def main(argv):
parser = argparse.ArgumentParser(
description=__DESCRIPTION__,
formatter_class=argparse.RawDescriptionHelpFormatter)
# name or flags - Either a name or a list of option strings, e.g. foo or -f, --foo.
# action - The basic type of action to be taken when this argument is encountered at the command line. (store, store_const, store_true, store_false, append, append_const, version)
# nargs - The number of command-line arguments that should be consumed. (N, ? (one or default), * (all 1 or more), + (more than 1) )
# const - A constant value required by some action and nargs selections.
# default - The value produced if the argument is absent from the command line.
# type - The type to which the command-line argument should be converted.
# choices - A container of the allowable values for the argument.
# required - Whether or not the command-line option may be omitted (optionals only).
# help - A brief description of what the argument does.
# metavar - A name for the argument in usage messages.
# dest - The name of the attribute to be added to the object returned by parse_args().
input_gr = parser.add_argument_group(
"TREE INPUT OPTIONS\n=================")
input_gr.add_argument(
'tree',
metavar='tree_file',
type=str,
nargs=1,
help='A tree file (or text string) in newick format.')
input_gr.add_argument("--raxml",
dest="raxml",
action="store_true",
help="""Process newick as raxml bootstrap values""")
img_gr = parser.add_argument_group("TREE IMAGE OPTIONS\n=================")
img_gr.add_argument("-m",
"--mode",
dest="mode",
choices=["c", "r"],
default="r",
help="""(r)ectangular or (c)ircular visualization""")
img_gr.add_argument(
"-i",
"--image",
dest="image",
type=str,
help="Render tree image instead of showing it. A filename "
" should be provided. PDF, SVG and PNG file extensions are"
" supported (i.e. -i tree.svg)")
img_gr.add_argument(
"--Iw",
"--width",
dest="width",
type=int,
default=0,
help="width of the rendered image in pixels (see --size-units).")
img_gr.add_argument(
"--Ih",
"--height",
dest="height",
type=int,
default=0,
help="height of the rendered image in pixels (see --size-units).")
img_gr.add_argument("--Ir",
"--resolution",
dest="resolution",
type=int,
default=300,
help="Resolution if the tree image (DPI)")
img_gr.add_argument("--Iu",
"--size-units",
dest="size_units",
choices=["px", "mm", "in"],
default="px",
help="Units used to specify the size of the image."
" (px:pixels, mm:millimeters, in:inches). ")
img_gr.add_argument(
"-mbs",
"--min-branch-separation",
dest="branch_separation",
type=int,
default=3,
help="Min number of pixels to separate branches vertically.")
img_gr.add_argument("--ss",
"--show-support",
dest="show_support",
action="store_true",
help="""Shows branch bootstrap/support values""")
img_gr.add_argument("--sbl",
"--branch-length",
dest="show_branch_length",
action="store_true",
help="""Show branch lengths.""")
img_gr.add_argument(
"--ft",
"--force-topology",
dest="force_topology",
action="store_true",
help="""Force branch length to have a minimum length in the image""")
img_gr.add_argument("--hln",
"--hide-leaf-names",
dest="hide_leaf_names",
action="store_true",
help="""Hide leaf names.""")
img_gr.add_argument(
"--sin",
"--show-internal-names",
dest="show_internal_names",
action="store_true",
help="""Show the name attribute of all internal nodes.""")
edit_gr = parser.add_argument_group("TREE EDIT OPTIONS\n=================")
edit_gr.add_argument(
"-r",
"--root",
dest="root",
type=str,
nargs="*",
help="Roots the tree to the node grouping the list"
" of node names provided (space separated). In example:"
"'--root human rat mouse'")
edit_gr.add_argument("-s",
"--sort-branches",
dest="sort",
action="store_true",
help="""Sort branches according to node names.""")
edit_gr.add_argument("-l",
"--ladderize",
dest="ladderize",
action="store_true",
help="""Sort branches by partition size.""")
