル: SNPlice.py プロジェクト: HorvathLab/NGS

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")
advanced.add_option("-R", "--readthrough", type="int", dest="readthrough", default=5, remember=True,
                    help="Number of bases aligning into intron. Default: 5bp.",
                    name="Read-Through")

コード例 #3

ファイル: readCounts.py プロジェクト: HorvathLab/NGS

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,
                    help="(Turn off) alignment filtering by length, edits, etc.", name="Filter Alignments")
advanced.add_option("-U", "--uniquereads", action="store_true", dest="unique", default=False, remember=True,
                    help="Consider only distinct reads.", name="Unique Reads")

コード例 #4

ファイル: RNA2DNAlign.py プロジェクト: HorvathLab/NGS

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")])
regexs.add_option("--normaldnare", type="str", dest="normaldnare", default='GDNA',
                  help="Germline/Normal DNA filename regular expression. Default: GDNA.",
                  remember=True, name="Germline DNA")
regexs.add_option("--normaltransre", type="str", dest="normaltransre", default='NRNA',
                  help="Normal transcriptome filename regular expression. Default: NRNA.",
                  remember=True, name="Normal Transcr.")

コード例 #5

ファイル: readCountsMatrix.py プロジェクト: qingnanl/NGS

    from optparse_gui import OptionParserGUI
    parser = OptionParserGUI(version=VERSION)
    error_kwargs = {'exit': False}
    sys.excepthook = excepthook
else:
    parser = OptionParser(version=VERSION)
    error_kwargs = {}

minreads_default = 0

parser.add_option("-c",
                  "--counts",
                  type="files",
                  dest="counts",
                  default=None,
                  help="ReadCounts files. Required.",
                  name="ReadCounts Files",
                  notNone=True,
                  remember=True,
                  filetypes=[("ReadCounts Files",
                              "*.csv;*.tsv;*.xls;*.xlsx;*.txt;")])
parser.add_option(
    "-M",
    "--matrix",
    type="choice",
    dest="matrix",
    default="Ref;Var",
    remember=True,
    help="Matrix output format: Ref;Var, Ref:Var, or VAF. Default: Ref;Var.",
    name="Matrix",
    choices=["Ref;Var", "Ref:Var", "VAF"])

コード例 #6

ファイル: SNPlice.py プロジェクト: qingnanl/NGS

    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",

コード例 #7

atexit.register(cleanup)

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 = {}

parser.add_option("-c",
                  "--counts",
                  type="files",
                  dest="counts",
                  default=None,
                  help="Read counts per SNP/Junction",
                  name="SNP/Junction Counts",
                  remember=True,
                  notNone=True,
                  filetypes=[("Read counts", "*.xlsx;*.xls;*.csv;*.tsv;*.txt"),
                             ("Excel", "*.xlsx"), ("Excel2003", "*.xls"),
                             ("CSV", "*.csv"), ("TSV", "*.tsv")])
parser.add_option("-q",
                  "--quiet",
                  action="store_true",
                  dest="quiet",
                  default=False,
                  remember=True,
                  help="Quiet.",
                  name="Quiet")
parser.add_option("-o",
                  "--output",

コード例 #8

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",
                  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")])

コード例 #9

ファイル: RNA2DNAlign.py プロジェクト: qingnanl/NGS

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")])
regexs.add_option("--normaldnare", type="str", dest="normaldnare", default='GDNA',
                  help="Germline/Normal DNA filename regular expression. Default: GDNA.",
                  remember=True, name="Germline DNA")
regexs.add_option("--normaltransre", type="str", dest="normaltransre", default='NRNA',
                  help="Normal transcriptome filename regular expression. Default: NRNA.",
                  remember=True, name="Normal Transcr.")

コード例 #10

ファイル: SNPlice-Combine.py プロジェクト: HorvathLab/NGS

    for d in toremove:
        shutil.rmtree(d, ignore_errors=True)

atexit.register(cleanup)

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 = {}

parser.add_option("-c", "--counts", type="files", dest="counts", default=None,
                  help="Read counts per SNP/Junction", name="SNP/Junction Counts",
                  remember=True, notNone=True,
                  filetypes=[("Read counts", "*.xlsx;*.xls;*.csv;*.tsv;*.txt"),
                             ("Excel", "*.xlsx"), ("Excel2003", "*.xls"),
                             ("CSV", "*.csv"), ("TSV", "*.tsv")])
parser.add_option("-q", "--quiet", action="store_true", dest="quiet", default=False, remember=True,
                  help="Quiet.", name="Quiet")
parser.add_option("-o", "--output", type="savefile", dest="output", remember=True,
                  help="Output file. Leave empty for console ouptut.", default="",
                  name="Output File", filetypes=[("All output formats", "*.xlsx;*.xls;*.csv;*.tsv;*.txt"),
                                                 ("Excel", "*.xlsx"), ("Excel2003", "*.xls"),
                                                 ("CSV", "*.csv"), ("TSV", "*.tsv"), ("Text", "*.txt")])

opt = None
while True:
    if 'exit' in error_kwargs:
        try:
            opt, args = parser.parse_args(opts=opt)