本文整理汇总了Python中ete3.Tree.get_midpoint_outgroup方法的典型用法代码示例。如果您正苦于以下问题：Python Tree.get_midpoint_outgroup方法的具体用法？Python Tree.get_midpoint_outgroup怎么用？Python Tree.get_midpoint_outgroup使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类ete3.Tree的用法示例。
在下文中一共展示了Tree.get_midpoint_outgroup方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: outgroup
# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_midpoint_outgroup [as 别名]
parser.add_argument(
'--verbose', action='store_true',
help=('Print information about the outgroup (if any) taxa to standard '
'error'))
args = parser.parse_args()
tree = Tree(args.treeFile.read())
if args.outgroupRegex:
from re import compile
regex = compile(args.outgroupRegex)
taxa = [leaf.name for leaf in tree.iter_leaves() if regex.match(leaf.name)]
if taxa:
ca = tree.get_common_ancestor(taxa)
if args.verbose:
print('Taxa for outgroup:', taxa, file=sys.stderr)
print('Common ancestor:', ca.name, file=sys.stderr)
print('Common ancestor is tree:', tree == ca, file=sys.stderr)
if len(taxa) == 1:
tree.set_outgroup(tree & taxa[0])
else:
if ca == tree:
tree.set_outgroup(tree.get_midpoint_outgroup())
else:
tree.set_outgroup(tree.get_common_ancestor(taxa))
print(tree.get_ascii())
示例2: main
# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_midpoint_outgroup [as 别名]
#.........这里部分代码省略.........
os.system(andi_c)
#Read in the andi dist matrix, convert to lower triangle
dm = read_file_lines(andi_mat)[1:]
dm = lower_tri(dm)
#Correct the names in the matrix
for iso in isos:
#Could do it this way, but this is slower than a nested loop
#dm.names[dm.names.index(iso_ID_trans[iso])] = iso
#real 0m9.417s
#user 1m18.576s
#sys 0m2.620s
#Nested loop is faster
for i in range(0, len(dm.names)):
#iso_ID_trans[iso] is the short_id
if dm.names[i] == iso_ID_trans[iso]:
dm.names[i] = iso
#real 0m8.789s
#user 1m14.637s
#sys 0m2.420s
#From the distance matrix in dm, infer the NJ tree
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
constructor = DistanceTreeConstructor()
njtree = constructor.nj(dm)
njtree.rooted = True
from Bio import Phylo
Phylo.write(njtree, 'temp.tre', 'newick')
from ete3 import Tree
t = Tree('temp.tre', format=1)
#Get rid of negative branch lengths (an artefact, not an error, of NJ)
for node in t.traverse():
node.dist = abs(node.dist)
t.set_outgroup(t.get_midpoint_outgroup())
t_out = base+'_andi_NJ_'+ARGS.model_andi_distance+'dist.nwk.tre'
t.write(format=1, outfile=t_out)
print('Final tree (midpoint-rooted, NJ under '+\
ARGS.model_andi_distance+' distance) looks like this:')
#Print the ascii tree
print(t)
#Remove the temp.tre
os.remove('temp.tre')
print('Tree (NJ under '+ARGS.model_andi_distance+\
' distance, midpoint-rooted) written to '+t_out+'.')
#Run roary?
if ARGS.roary_run:
roary_keepers = [
"accessory.header.embl",
"accessory.tab",
"accessory_binary_genes.fa",
"accessory_binary_genes.fa.newick",
"accessory_binary_genes_midpoint.nwk.tre",
"accessory_graph.dot",
"blast_identity_frequency.Rtab",
"clustered_proteins",
"core_accessory.header.embl",
"core_accessory.tab",
"core_accessory_graph.dot",
"core_gene_alignment.aln",
"gene_presence_absence.Ltab.csv",
"gene_presence_absence.Rtab",
"gene_presence_absence.csv",
"number_of_conserved_genes.Rtab",
"number_of_genes_in_pan_genome.Rtab",
"number_of_new_genes.Rtab",