edit_gr.add_argument("--color_by_rank",
dest="color_by_rank",
type=str,
nargs="+",
help="""If the attribute rank is present in nodes """)
phylo_gr = parser.add_argument_group(
"PHYLOGENETIC OPTIONS\n=================")
phylo_gr.add_argument("--alg",
dest="alg",
type=str,
help="""Multiple sequence alignment.""")
phylo_gr.add_argument(
"--alg-format",
dest="alg_format",
type=str,
default="fasta",
help="""fasta, phylip, iphylip, relaxed_iphylip, relaxed_phylip.""")
phylo_gr.add_argument(
"--sp-discovery",
dest="species_discovery_regexp",
type=str,
default="^[^_]+_(.+)",
help="Perl regular expression to capture species"
" code from node names. By default, node names"
" are expected to follow the NAME_SPCODE format = '^[^_]+_(.+)' ")
phylo_gr.add_argument(
"--dump-subtrees",
dest="subtrees_output_file",
type=str,
help="Returns a file containing all possible species subtrees"
" contained in a given gene tree ")
phylo_gr.add_argument(
"--newick",
dest="newick",
type=str,
help="dumps newick file after applying editing options")
args = parser.parse_args(argv)
tfile = args.tree[0]
if args.ladderize and args.sort:
raise ValueError(
"--sort-branches and --ladderize options are mutually exclusive")
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]",
open(tfile).read())
t = PhyloTree(nw)
#for n in t.traverse():
#n.support = getattr(n, "bootstrap", -1)
#
else:
t = PhyloTree(tfile)
if args.alg:
t.link_to_alignment(args.alg, alg_format=args.alg_format)
LEAF_ATTRIBUTES["sequence"] = 1
if args.species_discovery_regexp:
SPCODE_REGEXP = re.compile(args.species_discovery_regexp)
t.set_species_naming_function(user_species_naming_function)
if args.ladderize:
t.ladderize()
if args.sort:
t.sort_descendants()
if args.root:
if len(args.root) > 1:
outgroup = t.get_common_ancestor(args.root)
else:
outgroup = t & args.root[0]
t.set_outgroup(outgroup)
# EXTRACT INFO
if args.subtrees_output_file:
ntrees, ndups, treeiter = t.get_speciation_trees()
print >> sys.stderr, "Found %d duplication nodes. Dumping %d sutrees..." % (
ndups, ntrees)
OUT = open(args.subtrees_output_file, "w")
for tree in treeiter:
print >> OUT, tree.write()
OUT.close()
# VISUALIZATION
ts = TreeStyle()
ts.mode = args.mode
ts.show_leaf_name = False
ts.branch_vertical_margin = args.branch_separation
if args.show_support:
ts.show_branch_support = True
if args.show_branch_length:
ts.show_branch_length = True
if args.force_topology:
ts.force_topology = True
if args.hide_leaf_names:
del LEAF_ATTRIBUTES["name"]
if args.show_internal_names:
INTERNAL_ATTRIBUTES["name"] = 1
# scale the tree
if not args.height:
args.height = None
if not args.width:
args.width = None
ts.layout_fn = master_layout
if args.image:
t.render(args.image,
tree_style=ts,
w=args.width,
h=args.height,
units=args.size_units)
else:
t.show(None, tree_style=ts)
if args.newick:
t.write(features=[], outfile=args.newick)
print "Processed Newick dumped into", args.newick
def main(argv):
parser = argparse.ArgumentParser(
description=__DESCRIPTION__,
formatter_class=argparse.RawDescriptionHelpFormatter)
input_gr = parser.add_argument_group(
"TREE INPUT OPTIONS\n=================")
input_gr.add_argument(
'tree',
metavar='tree_file',
type=str,
nargs=1,
help='A tree file (or text string) in newick format.')
