import sys
import re
import fasta

#function that reads the enzyme list
def read_enzymes(file):
	#initialize dictionary
	resenz = {}
	start = False
	for line in file:
		#if we found the string we jump a line and start reading the list
		if line.find('Rich Roberts') >= 0:
			start = True
			line = file.next()
		if start == True and len(line) > 10:
			buffer = line.split()
			#populating the dictionary
			resenz[buffer[0]] = buffer[-1].replace('^', '')
 	return resenz

#function that checks if the input enzyme name was found in the list
def check_enzyme(input, set):
	if set.has_key(input):
		return True
	else:
		return False

def find_sites(input, set, sequence):
	#this is the IUPAC code
	iupacdict = {'A':'[A]',
	'C':'[C]',
	'G':'[G]',
	'T':'[T]',
	'M':'[AC]',
        'R':'[AG]',
        'W':'[AT]',
        'S':'[CG]',
        'Y':'[CT]',
        'K':'[GT]',
        'V':'[ACG]',
        'H':'[ACT]',
        'D':'[AGT]',
        'B':'[CGT]',
        'X':'[ACGT]',
        'N':'[ACGT]'}

	#we get the site
	site = set[input]
	pattern = ''
	positions = []
	#transform the site from IUPAC to nucleotides
	for i in site:
		pattern += iupacdict[i]
	#search the pattern
	searchpattern = re.compile(pattern)
	#search all entries of the pattern
	sites = searchpattern.findall(sequence)
	temppos = searchpattern.finditer(sequence)
	for i in temppos:
		begin, end = i.span()
		positions.append(begin)
	return sites, positions

#read the enzyme name
enzyme = sys.argv[1]
#read the list
enzymeset = read_enzymes(open('bionet.709', 'r'))
isname = check_enzyme(enzyme, enzymeset)

if isname:
	print 'Name found'
	#if we found the enzyme name we read the sequence file
	sequences = fasta.read_fasta(open(sys.argv[2], 'r').readlines())
	for item in sequences:
		#let's search
		sites, positions = find_sites(enzyme, enzymeset, item.sequence)
		#print the sequence name
		print item.name[:20]+'...'
		#and use the zip function to combine the lists and print
		for i in zip(sites,positions):
			print i[0], '->', i[1]
#if the name is not found, we bail out
else:
	print 'Enzyme name not found, please try again'