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phylolib2.py
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phylolib2.py
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#!/usr/bin/env python
import re
import copy
import numpy
class ascii_tree(object):
def __init__(self):
self.code = None
self.leaves = None
self.char_array = None
def code_to_number_of_leaves(self, code):
return len(self.code_to_char_list(code))
def create_empty_array(self, leaves=None):
if leaves is None:
leaves = self.leaves
#rows: 3->5, 4->7, 5->9 => rows = 2*leaves - 1
rows = 2*leaves - 1
#cols =
cols = 3*leaves + 3
char_array = numpy.empty((rows, cols), dtype='str')
char_array[:] = ' '
return char_array
def print_array(self):
lines = []
shape = self.char_array.shape
for rownum in range(shape[0]):
line = ''.join(self.char_array[rownum]) + ' '
print(line)
print("")
def code_to_char_list(self, code):
#print(code)
re_list = re.split("[^a-zA-Z]*", code)
#re_list has extra spaces
#char_str = ''.join(re_list)
#char_list = list(char_str)
char_list = list(filter(None, re_list))
return char_list
def get_edge_number_for_string(self, my_str, code):
if len(my_str) == self.leaves:
return None
index = code.find(my_str)
digit1 = code[index-1]
try:
digit2 = code[index+len(my_str)]
except IndexError:
digit2 = 'None'
if digit1.isdigit():
if digit2.isdigit():
print("character {0} has two edge numbers {1} and {2}".format(my_str, digit1, digit2))
raise
edge_number = int(digit1)
elif digit2.isdigit():
edge_number = int(digit2)
else:
print("character {0} has no edge number".format(my_str))
return None
return edge_number
def edge_number_to_line_length(self, edge_number):
#line_length = 3*edge_number + 1
#self.edge_number_to_line_length = {1:4, 2:7, 3:10, 4:13, 5:16, 6:19, 7:22}
line_length = 3*edge_number + 1
return line_length
def make_tree(self, code=None):
if code is None:
code = '(((a3b)4((c1d)2e))5f)'
code = '(((a1b)4((c2d)3e))5f)'
code = '(((a3b)5((c1d)4e))6(f2g))'
self.code = code
self.leaves = self.code_to_number_of_leaves(self.code)
self.char_array = self.create_empty_array(self.leaves)
char_list = self.code_to_char_list(code)
#print(char_list)
char_edge_number = {}
char_row_number = {}
edge_number_char_list = {}
for i,character in enumerate(char_list):
row = i*2
char_row_number[character] = row
self.char_array[row, -1] = character
edge_number = self.get_edge_number_for_string(character, code)
char_edge_number[character] = edge_number
edge_number_char_list[edge_number] = edge_number_char_list.get(edge_number, []) + [character]
line_length = self.edge_number_to_line_length(edge_number)
self.char_array[row, -line_length-2:-2] = '_'
#print(char_edge_number)
#print(edge_number_char_list)
newcode = copy.copy(code)
for edge_number in range(1, self.leaves):
#print("===========\nedge_number {0} of {1} for code: '{2}'".format(edge_number,self.leaves-1,newcode))
index = newcode.find(str(edge_number))
#char1 = newcode[index-1]
#char2 = newcode[index+1]
#if char1 in '()' or char2 in '()':
# continue
char1 = edge_number_char_list[edge_number][0]
char2 = edge_number_char_list[edge_number][1]
subcode = "({0}{1}{2})".format(char1,edge_number,char2)
if not subcode in newcode:
#swap order
char2, char1 = char1, char2
subcode = "({0}{1}{2})".format(char1,edge_number,char2)
if not subcode in newcode:
print('{0} not found in {1}'.format(subcode, newcode))
raise
#print(char1, char2)
row1 = char_row_number[char1]
row2 = char_row_number[char2]
midrow = (row1 + row2 + 1)//2
combined = "{0}{2}".format(char1,edge_number,char2)
#print("{0} -> {1},".format(subcode, combined))
newcode = newcode.replace(subcode, combined)
#print("{0} -> {1},".format(code, newcode))
new_edge_number = self.get_edge_number_for_string(combined, newcode)
if new_edge_number is not None:
edge_number_char_list[new_edge_number] = edge_number_char_list.get(new_edge_number, []) + [combined]
char_row_number[combined] = midrow
#print(char_row_number)
#print(row1, row2, midrow)
line_length = self.edge_number_to_line_length(edge_number)
if new_edge_number is not None:
next_line_length = self.edge_number_to_line_length(new_edge_number)
#print(line_length, next_line_length)
gap = next_line_length - line_length - 1
else:
gap = 2
#self.char_array[row1, -line_length-2:-2] = '_'
#self.char_array[row2, -line_length-2:-2] = '_'
self.char_array[midrow, -line_length-3-gap:-line_length-3] = '_'
self.char_array[row1+1:row2+1, -line_length-3] = '|'