input_gr.add_argument("--raxml",
dest="raxml",
action="store_true",
help="""Process newick as raxml bootstrap values""")
img_gr = parser.add_argument_group("TREE IMAGE OPTIONS\n=================")
img_gr.add_argument("-m",
"--mode",
dest="mode",
choices=["c", "r"],
default="r",
help="""(r)ectangular or (c)ircular visualization""")
img_gr.add_argument(
"-i",
"--image",
dest="image",
type=str,
help="Render tree image instead of showing it. A filename "
" should be provided. PDF, SVG and PNG file extensions are"
" supported (i.e. -i tree.svg)")
img_gr.add_argument("--text",
dest="text_mode",
action="store_true",
help="Shows the tree using ASCII characters")
img_gr.add_argument(
"--attr",
"--show_attributes",
dest="show_attributes",
nargs="+",
help="Display the value of the specified attributes, if available")
img_gr.add_argument(
"--Iw",
"--width",
dest="width",
type=int,
default=0,
help="width of the rendered image in pixels (see --size-units).")
img_gr.add_argument(
"--Ih",
"--height",
dest="height",
type=int,
default=0,
help="height of the rendered image in pixels (see --size-units).")
img_gr.add_argument("--Ir",
"--resolution",
dest="resolution",
type=int,
default=300,
help="Resolution if the tree image (DPI)")
img_gr.add_argument("--Iu",
"--size_units",
dest="size_units",
choices=["px", "mm", "in"],
default="px",
help="Units used to specify the size of the image."
" (px:pixels, mm:millimeters, in:inches). ")
img_gr.add_argument(
"-mbs",
"--min_branch_separation",
dest="branch_separation",
type=int,
default=3,
help="Min number of pixels to separate branches vertically.")
img_gr.add_argument("--ss",
"--show_support",
dest="show_support",
action="store_true",
help="""Shows branch bootstrap/support values""")
img_gr.add_argument("--sbl",
"--show_branch_length",
dest="show_branch_length",
action="store_true",
help="""Show branch lengths.""")
img_gr.add_argument(
"--ft",
"--force_topology",
dest="force_topology",
action="store_true",
help="""Force branch length to have a minimum length in the image""")
img_gr.add_argument("--hln",
"--hide_leaf_names",
dest="hide_leaf_names",
action="store_true",
help="""Hide leaf names.""")
img_gr.add_argument(
"--sin",
"--show_internal_names",
dest="show_internal_names",
action="store_true",
help="""Show the name attribute of all internal nodes.""")
edit_gr = parser.add_argument_group("TREE EDIT OPTIONS\n=================")
edit_gr.add_argument(
"-r",
"--root",
dest="root",
type=str,
nargs="*",
help="Roots the tree to the node grouping the list"
" of node names provided (space separated). In example:"
"'--root human rat mouse'")
edit_gr.add_argument("-s",
"--sort_branches",
dest="sort",
action="store_true",
help="""Sort branches according to node names.""")
edit_gr.add_argument("-l",
"--ladderize",
dest="ladderize",
action="store_true",
help="""Sort branches by partition size.""")
edit_gr.add_argument("--color_by_rank",
dest="color_by_rank",
type=str,
nargs="+",
help="""If the attribute rank is present in nodes """)
edit_gr.add_argument(
"--ncbi",
dest="ncbi",
action="store_true",
help=""" Annotate tree using the NCBI taxonomy database""")
edit_gr.add_argument(
"--taxid_attr",
dest="taxid_attr",
type=str,
default="name",
help="node attribute encoding for valid taxid numbers.")
edit_gr.add_argument(
"--taxid_attr_regexp",
dest="taxid_attr_regexp",
type=str,
help=
"If taxid number is encoded as part of another text string, i.e. gene name, use this argument to define a Perl regular expression to extract taxid numbers."
)
phylo_gr = parser.add_argument_group(
"PHYLOGENETIC OPTIONS\n=================")
phylo_gr.add_argument(
"--alg",
dest="alg",
type=str,
help="""Link tree to a multiple sequence alignment.""")
phylo_gr.add_argument(
"--alg_format",
dest="alg_format",
type=str,
default="fasta",
help="""fasta, phylip, iphylip, relaxed_iphylip, relaxed_phylip.""")
