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,
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,
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")])
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,
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",
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,
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"),
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
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="",