Python OptionParserGUIの例

コード例 #1

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

def cleanup():
    for d in toremove:
        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}
    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,

コード例 #2

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

toremove = []


def cleanup():
    for d in toremove:
        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,

コード例 #3

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

toremove = []


def cleanup():
    for d in toremove:
        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}
    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 #4

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

toremove = []


def cleanup():
    for d in toremove:
        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}
    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,

コード例 #5

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

def cleanup():
    for d in toremove:
        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}
    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",

コード例 #6

ファイル: SNPlice.py プロジェクト: qingnanl/NGS

def cleanup():
    for d in toremove:
        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,

コード例 #7

sys.excepthook = excepthook

toremove = []


def cleanup():
    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"),

コード例 #8

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


atexit.register(cleanup)

if len(sys.argv) == 2 and sys.argv[1] == '--GUI':
    from optparse_gui.needswx import *
    sys.exit(1)

if len(sys.argv) == 1:
    if not GUI():
        print("Graphical user-interface unavailable.", file=sys.stderr)
        sys.exit(1)
    from optparse_gui import OptionParserGUI
    parser = OptionParserGUI(version=VERSION)
    error_kwargs = {'exit': False}
    sys.excepthook = excepthook
else:
    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

コード例 #9

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

toremove = []


def cleanup():
    for d in toremove:
        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}
    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,

コード例 #10

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

    sys.stderr.flush()
    raw_input()
sys.excepthook = excepthook

toremove = []


def cleanup():
    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="",