Solution to rosalind's 'GRPH' problem

awSeqLib.py

class Dna:
	''' Object representing a FASTA record. '''
	def __init__(self, header, sequence):
		self.head = header
		self.seq = sequence
	def __str__(self, separator=''):
		return ">{0}\n{1}".format(self.head, separator.join(self.seq))
	def __len__(self):
		return len(''.join(self.seq))

	@property
	def name(self, separator=''):
		return self.head
	@property
	def sequence(self, separator=''):
		return separator.join(self.seq)

class Fasta:
	''' A FASTA iterator/generates DNA objects. '''
	def __init__(self, handle):
		self.handle = handle
		self.seqs   = []
	def __repr__(self):
		return '[HTML]' % (self.handle)
	def __iter__(self):
		header, sequence = '', []
		for line in self.handle:
			#print line
			if line[0] == '>':
				#print "...line start"
				if sequence: 
					#print "....","".join(sequence)
					yield Dna(header, "".join(sequence))
				header = line[1:-1]
				sequence = []
			else:
				sequence.append(line.strip())
		yield Dna(header, "".join(sequence))

	def initSeqList(self):
		header, sequence = '', []
		for line in self.handle:
			#print line
			if line[0] == '>':
				#print "...line start"
				if sequence: 
					#print "....","".join(sequence)
					self.seqs.append(Dna(header, "".join(sequence)))
				header = line[1:-1]
				sequence = []
			else:
				sequence.append(line.strip())
		self.seqs.append(Dna(header, "".join(sequence)))
		

def seqOverlap(s,t):
	sLen = len(s)
	tLen = len(t)
	seqLen = 0 
	if (sLen <= tLen):
		seqLen = sLen 
	else:
		seqLen = tLen
	seqLen = seqLen + 1
	for kk in reversed(range(1,seqLen)):
		suff = s[-kk:]
		pref = t[:kk]
		#print suff,pref
		if (suff == pref):
			return suff
	return None

# s[:(len(s) - k)] + s[-k:] == s
def prefix(s,t):
	return s[:(len(s) - len(seqOverlap(s,t)))]

def combinedOverlap(s,t):
	return prefix(s,t) + t

def incInt(i):
	return i + 1	


def revTransDNA(seq,lowerCaseReturn=False):
	bp = {'A':'T', 'C':'G', 'G':'C', 'T':'A', 'N':'N'}
	seqTemp = "".join([bp[x.upper()] for x in reversed(seq)])
	if (lowerCaseReturn == False):
		return seqTemp
	else:
		return seqTemp.lower()

def revTransRNA(seq,lowerCaseReturn=False):
	bp = {'A':'U', 'C':'G', 'G':'C', 'U':'A', 'N':'N'}
	seqTemp = "".join([bp[x.upper()] for x in reversed(seq)])
	if (lowerCaseReturn == False):
		return seqTemp
	else:
		return seqTemp.lower()

def getACGTcount(seq):
	seq = seq.lower()
	count = [0,0,0,0] # a c g t
	for s in seq:
		if (s == 'a'):
			count[0] = count[0] + 1
		if (s == 'c'):
			count[1] = count[1] + 1
		if (s == 'g'):
			count[2] = count[2] + 1
		if (s == 't'):
			count[3] = count[3] + 1
	return count

grph.py

import string
import itertools
from optparse import OptionParser
from awSeqLib import *

def prefSuffMatch(s,t,k=3,kRange=False):
	if(kRange == True):
		for kk in reversed(range(k,len(s))):
			suff = s[-kk:]
			pref = t[:kk]
			#print suff,pref
			if (suff == pref):
				return kk 
	else :
		if (s[-k:] == t[:k]):
			return k
	return 0

def createOverlapList(seqs):
	for seq1,seq2 in itertools.product(seqs, repeat=2): 
		yield [seq1, seq2, prefSuffMatch(seq1.seq, seq2.seq)]

def displayOverlapPair(seq1,seq2,match):
	print(seq1.name,seq2.name,match)

def main(): 
	parser = OptionParser()
	parser.add_option("-f","--file")
	(option, args ) = parser.parse_args()
	file = option.file 
	if file == None:
		print "Please specify a file" 
		exit(0)
	fileHandle = open(file, 'r')

	for s1,s2,m in createOverlapList(Fasta(fileHandle)):
		print(m)
		if (int(m) >= 3):
			displayOverlapPair(s1,s2,m)

if (__name__ == '__main__'):
	main()