return
code_library = {
### Number of types for number of leaves:
# Wedderburn-Etherington numbers
# https://oeis.org/A001190
# unlabeled binary rooted trees (every node has out-degree 0 or 2) with n endpoints (and 2n-1 nodes in all)
# 1, 1, 2, 3, 6, 11, 23, 46, 98, 207, 451, ...
### Number of edge-labeled for number of leaves:
# https://oeis.org/A000111
# 1, 1, 2, 5, 16, 61, 272, 1385, 7936, 50521, ...
# 10: 98
# 9+1: 46, 8+2: 23, 7+3: 11, 6+4: 6*2, 5+5: 3*3 - 3
# 46 + 23 + 11 + 6*2 + 3*3 - 3 = 98
# subtraction is (n*n - n)//2; n = 3
# 11: 207
# 10+1: 98, 9+2: 46, 8+3: 23, 7+4: 2*11, 6+5: 3*6
# 98 + 46 + 23+ 2*11 + 3*6 = 207
# 12: 451
# 11+1: 207, 10+2: 98, 9+3: 46, 8+4: 2*23, 7+5: 3*11, 6+6: 6*6 - 15
# 207 + 98 + 46 + 2*23+ 3*11 + 6*6 - 15 = 451
# subtraction is (n*n - n)//2; n = 6
# 13: 983
# 12+1: 451, 11+2: 207, 10+3: 98, 9+4: 2*46, 8+5: 3*23, 7+6: 6*11
# 451 + 207 + 98 + 2*46 + 3*23 + 6*11 = 983
# 14: 2179
# 13+1: 983, 12+2: 451, 11+3: 207, 10+4: 2*98, 9+5: 3*46, 8+6: 6*23, 7+7: 11*11 - 55
# 983 + 451 + 207 + 2*98 + 3*46 + 6*23 + 11*11 - 55 = 2179
# subtraction is (n*n - n)//2; n = 11
## 2 leaves -- 1 type / 1 edge-labeled
'pair': '(a1b)',
## 3 leaves -- 1 type / 1 edge-labeled
'3comb': '((a1b)2c)',
#'3comb*': '(a2(b1c))',
## 4 leaves -- 2 type / 2 edge-labeled
'4comb': '(((a1b)2c)3d)', #type 1
#'4comb*': '(a3(b2(c1d)))',
'4balanced': '((a1b)3(c2d))', #type 2
#'4balanced*': '((a2b)3(c1d))',
## 5 leaves -- 3 type / 5 edge-labeled
'5comb': '((((a1b)2c)3d)4e)', #type 1
'5giraffe': '(((a1b)3(c2d))4e)', #type 2
#'5giraffe*': '(((a2b)3(c1d))4e)',
'3comb+pair1': '(((a1b)2c)4(d3e))', #type 3 / 3 edge-labels
'3comb+pair2': '(((a1b)3c)4(d2e))',
'3comb+pair3': '(((a2b)3c)4(d1e))',
###================================================
## 6 leaves -- 6 type / 16 edge-labeled
'6comb': '(((((a1b)2c)3d)4e)5f)', #type 1
'5giraffe+1': '((((a1b)3(c2d))4e)5f)', #type 2
#'5giraffe*+1': '((((a2b)3(c1d))4e)5f)',
'3comb+pair1+1': '((((a1b)2c)4(d3e))5f)', #type 3 / 3 edge-labels
'3comb+pair2+1': '((((a1b)3c)4(d2e))5f)',
'3comb+pair3+1': '((((a2b)3c)4(d1e))5f)',
'4comb+pair1': '((((a1b)2c)3d)5(e4f))', #type 4 / 4 edge-labels
'4comb+pair2': '((((a1b)2c)4d)5(e3f))',
'4comb+pair3': '((((a1b)3c)4d)5(e2f))',
'4comb+pair4': '((((a2b)3c)4d)5(e1f))',
'6twohead1': '(((a1b)3(c2d))5(e4f))', #type 5 / 4 edge-labels
'6twohead2': '(((a1b)4(c2d))5(e3f))',
'6twohead3': '(((a1b)4(c3d))5(e2f))',
'6twohead4': '(((a2b)4(c3d))5(e1f))',
#'6twohead*1': '(((a2b)3(c1d))5(e4f))',
#'6twohead*2': '(((a2b)4(c1d))5(e3f))',
#'6twohead*3': '(((a3b)4(c1d))5(e2f))',
#'6twohead*4': '(((a3b)4(c2d))5(e1f))',
'6balanced1': '(((a1b)2c)5((d3e)4f))', #type 6 / 3 edge-labels
'6balanced2': '(((a1b)3c)5((d2e)4f))',
'6balanced3': '(((a2b)3c)5((d1e)4f))',
#'6balanced3*': '(((a1b)4c)5((d2e)3f))',
#'6balanced2*': '(((a2b)4c)5((d1e)3f))',
#'6balanced1*': '(((a3b)4c)5((d1e)2f))',
###================================================
## 7 leaves -- 11 type / 61 edge-labeled
'7comb': '((((((a1b)2c)3d)4e)5f)6g)', #type 1 / 1 edge-labels
'5giraffe+1+1': '(((((a1b)3(c2d))4e)5f)6g)', #type 2 / 1 edge-labels
'3comb+pair1+1+1': '(((((a1b)2c)4(d3e))5f)6g)', #type 3 / 3 edge-labels
'4comb+pair1+1': '(((((a1b)2c)3d)5(e4f))6g)', #type 4 / 4 edge-labels
'6twohead1+1': '((((a1b)3(c2d))5(e4f))6g)', #type 5 / 4 edge-labels
'6balanced1+1': '((((a1b)2c)5((d3e)4f))6g)', #type 6 / 3 edge-labels
'5comb+pair': '(((((a1b)2c)3d)4e)6(f5g))', #type 7 / 5 edge-labels
'5giraffe+pair': '((((a1b)3(c2d))4e)6(f5g))', #type 8 / 5 edge-labels
'3comb+pair1+pair': '((((a1b)2c)4(d3e))6(f5g))', #type 9 / 5x3 = 15 edge-labels
'4comb+3comb': '((((a1b)2c)3d)6((e4f)5g))', #type 10 / (4+3+2+1) = 10 edge-labels
'4balanced+3comb': '(((a1b)3(c2d))6((e4f)5g))', #type 11 / (4+3+2+1) = 10 edge-labels
###================================================
## 8 leaves -- 24 type / 272 edge-labeled
# 11 from 7 leaves
'8comb': '(((((((a1b)2c)3d)4e)5f)6g)7h)', #type 1 / 1 edge-labels
'5giraffe+1+1+1': '((((((a1b)3(c2d))4e)5f)6g)7h)', #type 2 / 1 edge-labels
'3comb+pair1+1+1+1': '((((((a1b)2c)4(d3e))5f)6g)7h)', #type 3 / 3 edge-labels
'4comb+pair1+1+1': '((((((a1b)2c)3d)5(e4f))6g)7h)', #type 4 / 4 edge-labels
'6twohead1+1+1': '(((((a1b)3(c2d))5(e4f))6g)7h)', #type 5 / 4 edge-labels
'6balanced1+1+1': '(((((a1b)2c)5((d3e)4f))6g)7h)', #type 6 / 3 edge-labels
'5comb+pair+1': '((((((a1b)2c)3d)4e)6(f5g))7h)', #type 7 / 5 edge-labels
'5giraffe+pair+1': '(((((a1b)3(c2d))4e)6(f5g))7h)', #type 8 / 5 edge-labels
'3comb+pair1+pair+1': '(((((a1b)2c)4(d3e))6(f5g))7h)', #type 9 / 15 edge-labels
'4comb+3comb+1': '(((((a1b)2c)3d)6((e4f)5g))7h)', #type 10 / 10 edge-labels
'4balanced+3comb+1': '((((a1b)3(c2d))6((e4f)5g))7h)', #type 11 / 10 edge-labels
# 6 from 6 leaves
'6comb+pair': '((((((a1b)2c)3d)4e)5f)7(g6h))', #type 12 / 6 edge-labels
'5giraffe+1+pair': '(((((a1b)3(c2d))4e)5f)7(g6h))', #type 13 / 6 edge-labels
'3comb+pair1+1+pair': '(((((a1b)2c)4(d3e))5f)7(g6h))', #type 14 / 18 edge-labels
'4comb+pair1+pair': '(((((a1b)2c)3d)5(e4f))7(g6h))', #type 15 / 24 edge-labels
'6twohead1+pair': '((((a1b)3(c2d))5(e4f))7(g6h))', #type 16 / 24 edge-labels
'6balanced1+pair': '((((a1b)2c)5((d3e)4f))7(g6h))', #type 17 / 18 edge-labels
# 3 from 5 leaves
'5comb+3comb': '(((((a1b)2c)3d)4e)7((f5g)6h))', #type 18 / 15 edge-labels
'5giraffe+3comb': '((((a1b)3(c2d))4e)7((f5g)6h))', #type 19 / 15 edge-labels
'3comb+pair1+3comb': '((((a1b)2c)4(d3e))7((f5g)6h))', #type 20 / 45 edge-labels
# 2x2 from 4 leaves
'8hanukkah': '((((a1b)3c)5d)7(e6(f4(g2h))))', #type 21 / 10 edge-labels
'8balanced': '(((a1b)5(c3d))7((e4f)6(g2h)))', #type 22 / 10 edge-labels
#'4balanced+4comb': '(((a1b)3(c2d))7(((e4f)5g)6h))', #duplicate
'4comb+4balanced': '((((a1b)2c)3d)7((e4f)6(g5h)))', #type 23 / 20 edge-labels
###================================================
## 9 leaves -- 24 type / 272 edge-labeled
# 23 from 8 leaves
'9comb': '((((((((a1b)2c)3d)4e)5f)6g)7h)8i)', #type 1 / 1 edge-labels
'5giraffe+1+1+1+1': '(((((((a1b)3(c2d))4e)5f)6g)7h)8i)', #type 2 / 1 edge-labels
'3comb+pair1+1+1+1+1': '(((((((a1b)2c)4(d3e))5f)6g)7h)8i)', #type 3 / 3 edge-labels
'4comb+pair1+1+1+1': '(((((((a1b)2c)3d)5(e4f))6g)7h)8i)', #type 4 / 4 edge-labels
'6twohead1+1+1+1': '((((((a1b)3(c2d))5(e4f))6g)7h)8i)', #type 5 / 4 edge-labels
'6balanced1+1+1+1': '((((((a1b)2c)5((d3e)4f))6g)7h)8i)', #type 6 / 3 edge-labels
'5comb+pair+1+1': '(((((((a1b)2c)3d)4e)6(f5g))7h)8i)', #type 7 / 5 edge-labels
'5giraffe+pair+1+1': '((((((a1b)3(c2d))4e)6(f5g))7h)8i)', #type 8 / 5 edge-labels
'3comb+pair1+pair+1+1': '((((((a1b)2c)4(d3e))6(f5g))7h)8i)', #type 9 / 15 edge-labels
'4comb+3comb+1+1': '((((((a1b)2c)3d)6((e4f)5g))7h)8i)', #type 10 / 10 edge-labels
'4balanced+3comb+1+1': '(((((a1b)3(c2d))6((e4f)5g))7h)8i)', #type 11 / 10 edge-labels
'6comb+pair+1': '(((((((a1b)2c)3d)4e)5f)7(g6h))8i)', #type 12 / 6 edge-labels
'5giraffe+1+pair+1': '((((((a1b)3(c2d))4e)5f)7(g6h))8i)', #type 13 / 6 edge-labels
'3comb+pair1+1+pair+1': '((((((a1b)2c)4(d3e))5f)7(g6h))8i)', #type 14 / 18 edge-labels
'4comb+pair1+pair+1': '((((((a1b)2c)3d)5(e4f))7(g6h))8i)', #type 15 / 24 edge-labels
'6twohead1+pair+1': '(((((a1b)3(c2d))5(e4f))7(g6h))8i)', #type 16 / 24 edge-labels
'6balanced1+pair+1': '(((((a1b)2c)5((d3e)4f))7(g6h))8i)', #type 17 / 18 edge-labels
'5comb+3comb+1': '((((((a1b)2c)3d)4e)7((f5g)6h))8i)', #type 18 / 15 edge-labels
'5giraffe+3comb+1': '(((((a1b)3(c2d))4e)7((f5g)6h))8i)', #type 19 / 15 edge-labels
'3comb+pair1+3comb+1': '(((((a1b)2c)4(d3e))7((f5g)6h))8i)', #type 20 / 45 edge-labels
'8hanukkah+1': '(((((a1b)3c)5d)7(e6(f4(g2h))))8i)', #type 21 / 10 edge-labels
'8balanced+1': '((((a1b)5(c3d))7((e4f)6(g2h)))8i)', #type 22 / 10 edge-labels
'4comb+4balanced+1': '(((((a1b)2c)3d)7((e4f)6(g5h)))8i)', #type 23 / 10 edge-labels
# 11 from 7 leaves
'7comb+pair': '(((((((a1b)2c)3d)4e)5f)6g)8(h7i))', #type 24 / 7 edge-labels
'5giraffe+1+1+pair': '((((((a1b)3(c2d))4e)5f)6g)8(h7i))', #type 25 / 7 edge-labels
'3comb+pair1+1+1+pair': '((((((a1b)2c)4(d3e))5f)6g)8(h7i))', #type 26 / 21 edge-labels
'4comb+pair1+1+pair': '((((((a1b)2c)3d)5(e4f))6g)8(h7i))', #type 27 / 28 edge-labels
'6twohead1+1+pair': '(((((a1b)3(c2d))5(e4f))6g)8(h7i))', #type 28 / 28 edge-labels
'6balanced1+1+pair': '(((((a1b)2c)5((d3e)4f))6g)8(h7i))', #type 29 / 21 edge-labels
'5comb+pair+pair': '((((((a1b)2c)3d)4e)6(f5g))8(h7i))', #type 30 / 35 edge-labels
'5giraffe+pair+pair': '(((((a1b)3(c2d))4e)6(f5g))8(h7i))', #type 31 / 35 edge-labels
'3comb+pair1+pair+pair': '(((((a1b)2c)4(d3e))6(f5g))8(h7i))', #type 32 /105 edge-labels
'4comb+3comb+pair': '(((((a1b)2c)3d)6((e4f)5g))8(h7i))', #type 33 / 70 edge-labels
'4balanced+3comb+pair': '((((a1b)3(c2d))6((e4f)5g))8(h7i))', #type 34 / 70 edge-labels
# 6 from 6 leaves
'6comb+3comb': '((((((a1b)2c)3d)4e)5f)8((g6h)7i))', #type 35 / 21 edge-labels
'5giraffe+1+3comb': '(((((a1b)3(c2d))4e)5f)8((g6h)7i))', #type 36 / 21 edge-labels
'3comb+pair1+1+3comb': '(((((a1b)2c)4(d3e))5f)8((g6h)7i))', #type 37 / 63 edge-labels
'4comb+pair1+3comb': '(((((a1b)2c)3d)5(e4f))8((g6h)7i))', #type 38 / 84 edge-labels
'6twohead1+3comb': '((((a1b)3(c2d))5(e4f))8((g6h)7i))', #type 39 / 84 edge-labels
'6balanced1+3comb': '((((a1b)2c)5((d3e)4f))8((g6h)7i))', #type 40 / 63 edge-labels
# 2x3 from 5 leaves
'5comb+4comb': '(((((a1b)2c)3d)4e)8(((f5g)6h)7i))', #type 41 / 15 edge-labels
'5giraffe+4comb': '((((a1b)3(c2d))4e)8(((f5g)6h)7i))', #type 42 / 15 edge-labels
'3comb+pair1+4comb': '((((a1b)2c)4(d3e))8(((f5g)6h)7i))', #type 43 / 45 edge-labels
'5comb+4balanced': '(((((a1b)2c)3d)4e)8(((f5g)6h)7i))', #type 44 / 15 edge-labels
'5giraffe+4balanced': '((((a1b)3(c2d))4e)8(((f5g)6h)7i))', #type 45 / 15 edge-labels
'3comb+pair1+4balanced': '((((a1b)2c)4(d3e))8(((f5g)6h)7i))', #type 46 / 45 edge-labels
}
if __name__ == '__main__':
a = ascii_tree()
for name in code_library:
code = code_library[name]
if a.code_to_number_of_leaves(code) < 9:
continue
print('=====\n{0}'.format(name))
a.make_tree(code)
a.print_array()