Python script for transmembrane region calcuations

tmpred.py

#!/usr/bin/env python3.1
# cc attribution-sharealike // max [@] maxnanis.com
#transmembrane
import re
def tmpred(aa):
	aa = aa.upper()
	engine = re.compile("[^A-Z]")
	aa = engine.sub("", aa)
	ruler = ''
	count = 1
	while len(ruler) < len(aa):
		ruler = ruler + "----+----"
		ruler = ruler + str(count)
		if count == 9:
			count = 0
		else:
			count = count + 1
	print(ruler)
	print(aa)
	
	result = ''
	for c in aa:
		if c in "VWFAMILY":
			result = result + "-"
		else:
			result = result + "+"
	aa = result
	print (aa)

	tmPattern = re.compile("(\+{3,})((\+{0,2}-)+)")
	seq_iter = tmPattern.finditer(aa)	

	for pattern in seq_iter:
		upstream = pattern.group(1)
		seq = pattern.group(2)
		if len(seq) < 17:
			continue
		score = 0.0
		for c in seq:
			if c == "+":
				score = score + 1.0
		score = score/len(seq)
		if score > .43:
			continue
		print("{}: {}[{}]{} score = {}".format(len(seq), pattern.start()+len(upstream)+1, seq, pattern.end(), score))

if __name__ == "__main__":
	from sys import stdin
	seqs = stdin.readlines()
	for aa in seqs:
		tmpred(aa)