How to return string area between two matches in Python?

Question

I am looking for a way (using python 3) to iterate over a certain string and to hand back another string with the two framing matches and the area in between.

seq="TCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGT"

In seq I want to find start (ATG) and stop (TGA) codons and extract the possible reading frames for further analysis.

It should give me this:

newstring="ATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGA"

So, when my original sequence is this:

GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCCCACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTGGCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGGGAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAACCAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACCTGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTGGCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTCTGCTCCACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGGCTGGGGTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGGGAGTGGCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGGAGAGGAGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCGGATCCCCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTTCAGGAGGCCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTGCTCCTCTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCCCCATCATCCCAGCTGCTCCCAAATAAACTCCAGAAG

I want to extract all possible varieties starting with ATG and ending with TGA (and later with other stop codons TAA and TAG.

It is probably a quite easy question, sorry in advance.

Not close enough to be a duplicate, but [here's a similar question about lists](https://stackoverflow.com/questions/51327792/python-extracting-lists-from-list-with-module-or-regular-expression/51328145) — Patrick Haugh, Aug 05 '18 at 20:34
regex can help you. Pattern being `(ATG.*?TGA)` [demo](https://regexr.com/3tg2c) — Madhan Varadhodiyil, Aug 05 '18 at 20:37
@N.Brue What should string 'ATGA' return? It starts with ATG and ends TGA... — Andrej Kesely, Aug 06 '18 at 05:55

Andrej Kesely · Answer 1 · 2018-08-06T06:11:37.203

You can use Python's re module for matching the strings (explanation of this regexp here):

import re

seq="TCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGT"

print(re.findall(r'(ATG.*?TGA)', seq))

Prints:

['ATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGA']

EDIT:

To get all substrings starting with ATG end ending with TGA, you can use this:

import re

seq="GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCCCACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTGGCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGGGAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAACCAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACCTGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTGGCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTCTGCTCCACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGGCTGGGGTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGGGAGTGGCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGGAGAGGAGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCGGATCCCCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTTCAGGAGGCCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTGCTCCTCTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCCCCATCATCCCAGCTGCTCCCAAATAAACTCCAGAAG"

def get_substrings(seq, start_string, end_string):
    r_start = re.compile(r'({})'.format(start_string))
    r_end = re.compile(r'({})'.format(end_string))

    for start in r_start.finditer(seq):
        s = start.start(1)
        for end in r_end.finditer(seq, s):
            e = end.end(1)
            yield s, e, seq[s:e]

for start, end, s in get_substrings(seq, 'ATG', 'TGA'):
    print('{} at [{}:{}]'.format(s, start, end))
    print('-' * 80)

This prints:

ATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGA at [29:113]
--------------------------------------------------------------------------------
ATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGA at [29:120]
--------------------------------------------------------------------------------
ATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACCATGA at [29:154]
--------------------------------------------------------------------------------
ATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGA at [29:218]
--------------------------------------------------------------------------------
ATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGTATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACCATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCCCACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGA at [29:260]          
...and so on.

This actually won't work for what the OP is actually trying to do, this will catch stop codons that are frame-shifted from the reading frame. Of course, the OP hasn't properly specified this question if indeed that is what they want, (I can only assume that is what they want if they are doing a typical genetics exercise) — juanpa.arrivillaga, Aug 05 '18 at 20:59
@juanpa.arrivillaga I need to confess my genetics is not my cup of tea ;) But yeah, OP needs to edit his question and specify it properly if he wants something different. — Andrej Kesely, Aug 05 '18 at 21:02
First of all, thank you; it looks not to bad. My idea was to print out all possible sequences and subsequently check the length to clarify whether they can be really coding or not and to translate its sequences. — N.Brue, Aug 06 '18 at 04:30
The only problem is now that only some reading frames are printed, in-frame and not in-frame. Any ideas how I can achieve this? — N.Brue, Aug 06 '18 at 05:07
@N.Brue I'm not geneticist so I don't know what do you want. If you edit your question, write there your inputs and desired outputs, maybe I'm able to help you. — Andrej Kesely, Aug 06 '18 at 05:33
@N.Brue I updated my answer, I hope now it's what do you want. — Andrej Kesely, Aug 06 '18 at 06:12

How to return string area between two matches in Python?

1 Answers1