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polyAsig.py
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polyAsig.py
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from __future__ import print_function
########################################################################
# File: polyAsig.py
# executable: polyAsig.py
# Purpose:
#
#
# Author: Cameron M. Soulette
# History: cms 01/17/2019 Created
#
########################################################################
import sys, os
from Bio import motifs
import re
import random
random.seed(123)
fasta = sys.argv[1]
seqs = list()
signal1 = "AATAAA"[::-1]
signal2 = "ATTAAA"[::-1]
signal3 = "AGTAAA"[::-1]
random4 = "".join([random.choice('TCAG') for _ in range(6)])[::-1]
with open(fasta) as lines:
for header in lines:
sequence = next(lines).rstrip()
if len(sequence)<150: continue
endChunk = sequence[-150:]
endChunk = endChunk[::-1]
seqs.append(endChunk)
try:
print(re.search(signal1, endChunk).start(),signal1[::-1])
print(re.search(signal2, endChunk).start(),signal2[::-1])
print(re.search(signal3, endChunk).start(),signal3[::-1])
print(re.search(random4, endChunk).start(),random4[::-1])
except:
continue