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genus.py
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genus.py
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#!/usr/bin/python
# ------------------------------------------------------------------
# genus.py
# ------------------------------------------------------------------
# purpose: to compute the genus range of double occurrence words
# ------------------------------------------------------------------
# usage: 1) genus.py w1 [w2 w3 ...]
# where w1 is non-delimited or comma-delimited dow
# 2) genus.py -t dows1.txt [dows2.txt dows3.txt ...]
# where dows1.txt is a text file in which each line is dow
# of the format specified for w1 above
# 3) use optional argument "-r" to print range rather than
# spectrum
# 4) use optional argument '-v' to print verbosely
# the genus for every connection
# 5) use optional argument '-e' to consider assembly graphs
# with endpoints
# ------------------------------------------------------------------
# author: Ryan Arredondo
# email: [email protected]
# date: 6/2/2013
# ------------------------------------------------------------------
# updates:
# 12/31/2016 - Made PEP8 compliant - Ryan Arredondo
# 12/31/2016 - Made Python 3 compatible - Ryan Arredondo
# ------------------------------------------------------------------
import itertools
import sys # For argv containing commandline args
from dowlib import *
def main(argv):
printrange = False
verbose = False
hasEndpoints = False
if "-r" in argv:
printrange = True
argv.pop(argv.index("-r"))
if "-v" in argv:
verbose = True
argv.pop(argv.index("-v"))
if "-e" in argv:
hasEndpoints = True
argv.pop(argv.index("-e"))
if len(argv) == 1 or "-h" in argv:
print_usage()
exit(1)
elif argv[1] == "-t":
for filename in argv[2:]:
words = importDOWs(filename)
for word in words:
if isDOW(word):
if printrange:
genera = getGenera(word, hasEndpoints, verbose)
genusrange = list(set(genera))
print("%s: %s" % (dow2str(word), genusrange))
else:
genera = getGenera(word, hasEndpoints, verbose)
genusspectrum = getCounts(genera)
print("%s: %s" % (dow2str(word), genusspectrum))
else:
print("%s: not dow" % dow2str(word))
else:
for wordstr in argv[1:]:
word = str2dow(wordstr)
if isDOW(word):
if printrange:
genera = getGenera(word, hasEndpoints, verbose)
genusrange = list(set(genera))
print("%s: %s" % (dow2str(word), genusrange))
else:
genera = getGenera(word, hasEndpoints, verbose)
genusspectrum = getCounts(genera)
print("%s: %s" % (dow2str(word), genusspectrum))
else:
print("%s: not dow" % wordstr)
def print_usage():
"""Prints Description of how the program should be used.
"""
print("usage: 1) genus.py w1 [w2 w3 ...]")
print(" where w1 is non-delimited or comma-delimited dow")
print(" 2) genus.py -t dows1.txt [dows2.txt dows3.txt ...]")
print(" where dows1.txt is a text file in which each line is dow")
print(" of the format specified for w1 above")
print(" 3) use optional argument '-r' to print range rather")
print(" than spectrum")
print(" 4) use optional argument '-v' to print verbosely")
print(" the genus for every connection")
print(" 5) use optional argument '-e' to consider assembly graphs")
print(" with endpoints")
def getCounts(genera):
"""Takes the output of getGenera and presents it so that the
counts of the genera are shown.
"""
if type(genera[0]) == list:
if len(genera[0]) == 0:
counts = [[], [0]*(max(genera[1])+1)]
elif len(genera[1]) == 0:
counts = [[0]*(max(genera[0])+1), []]
else:
counts = [[0]*(max(genera[0])+1), [0]*(max(genera[1])+1)]
for i in range(2):
for g in genera[i]:
counts[i][g] += 1
return [[(g, counts[i][g]) for g in set(genera[i])] for i in range(2)]
else:
counts = [0]*(max(genera)+1)
for g in genera:
counts[g] += 1
return [(g, counts[g]) for g in set(genera)]
def getGenera(w, hasEndpoints, verbose):
"""Returns list of all genera for all possible connections of
graph with corresponding edges E and cyclical arrangement Arr
"""
ESet = getEdges(w)
Arr = getCyclicArrangement(ESet)
if hasEndpoints:
genera = [[], []]
else:
genera = []
numberOfVertices = len(set(flatten(ESet)))
for connection in itertools.product(range(2), repeat=numberOfVertices):
BSet = getBoundaries(ESet, Arr, connection)
numberOfBoundaries = len(BSet)
genus = int((numberOfVertices - numberOfBoundaries + 2)/2)
if not hasEndpoints:
genera.append(genus)
elif 2 in [count(B, ESet[-1]) for B in BSet]:
genera[0].append(genus)
else:
genera[1].append(genus)
if verbose:
print("%s: %d" % (connection, genus))
return genera
def getBoundaries(ESet, Arr, connection):
"""returns list of lists of edges in which each list represents
a boundary component of graph with connections described by connection,
edges E and cyclical arrangement of edges Arr
"""
# Boundary set is initialized with loops since a loop will always
# form its own boundary regardless of connection
BSet = [[e] for e in ESet if e[0] == e[1]]
