# advanced.add_option("-d", "--debug", action="store_true", dest="debug", default=False, remember=True, # help="Debug.", name="Debug") 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")]) parser.add_option_group(advanced) opt = None while True: if 'exit' in error_kwargs: try: opt, args = parser.parse_args(opts=opt) except UserCancelledError: sys.exit(0) else: opt, args = parser.parse_args() break progress = None if not opt.output:
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") readcounts.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") readcounts.add_option("-U", "--uniquereads", action="store_true", dest="unique", default=False, remember=True, help="Consider only distinct reads.", name="Unique Reads") readcounts.add_option("-t", "--threadsperbam", type="int", dest="tpb", default=1, remember=True, help="Worker threads per alignment file. Indicate no threading with 0. Default=1.", name="Threads/BAM") readcounts.add_option("-q", "--quiet", action="store_true", dest="quiet", default=False, remember=True, help="Quiet.", name="Quiet") parser.add_option("-o", "--output", type="savedir", dest="output", remember=True, help="Output folder. Required.", default=None, notNone=True, name="Output Folder") parser.add_option_group(exfilt) parser.add_option_group(readcounts) parser.add_option_group(regexs) parser.add_option_group(snvannot) opt = None while True: if 'exit' in error_kwargs: try: opt, args = parser.parse_args(opts=opt) except UserCancelledError: sys.exit(0) else: opt, args = parser.parse_args() break
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") advanced.add_option("-t", "--threadsperbam", type="int", dest="tpb", default=0, remember=True, help="Worker threads per alignment file. Indicate no threading with 0. Default=0.", name="Threads/BAM") advanced.add_option("-q", "--quiet", action="store_true", dest="quiet", default=False, remember=True, help="Quiet.", name="Quiet") advanced.add_option("-d", "--debug", action="store_true", dest="debug", default=False, remember=True, help="Debug.", name="Debug") 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")]) parser.add_option_group(advanced) opt = None while True: if 'exit' in error_kwargs: try: opt, args = parser.parse_args(opts=opt) except UserCancelledError: sys.exit(0) else: opt, args = parser.parse_args() break progress = None if not opt.output: