add NWCK

NWCK/NWCK.px~

@@ -0,0 +1,97 @@
+#!/usr/bin/python
+
+
+#########################################################################
+# Author:
+#
+# Sanyk28 ([email protected])
+#
+# Date created:
+#
+# 19 Oct 2013
+#
+# Rosalind problem:
+#
+# Distances in Trees
+#
+# Given: A collection of n trees (n<=40) in Newick format, with each tree 
+#        containing at most 200 nodes; each tree Tk is followed by a pair 
+#        of nodes xk and yk in Tk.
+#
+# Return: A collection of n positive integers, for which the kth integer 
+#         represents the distance between xk and yk in Tk.
+#
+# Usage:
+#
+# python NWCK.py [Input File]
+#
+########################################################################
+
+import sys
+
+def read_file(filename):
+    '''
+    Given: input file filename in plain text format.
+    Return: file contents from input file.
+    
+    Example:
+    >>> read_file(test.txt)
+    ['(cat)dog;\n', 'dog cat\n', '\n', '(dog,cat);\n', 'dog cat\n']
+    '''
+    f = open(filename)
+    raw_data = f.readlines()
+    f.close()
+    return raw_data
+
+def parse_data(data):
+    '''
+    Given: file content from read_file(filename).
+    Return: a dictionary where Newick format Trees are dictionary keys, 
+            and nodes that need to calcuate the distance in between are 
+            dictionary values.
+    
+    Example:
+    >>> parse_data(['(cat)dog;\n', 'dog cat\n', '\n', '(dog,cat);\n', 
+                    'dog cat\n'])
+    {'(dog,cat);': 'dog cat', '(cat)dog;': 'dog cat'}
+    '''
+
+    Trees = {}
+    tree = ''
+    for row in data:
+        if len(row.strip()) == 0:
+            continue
+        elif row.strip()[-1:] == ';':
+            tree = row.strip()
+            Trees[tree] = ''
+        else:
+            Trees[tree] = row.strip()
+    return Trees
+
+def distance(tree, nodes):
+    '''
+    Given: a Newick format tree and a string of two nodes from the tree.
+    Return: the distance between the nodes.
+
+    Examples:
+    >>> 
+    '''
+
+    distance = 0
+    nodes = nodes.split(' ')
+    if ','.join([nodes[0],nodes[1]]) or ','.join([nodes[1],nodes[0]]) in tree:
+        distance = 2
+    return distance
+
+'''
+def result(data_dict):
+    for key, value in data_dict:
+        distance
+    return 
+'''
+
+if __name__ == '__main__':
+
+    raw_data = read_file(sys.argv[-1])
+    Trees = parse_data(raw_data)
+    print distance('(dog,cat);','dog cat')