phylo_gr.add_argument(
"--sp_discovery",
dest="species_discovery_regexp",
type=str,
default="^[^_]+_(.+)",
help="Perl regular expression used to capture species"
" code from node names. By default, node names"
" are expected to follow the NAME_SPCODE format = '^[^_]+_(.+)' ")
args = parser.parse_args(argv)
tfile = args.tree[0]
if args.ladderize and args.sort:
raise ValueError(
"--sort-branches and --ladderize options are mutually exclusive")
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]",
open(tfile).read())
t = PhyloTree(nw)
else:
t = PhyloTree(tfile)
if args.ncbi:
if args.taxid_attr_regexp:
TAXIDMATCHER = re.compile(args.taxid_attr_regexp)
for lf in t:
if args.taxid_attr_regexp:
lf.taxid = re.search(TAXIDMATCHER,
getattr(lf, args.taxid_attr)).groups()[0]
else:
lf.taxid = getattr(lf, args.taxid_attr)
t.annotate_ncbi_taxa(taxid_attr="taxid")
if args.alg:
t.link_to_alignment(args.alg, alg_format=args.alg_format)
LEAF_ATTRIBUTES["sequence"] = 1
if args.species_discovery_regexp:
SPCODE_REGEXP = re.compile(args.species_discovery_regexp)
t.set_species_naming_function(user_species_naming_function)
if args.ladderize:
t.ladderize()
if args.sort:
t.sort_descendants()
if args.root:
if len(args.root) > 1:
outgroup = t.get_common_ancestor(args.root)
else:
outgroup = t & args.root[0]
t.set_outgroup(outgroup)
# VISUALIZATION
ts = TreeStyle()
ts.mode = args.mode
ts.show_leaf_name = False
ts.branch_vertical_margin = args.branch_separation
if args.show_support:
ts.show_branch_support = True
if args.show_branch_length:
ts.show_branch_length = True
if args.force_topology:
ts.force_topology = True
if args.hide_leaf_names:
del LEAF_ATTRIBUTES["name"]
if args.show_internal_names:
INTERNAL_ATTRIBUTES["name"] = 1
# scale the tree
if not args.height:
args.height = None
if not args.width:
args.width = None
if args.text_mode:
print t.get_ascii(show_internal=args.show_internal_names,
attributes=args.show_attributes)
else:
ts.layout_fn = master_layout
if args.image:
t.render(args.image,
tree_style=ts,
w=args.width,
h=args.height,
units=args.size_units)
else:
t.show(None, tree_style=ts)
def main(argv):
parser = argparse.ArgumentParser(description=__DESCRIPTION__,
formatter_class=argparse.RawDescriptionHelpFormatter)
# name or flags - Either a name or a list of option strings, e.g. foo or -f, --foo.
# action - The basic type of action to be taken when this argument is encountered at the command line. (store, store_const, store_true, store_false, append, append_const, version)
# nargs - The number of command-line arguments that should be consumed. (N, ? (one or default), * (all 1 or more), + (more than 1) )
# const - A constant value required by some action and nargs selections.
# default - The value produced if the argument is absent from the command line.
# type - The type to which the command-line argument should be converted.
# choices - A container of the allowable values for the argument.
# required - Whether or not the command-line option may be omitted (optionals only).
# help - A brief description of what the argument does.
# metavar - A name for the argument in usage messages.
# dest - The name of the attribute to be added to the object returned by parse_args().
input_gr = parser.add_argument_group("TREE INPUT OPTIONS\n=================")
input_gr.add_argument('tree', metavar='tree_file', type=str, nargs=1,
help='A tree file (or text string) in newick format.')
input_gr.add_argument("--raxml", dest="raxml",
action="store_true",
help="""Process newick as raxml bootstrap values""")
img_gr = parser.add_argument_group("TREE IMAGE OPTIONS\n=================")
img_gr.add_argument("-m", "--mode", dest="mode",
choices=["c", "r"], default="r",
help="""(r)ectangular or (c)ircular visualization""")
img_gr.add_argument("-i", "--image", dest="image",
type=str,
help="Render tree image instead of showing it. A filename "
" should be provided. PDF, SVG and PNG file extensions are"
" supported (i.e. -i tree.svg)"
)
img_gr.add_argument("--Iw", "--width", dest="width",
type=int, default=0,
help="width of the rendered image in pixels (see --size-units)."
)
img_gr.add_argument("--Ih", "--height", dest="height",
type=int, default=0,
help="height of the rendered image in pixels (see --size-units)."
)
img_gr.add_argument("--Ir", "--resolution", dest="resolution",
type=int, default=300,
help="Resolution if the tree image (DPI)"
)
img_gr.add_argument("--Iu", "--size-units", dest="size_units",
choices=["px", "mm", "in"], default="px",
help="Units used to specify the size of the image."
" (px:pixels, mm:millimeters, in:inches). "
)
img_gr.add_argument("-mbs", "--min-branch-separation", dest="branch_separation",
type=int, default = 3,
help="Min number of pixels to separate branches vertically."
)
img_gr.add_argument("--ss", "--show-support", dest="show_support",
action="store_true",
help="""Shows branch bootstrap/support values""")
img_gr.add_argument("--sbl", "--branch-length", dest="show_branch_length",
action="store_true",
help="""Show branch lengths.""")
img_gr.add_argument("--ft", "--force-topology", dest="force_topology",
action="store_true",
help="""Force branch length to have a minimum length in the image""")
img_gr.add_argument("--hln", "--hide-leaf-names", dest="hide_leaf_names",
action="store_true",
help="""Hide leaf names.""")
img_gr.add_argument("--sin", "--show-internal-names", dest="show_internal_names",
action="store_true",
help="""Show the name attribute of all internal nodes.""")
edit_gr = parser.add_argument_group("TREE EDIT OPTIONS\n=================")
edit_gr.add_argument("-r", "--root", dest="root",
type=str, nargs="*",
help="Roots the tree to the node grouping the list"
" of node names provided (space separated). In example:"
"'--root human rat mouse'")
edit_gr.add_argument("-s", "--sort-branches", dest="sort",
action="store_true",
help="""Sort branches according to node names.""")
edit_gr.add_argument("-l", "--ladderize", dest="ladderize",
action="store_true",
help="""Sort branches by partition size.""")
edit_gr.add_argument("--color_by_rank", dest="color_by_rank",
type=str, nargs="+",
help="""If the attribute rank is present in nodes """)
phylo_gr = parser.add_argument_group("PHYLOGENETIC OPTIONS\n=================")
phylo_gr.add_argument("--alg", dest="alg",
type=str,
help="""Multiple sequence alignment.""")
phylo_gr.add_argument("--alg-format", dest="alg_format",
type=str, default="fasta",
help="""fasta, phylip, iphylip, relaxed_iphylip, relaxed_phylip.""")
phylo_gr.add_argument("--sp-discovery", dest="species_discovery_regexp",
type=str, default="^[^_]+_(.+)",
help="Perl regular expression to capture species"
" code from node names. By default, node names"
" are expected to follow the NAME_SPCODE format = '^[^_]+_(.+)' ")
phylo_gr.add_argument("--dump-subtrees", dest="subtrees_output_file",
type=str,
help="Returns a file containing all possible species subtrees"
" contained in a given gene tree ")
phylo_gr.add_argument("--newick", dest="newick",
type=str,
help="dumps newick file after applying editing options")
args = parser.parse_args(argv)
tfile = args.tree[0]
if args.ladderize and args.sort:
raise ValueError("--sort-branches and --ladderize options are mutually exclusive")
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
t = PhyloTree(nw)
#for n in t.traverse():
#n.support = getattr(n, "bootstrap", -1)
#
else:
t = PhyloTree(tfile)
if args.alg:
t.link_to_alignment(args.alg, alg_format=args.alg_format)
LEAF_ATTRIBUTES["sequence"] = 1
if args.species_discovery_regexp:
SPCODE_REGEXP = re.compile(args.species_discovery_regexp)
t.set_species_naming_function(user_species_naming_function)
if args.ladderize:
t.ladderize()
if args.sort:
t.sort_descendants()
if args.root:
if len(args.root) > 1:
outgroup = t.get_common_ancestor(args.root)
else:
outgroup = t & args.root[0]
t.set_outgroup(outgroup)
# EXTRACT INFO
if args.subtrees_output_file:
ntrees, ndups, treeiter = t.get_speciation_trees()
print >>sys.stderr, "Found %d duplication nodes. Dumping %d sutrees..." %(ndups, ntrees)
OUT = open(args.subtrees_output_file, "w")
for tree in treeiter:
print >>OUT, tree.write()
OUT.close()
# VISUALIZATION
ts = TreeStyle()
ts.mode = args.mode
ts.show_leaf_name = False
ts.branch_vertical_margin = args.branch_separation
if args.show_support:
ts.show_branch_support = True
if args.show_branch_length:
ts.show_branch_length = True
if args.force_topology:
ts.force_topology = True
if args.hide_leaf_names:
del LEAF_ATTRIBUTES["name"]
if args.show_internal_names:
INTERNAL_ATTRIBUTES["name"] = 1
# scale the tree
if not args.height:
args.height = None
if not args.width:
args.width = None
ts.layout_fn = master_layout
if args.image:
t.render(args.image, tree_style=ts, w=args.width, h=args.height, units=args.size_units)
else:
t.show(None, tree_style=ts)
if args.newick:
t.write(features=[], outfile=args.newick)
print "Processed Newick dumped into", args.newick
def main(argv):
parser = argparse.ArgumentParser(description=__DESCRIPTION__,
formatter_class=argparse.RawDescriptionHelpFormatter)
input_gr = parser.add_argument_group("TREE INPUT OPTIONS\n=================")
input_gr.add_argument('tree', metavar='tree_file', type=str, nargs=1,
help='A tree file (or text string) in newick format.')
input_gr.add_argument("--raxml", dest="raxml",
action="store_true",
help="""Process newick as raxml bootstrap values""")
img_gr = parser.add_argument_group("TREE IMAGE OPTIONS\n=================")
img_gr.add_argument("-m", "--mode", dest="mode",
choices=["c", "r"], default="r",
help="""(r)ectangular or (c)ircular visualization""")
img_gr.add_argument("-i", "--image", dest="image",
type=str,
help="Render tree image instead of showing it. A filename "
" should be provided. PDF, SVG and PNG file extensions are"
" supported (i.e. -i tree.svg)"
)
img_gr.add_argument("--text", dest="text_mode",
action="store_true",
help="Shows the tree using ASCII characters")
img_gr.add_argument("--attr", "--show_attributes", dest="show_attributes",
nargs="+",
help="Display the value of the specified attributes, if available")
img_gr.add_argument("--Iw", "--width", dest="width",
type=int, default=0,
help="width of the rendered image in pixels (see --size-units)."
)
img_gr.add_argument("--Ih", "--height", dest="height",
type=int, default=0,
help="height of the rendered image in pixels (see --size-units)."
)
img_gr.add_argument("--Ir", "--resolution", dest="resolution",
type=int, default=300,
help="Resolution if the tree image (DPI)"
)
img_gr.add_argument("--Iu", "--size_units", dest="size_units",
choices=["px", "mm", "in"], default="px",
help="Units used to specify the size of the image."
" (px:pixels, mm:millimeters, in:inches). "
)
img_gr.add_argument("-mbs", "--min_branch_separation", dest="branch_separation",
type=int, default = 3,
help="Min number of pixels to separate branches vertically."
)
img_gr.add_argument("--ss", "--show_support", dest="show_support",
action="store_true",
help="""Shows branch bootstrap/support values""")
img_gr.add_argument("--sbl", "--show_branch_length", dest="show_branch_length",
action="store_true",
help="""Show branch lengths.""")
img_gr.add_argument("--ft", "--force_topology", dest="force_topology",
action="store_true",
help="""Force branch length to have a minimum length in the image""")
img_gr.add_argument("--hln", "--hide_leaf_names", dest="hide_leaf_names",
action="store_true",
help="""Hide leaf names.""")
img_gr.add_argument("--sin", "--show_internal_names", dest="show_internal_names",
action="store_true",
help="""Show the name attribute of all internal nodes.""")