# DirSet holds the directions in which an edge is being traced.
# Used by function tracedOnRightOnly
DirSet = [e[0] for e in flatten(BSet)]
# For readability, returns True if connection is flipped or False o.w.
def flipped(val):
return bool(val)
# Constructs all boundaries by taking a "left" at each vertex
edgesNotTracedOnLeft = [notTracedOnLeft(e, BSet, DirSet) for e in ESet]
while any(edgesNotTracedOnLeft):
e1 = ESet[edgesNotTracedOnLeft.index(True)]
B = [e1]
towards = e1[1]
DirSet.append(towards)
# If connection is flipped, we turn right (o.w., turn left) at
# vertex=towards
if flipped(connection[towards - 1]):
e, towards = turnRight(e1, towards, Arr)
else:
e, towards = turnLeft(e1, towards, Arr)
# Repeat until we get back to starting edge in same direction
while e1 is not e or e1[1] != towards:
B.append(e)
DirSet.append(towards)
if flipped(connection[towards - 1]):
e, towards = turnRight(e, towards, Arr)
else:
e, towards = turnLeft(e, towards, Arr)
BSet.append(B)
edgesNotTracedOnLeft = [notTracedOnLeft(e, BSet, DirSet) for e in ESet]
# Constructs all boundaries by taking a "right" at each vertex
edgesNotTracedOnRight = [count(flatten(BSet), e) != 2 for e in ESet]
while any(edgesNotTracedOnRight):
e1 = ESet[edgesNotTracedOnRight.index(True)]
B = [e1]
towards = e1[1]
# If connection is flipped, we turn left (o.w., turn right) at
# vertex=towards
if flipped(connection[towards - 1]):
e, towards = turnLeft(e1, towards, Arr)
else:
e, towards = turnRight(e1, towards, Arr)
# Repeat until we get back to starting edge in same direction
while e1 is not e or e1[1] != towards:
B.append(e)
if flipped(connection[towards - 1]):
e, towards = turnLeft(e, towards, Arr)
else:
e, towards = turnRight(e, towards, Arr)
BSet.append(B)
edgesNotTracedOnRight = [count(flatten(BSet), e) != 2 for e in ESet]
return BSet
def notTracedOnLeft(e, BSet, Directions):
"""Determines whether an edge e has NOT been traced on the left.
"""
FlatBSet = list(flatten(BSet))
c = count(FlatBSet, e)
if c == 0:
return True
elif c == 2:
return False
else:
# Check if edge is traced on right only
for i in range(len(FlatBSet)):
if FlatBSet[i] is e:
ind = i
return Directions[ind] == e[0]
def turnLeft(e, towards, Arr):
"""Given graphs cylical arrangement Arr we turn "left" from edge e
towards vertex=towards and return new edge and vertex towards.
"""
for i in range(4):
if Arr[towards-1][i] is e and Arr[towards-1][(i+1) % 4] is not e:
idx = i
nextEdge = Arr[towards-1][(idx+1) % 4]
if towards != nextEdge[0]:
return nextEdge, nextEdge[0]
else:
return nextEdge, nextEdge[1]
def turnRight(e, towards, Arr):
"""Given graphs cylical arrangement Arr we turn "right" from edge e
towards vertex=towards and return new edge and vertex towards.
"""
for i in range(4):
if Arr[towards-1][i] is e and Arr[towards-1][i-1] is not e:
ind = i
nextEdge = Arr[towards-1][ind-1]
if towards != nextEdge[0]:
return nextEdge, nextEdge[0]
else:
return nextEdge, nextEdge[1]
def getCyclicArrangement(E):
"""Returns list of edges as they appear cyclically around each vertex.
"""
Arr = [[] for _ in set(flatten(E))]
for e in E:
Arr[e[0]-1].append(e)
for e in E:
Arr[e[1]-1].append(e)
# Edges must be swapped for proper cyclic arrangement
Arr[0][2], Arr[0][3] = Arr[0][3], Arr[0][2]
return Arr
def getEdges(w):
"""Returns edges (pairs of vertices) of assembly graph corresponding to w.
"""
w2 = 2*w
return [w2[i:i+2] for i in range(len(w))]
def count(listOflists, myList):
"""Counts occurrence of myList in listOflists by reference, not value."""
return sum(1 and int(myList is l) for l in listOflists)
def flatten(listOflists):
"""Removes outtermost pairs of braces in a nested list."""
return itertools.chain.from_iterable(listOflists)
if __name__ == "__main__":
main(sys.argv)