def run(): parser = optparse.OptionParser(__doc__) options, files = parser.parse_args() dedupe = Dedupe() plumb(dedupe, files)
def run(): parser = optparse.OptionParser(__doc__) parser.add_option('-a', '--attribute', default=None) parser.add_option('-f', '--file', dest="filename", help='Specifies a file from which to read taxa') parser.add_option('-i', '--inverse', action="store_true", default=False, dest="inverse") parser.add_option('-v', '--value', default=None) options, files = parser.parse_args() if (options.attribute and options.value) or options.filename: taxa = [] else: if files: taxa = set(files[0].split(",")) files = files[1:] else: sys.stderr.write( "Must specify either a list of taxa, a file of taxa, or an attribute and value.\n" ) sys.exit(1) prune = Prune(taxa, options.filename, options.attribute, options.value, options.inverse) plumb(prune, files)
def run(): # Parse options parser = optparse.OptionParser(__doc__) parser.add_option('-a', '--age', action="store_true", dest="age", default=False, help="Include age information in report.") parser.add_option('-f', '--frequency', type="float", dest="frequency", default=1.0, help='Minimum clade frequency to report.') parser.add_option("-o", "--output", action="store", dest="filename", help="save clades to FILE", metavar="FILE") parser.add_option('-s', '--sort', action="store_true", dest="sort", default=False) options, files = parser.parse_args() support = Support(options.frequency, options.age, options.sort, options.filename) plumb(support, files)
def run(): # Parse options parser = optparse.OptionParser(__doc__) options, files = parser.parse_args() stat = Stat() plumb(stat, files)
def run(): parser = optparse.OptionParser(__doc__) options, files = parser.parse_args() height = Height() plumb(height, files)
def run(): # Parse options parser = optparse.OptionParser(__doc__) options, files = parser.parse_args() taxa = Taxa() plumb(taxa, files)
def run(): parser = optparse.OptionParser(__doc__) parser.add_option('-a', '--attribute', dest="attribute", default=None) parser.add_option('-t', '--translate', help='Specifies the translation file.',default=None) options, files = parser.parse_args() collapse = Collapse(options.translate, options.attribute) plumb(collapse, files)
def run(): # Parse options parser = optparse.OptionParser(__doc__) parser.add_option('-a', '--ages', action="store_true", dest="age", default=False, help="Include age information in report.") parser.add_option('-f', '--frequency', type="float", dest="frequency", default=1.0, help='Minimum clade frequency to report.') options, files = parser.parse_args() clades = Clades(options.frequency, options.age) plumb(clades, files)
def run(): # Parse options parser = optparse.OptionParser(__doc__) parser.add_option('-c', '--compress', action="store_true", dest="compress", default=False) options, files = parser.parse_args() pretty = Pretty(compress=options.compress) plumb(pretty, files)
def run(): # Parse options parser = optparse.OptionParser(__doc__) parser.add_option('-s', '--scale', type="float", default=1.0, help='Scaling factor.') options, files = parser.parse_args() scale = Scale(options.scale) plumb(scale, files)
def run(): # Parse options parser = optparse.OptionParser(__doc__) parser.add_option('-f', '--file', dest="filename", help='Specifies the translation file.') print(sys.argv) options, files = parser.parse_args() rename = Rename(options.filename) plumb(rename, files)
def run(): parser = optparse.OptionParser(__doc__) parser.add_option('-f', '--frequency', type="float", dest="frequency", default=0.5, help="Minimum clade support to include in tree.") options, files = parser.parse_args() consensus = Consensus(options.frequency) plumb(consensus, file)
def run(): # Parse options parser = optparse.OptionParser(__doc__) parser.add_option('-l', '--lengths', action="store", dest="lengths", default="mean") options, files = parser.parse_args() uniq = Uniq(options.lengths) plumb(uniq, files)
def run(): # Parse options parser = optparse.OptionParser(__doc__) parser.add_option('-n', action="store", dest="iterations", type="int", default=1) parser.add_option('-g', "--guard", action="store", dest="guarded") options, files = parser.parse_args() rogue = Rogue(options.iterations, options.guarded) plumb(rogue, files)
def run(): # Parse options parser = optparse.OptionParser(__doc__) parser.add_option('-e', '--extract', action="store_true", help="Extract data from annotated tree to file.") parser.add_option('-f', '--file', dest="filename", help="File to read/write annotation data from/to.") parser.add_option( '-k', '--key', dest="key", help="Name of column in annotation file to match against taxon names") parser.add_option('-m', '--multiple', default=False, action="store_true") options, files = parser.parse_args() annotate = Annotate(options.filename, options.key, options.extract, options.multiple) plumb(annotate, files)