edit_gr = parser.add_argument_group("TREE EDIT OPTIONS\n=================")
edit_gr.add_argument("-r", "--root", dest="root",
type=str, nargs="*",
help="Roots the tree to the node grouping the list"
" of node names provided (space separated). In example:"
"'--root human rat mouse'")
edit_gr.add_argument("-s", "--sort_branches", dest="sort",
action="store_true",
help="""Sort branches according to node names.""")
edit_gr.add_argument("-l", "--ladderize", dest="ladderize",
action="store_true",
help="""Sort branches by partition size.""")
edit_gr.add_argument("--color_by_rank", dest="color_by_rank",
type=str, nargs="+",
help="""If the attribute rank is present in nodes """)
edit_gr.add_argument("--ncbi", dest="ncbi",
action="store_true",
help=""" Annotate tree using the NCBI taxonomy database""")
edit_gr.add_argument("--taxid_attr", dest="taxid_attr",
type=str, default="name",
help="node attribute encoding for valid taxid numbers.")
edit_gr.add_argument("--taxid_attr_regexp", dest="taxid_attr_regexp",
type=str,
help="If taxid number is encoded as part of another text string, i.e. gene name, use this argument to define a Perl regular expression to extract taxid numbers.")
phylo_gr = parser.add_argument_group("PHYLOGENETIC OPTIONS\n=================")
phylo_gr.add_argument("--alg", dest="alg",
type=str,
help="""Link tree to a multiple sequence alignment.""")
phylo_gr.add_argument("--alg_format", dest="alg_format",
type=str, default="fasta",
help="""fasta, phylip, iphylip, relaxed_iphylip, relaxed_phylip.""")
phylo_gr.add_argument("--sp_discovery", dest="species_discovery_regexp",
type=str, default="^[^_]+_(.+)",
help="Perl regular expression used to capture species"
" code from node names. By default, node names"
" are expected to follow the NAME_SPCODE format = '^[^_]+_(.+)' ")
args = parser.parse_args(argv)
tfile = args.tree[0]
if args.ladderize and args.sort:
raise ValueError("--sort-branches and --ladderize options are mutually exclusive")
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
t = PhyloTree(nw)
else:
t = PhyloTree(tfile)
if args.ncbi:
if args.taxid_attr_regexp:
TAXIDMATCHER = re.compile(args.taxid_attr_regexp)
for lf in t:
if args.taxid_attr_regexp:
lf.taxid = re.search(TAXIDMATCHER, getattr(lf, args.taxid_attr)).groups()[0]
else:
lf.taxid = getattr(lf, args.taxid_attr)
t.annotate_ncbi_taxa(taxid_attr="taxid")
if args.alg:
t.link_to_alignment(args.alg, alg_format=args.alg_format)
LEAF_ATTRIBUTES["sequence"] = 1
if args.species_discovery_regexp:
SPCODE_REGEXP = re.compile(args.species_discovery_regexp)
t.set_species_naming_function(user_species_naming_function)
if args.ladderize:
t.ladderize()
if args.sort:
t.sort_descendants()
if args.root:
if len(args.root) > 1:
outgroup = t.get_common_ancestor(args.root)
else:
outgroup = t & args.root[0]
t.set_outgroup(outgroup)
# VISUALIZATION
ts = TreeStyle()
ts.mode = args.mode
ts.show_leaf_name = False
ts.branch_vertical_margin = args.branch_separation
if args.show_support:
ts.show_branch_support = True
if args.show_branch_length:
ts.show_branch_length = True
if args.force_topology:
ts.force_topology = True
if args.hide_leaf_names:
del LEAF_ATTRIBUTES["name"]
if args.show_internal_names:
INTERNAL_ATTRIBUTES["name"] = 1
# scale the tree
if not args.height:
args.height = None
if not args.width:
args.width = None
if args.text_mode:
print t.get_ascii(show_internal=args.show_internal_names, attributes = args.show_attributes)
else:
ts.layout_fn = master_layout
if args.image:
t.render(args.image, tree_style=ts, w=args.width, h=args.height, units=args.size_units)
else:
t.show(None, tree_style=ts)
