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()
# Read trees
first = True
for count, line in enumerate(fileinput.input(files),1):
t = ete2.Tree(line)
leaves = t.get_leaves()
# If first tree, get names
if first:
names = sorted([l.name for l in leaves])
print_middle(names)
first = False
for l in leaves:
if l.name in names:
l.name = str(names.index(l.name)+1)
# Print tree line
print "TREE tree_%d = %s" % (count, t.write())
print_footer()
# Done
return 0
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():
parser = optparse.OptionParser(__doc__)
options, files = parser.parse_args()
dedupe = Dedupe()
plumb(dedupe, 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()
taxa = Taxa()
plumb(taxa, files)
def run():
# Parse options
parser = optparse.OptionParser(__doc__)
parser.add_option('-a', '--attribute', dest="attribute", default=None)
parser.add_option('-d', '--dpi', type="int", default=None)
parser.add_option('-H', '--height', type="int", dest="h", default=None)
parser.add_option('-l', '--label', default="name")
parser.add_option('-m', '--multiple', default=False, action="store_true")
parser.add_option('-o', '--output', default=None)
parser.add_option('-u', '--units', default="px")
parser.add_option('-w', '--width', type="int", dest="w", default=None)
options, files = parser.parse_args()
# Setup TreeStyle
ts = ete2.TreeStyle()
ts.show_scale = False
ts.show_branch_support = True
# Read trees
for n, line in enumerate(fileinput.input(files)):
t = ete2.Tree(line)
# Add faces
if options.attribute:
values = set(
[getattr(l, options.attribute) for l in t.get_leaves()])
colours = get_colour_set(len(values))
colour_map = dict(zip(values, colours))
for l in t.iter_leaves():
mycolour = colour_map[getattr(l, options.attribute)]
l.add_face(
ete2.CircleFace(radius=10, color=mycolour, style="sphere"),
0)
for l in t.iter_leaves():
l.add_face(ete2.TextFace(getattr(l, options.label)), 1)
# Plot or save
if options.output:
kw = {}
if options.h or options.w:
for o in ("h", "w", "units", "dpi"):
if getattr(options, o):
kw[o] = getattr(options, o)
if options.multiple:
base, ext = os.path.splitext(options.output)
filename = base + ("_%06d" % (n + 1)) + ext
else:
filename = options.output
t.render(filename, ultrametric, tree_style=ts, **kw)
else:
t.show(ultrametric, tree_style=ts)
if not options.multiple:
return 0
return 0
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():
# 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():
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('-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)
def run():
# Parse options
parser = optparse.OptionParser(__doc__)
parser.add_option('-b',
'--burnin',
action="store",
dest="burnin",
type="int",
default=0)
parser.add_option('-s',
'--subsample',
action="store",
dest="subsample",
type="int",
default=1)
parser.add_option('--no-annotations',
action="store_true",
dest="no_annotations",
default=False)
options, files = parser.parse_args()
if not files:
files = ["-"]
# Read files
for filename in files:
if filename == "-":
fp = sys.stdin
else:
fp = open(filename, "r")
tree_strings = []
firstline = True
for line in fp:
# Skip blank lines
if not line:
continue
# Detect Nexus file format by checking first line
if firstline:
if line.strip() == "#NEXUS":
isNexus = True
inTranslate = False
nexus_trans = {}
else:
isNexus = False
firstline = False
# Detect beginning of Nexus translate block
if isNexus and "translate" in line.lower():
inTranslate = True
continue
# Handle Nexus translate block
if isNexus and inTranslate:
# Detect ending of translate block...
if line.strip() == ";":
inTranslate = False
# ...or handle a line of translate block
else:
if line.strip().endswith(";"):
line = line[:-1]
inTranslate = False
index, name = line.strip().split()
if name.endswith(","):
name = name[:-1]
nexus_trans[index] = name
# Try to find a likely tree on this line and extract it
if (")" in line and ";" in line
and line.count("(") == line.count(")")):
# Smells like a tree!
start = line.index("(")
end = line.rindex(";") + 1
tree_strings.append(line[start:end])
burnin = int(round((options.burnin / 100.0) * len(tree_strings)))
tree_strings = tree_strings[burnin::options.subsample]
while tree_strings:
tree_string = tree_strings.pop(0)
t = get_tree(tree_string)
if not t:
continue
if isNexus and nexus_trans:
for node in t.traverse():
if node.name and node.name in nexus_trans:
node.name = nexus_trans[node.name]
if options.no_annotations:
print t.write(format_root_node=True)
else:
print t.write(features=[], format_root_node=True)
# Done
return 0
