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)
