Question

Please provide the general python code needed:

Use regular expression to find all of the genes that meet the following criteria. You just have to print out the number of matched genes to standard output (i.e. console).

a sequence that is between 10 to 50 bp that has no A or Ts.
any nucleotide repeated three times followed by any nucleotide repeated three times.
A one or more times, followed by T one or more times, followed by G one or more times, followed by C one or more times
one T followed by one A followed by five bases followed by one A followed by one T.

Answer 1

Please find the answers as below::

Note that for each, I am assuming we are checking only one end of the string, and thus, its corresponding pair would occur on the other end. Please accommodate any changes that the biology of the problem might require.

a) check for a length of 10 to 50 basepairs, that they do not comprise of A or T.

String checker::: [^AT]{10, 50}

This means that the string should not contain the characters A and T and must be of a length of 10 to 50 characters.  

Code:::

import re

txt = "GCGCGCCGGCGCGGCGCC"
x = re.search("[^AT]{10,50}", txt)

if (x):
print("YES! We have a match!")
else:
print("No match")

b) A nucleotide repeated thrice followed by a nucleotide repeated thrice.

String checker ::: (A|T|G|C){3}(A|T|G|C){3}

note that the problem does not mention that the two nucleotides must be different. Hence a repetition of G six times is also a valid string.

Code:::

import re

txt = "GCGCGCCGGCGCGGGCCCGCC"
x = re.search("(A|T|G|C){3}(A|T|G|C){3}", txt)

if (x):
print("YES! We have a match!")
else:
print("No match")

c) One or more instances of A then T then G then C

String checker ::: A+T+G+C+

Code :::

import re

txt = "ATGCC"
x = re.search("A+T+G+C+", txt)

if (x):
print("YES! We have a match!")
else:
print("No match")

d) TA followed by 5 bases followed by AT

String checker ::: TA.....AT

Code :::

import re

txt = "TA.....AT"
x = re.search("TAGGCGCATGGA", txt)

if (x):
print("YES! We have a match!")
else:
print("No match")

Hopefully, this is helpful.