NWCK/NWCK.py

@@ -0,0 +1,138 @@
+#!/usr/bin/python
+
+
+#########################################################################
+# Author:
+#
+# Sanyk28 ([email protected])
+#
+# Date created:
+#
+# 20 Oct 2013
+#
+# Rosalind problem:
+#
+# Distances in Trees
+#
+# Given: A collection of n trees (n<=40) in Newick format, with each tree 
+#        containing at most 200 nodes; each tree Tk is followed by a pair 
+#        of nodes xk and yk in Tk.
+#
+# Return: A collection of n positive integers, for which the kth integer 
+#         represents the distance between xk and yk in Tk.
+#
+# Usage:
+#
+# python NWCK.py [Input File]
+#
+########################################################################
+
+import sys
+import re
+
+def read_file(filename):
+    '''
+    Given: input file filename in plain text format.
+    Return: file contents from input file.
+    
+    Example:
+    >>> read_file(test.txt)
+    ['(cat)dog;\n', 'dog cat\n', '\n', '(dog,cat);\n', 'dog cat\n']
+    '''
+    f = open(filename)
+    raw_data = f.readlines()
+    f.close()
+    return raw_data
+
+def parse_data(data):
+    '''
+    Given: file content from read_file(filename).
+    Return: a dictionary where Newick format Trees are dictionary keys, 
+            and nodes that need to calcuate the distance in between are 
+            dictionary values.
+    
+    Example:
+    >>> parse_data(['(cat)dog;\n', 'dog cat\n', '\n', '(dog,cat);\n', 
+                    'dog cat\n'])
+    [('(cat)dog;', ['dog', 'cat']), ('(dog,cat);', ['dog', 'cat'])]
+    '''
+
+    Trees,tree,nodes = [],'',[]
+    for row in data:
+        if len(row.strip()) == 0:
+            continue
+        elif row.strip()[-1:] == ';':
+            tree = row.strip()
+        else:
+            nodes = row.strip().split(' ')
+            Trees.append((tree,nodes))
+    return Trees
+
+def count_pattern(string, pattern):
+    return re.subn(pattern, '', string)[1]
+
+def NWCK_distance(tree, nodes):
+    '''
+    Given: a Newick format tree and a string of two nodes from the tree.
+    Return: the distance between the nodes.
+
+    Examples:
+    >>> distance('(dog,cat);','dog cat')
+    2
+    >>> distance('(,,,,,,,,,,dog,,,,)cat', 'cat dog')
+    1
+    >>> distance('(elephant,rabbit,cat,monkey,pig)dog;', 'dog cat')
+    1
+    >>> distance('(rabbit,cat,monkey)dog;', 'cat dog')
+    1
+    >>> distance('(dog)cat;', 'cat dog')
+    1
+    >>> distance('cat,(dog,monkey),elephant;', 'elephant cat')
+    2
+    >>> distance('(,,,,,,,,,,Bradyporus_saxatilis,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Thymallus_platycephala,,,);', 'Thymallus_platycephala Bradyporus_saxatilis')
+    2
+    >> distance()
+    1
+    '''
+
+    distance = 0
+    n1, n2 = nodes[0], nodes[1]
+    i1, i2 = tree.find(n1), tree.find(n2)
+    # '(cat)dog;','(zebra,(cat,rat))dog;', '(((zebra,panda),rabbit),(cat,sheep))dog;'
+    prog1 = re.compile('\)'+n1+';$')
+    prog2 = re.compile('\)'+n2+';$')
+    # '(cat,dog);', '(cat,zebra,dog)monkey;', '(cat,(monkey,ant),(dog,rabbit));', '(((pig,cat,rat),monkey),(zebra,giraff,dog));'
+    prog3 = re.compile('\([\(\),\w]*'+n1+'[\(\),\w]*'+n2+'[\(\),\w]*\)\w*;$')
+    # '(monkey,((zebra,rat),rabbit),(elephant,(pig,cat,giraff)),((ants,(dog,tiger)),((hippo,dragon),sheep)));'
+    prog4 = re.compile('\([\(\),\w]*'+n2+'[\(\),\w]*'+n1+'[\(\),\w]*\)\w*;$')
+    if prog1.search(tree):
+        distance = count_pattern(tree[:i2],'\(')-count_pattern(tree[:i2],'\)')
+    elif prog2.search(tree):
+        distance = count_pattern(tree[:i1],'\(')-count_pattern(tree[:i1],'\)')
+    elif prog3.search(tree):
+        distance = count_pattern(tree[:i1],'\(')-count_pattern(tree[:i1],'\)')-count_pattern(tree[i2:],'\(')+count_pattern(tree[i2:],'\)')
+    elif prog4.search(tree):
+        distance = count_pattern(tree[:i2],'\(')-count_pattern(tree[:i2],'\)')-count_pattern(tree[i1:], '\(')+count_pattern(tree[i1:],'\)')
+    return distance
+
+def result(Trees):
+    '''
+    Given: a dictionary where Newick format Trees are dictionary keys, 
+           and nodes that need to calcuate the distance in between are 
+           dictionary values.
+    Return: the distance between the two nodes in coresponding Newick 
+            format Tree
+    
+    Example:
+    '''
+
+    Distances = []
+    for tree, nodes in Trees:
+        Distances.append((NWCK_distance(tree, nodes)))
+    return Distances
+
+if __name__ == '__main__':
+
+    raw_data = read_file(sys.argv[-1])
+    Trees = parse_data(raw_data)
+    print ' '.join(map(str, result(Trees)))

NWCK/NWCK.py~

@@ -0,0 +1,76 @@
+#!/usr/bin/python
+
+
+#########################################################################
+# Author:
+#
+# Sanyk28 ([email protected])
+#
+# Date created:
+#
+# 19 Oct 2013
+#
+# Rosalind problem:
+#
+# Distances in Trees
+#
+# Given: A collection of n trees (n<=40) in Newick format, with each tree 
+#        containing at most 200 nodes; each tree Tk is followed by a pair 
+#        of nodes xk and yk in Tk.
+#
+# Return: A collection of n positive integers, for which the kth integer 
+#         represents the distance between xk and yk in Tk.
+#
+# Usage:
+#
+# python NWCK.py [Input File]
+#
+########################################################################
+
+import sys
+
+def read_file(filename):
+    '''
+    Given: input file filename in plain text format.
+    Return: file contents from input file.
+    
+    Example:
+    >>> read_file(test.txt)
+    ['(cat)dog;\n', 'dog cat\n', '\n', '(dog,cat);\n', 'dog cat\n']
+    '''
+    f = open(filename)
+    raw_data = f.readlines()
+    f.close()
+    return raw_data
+
+def parse_data(data):
+    '''
+    Given: file content from read_file(filename).
+    Return: a dictionary where Newick format Trees are dictionary keys, 
+            and nodes that need to calcuate the distance are dictionary 
+            values.
+    
+    Examples:
+    >>> parse_data(['(cat)dog;\n', 'dog cat\n', '\n', '(dog,cat);\n', 
+                    'dog cat\n'])
+    {'(dog,cat);': 'dog cat', '(cat)dog;': 'dog cat'}
+    '''
+
+    Trees = {}
+    tree = ''
+    for row in data:
+        if len(row.strip()) == 0:
+            continue
+        elif row.strip()[-1:] == ';':
+            tree = row.strip()
+            Trees[tree] = ''
+        else:
+            Trees[tree] = row.strip()
+    return Trees
+
+
+
+if __name__ == '__main__':
+
+    raw_data = read_file(sys.argv[-1])
+    print parse_data(raw_data)