Created
October 5, 2011 19:12
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Python script for transmembrane region calcuations
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#!/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) |
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