rosalind_find_motif(subs).py

# -*- coding: utf-8 -*-
# Diane Kaplan
# Rosalind Problem: finding motif (subs)
# http://rosalind.info/problems/subs/
# Aug 14, 2015

# Rules:
#Given: Two DNA strings s and t (each of length at most 1 kbp).
#Return: All locations of t as a substring of s.
#    
DEBUG = False


def find_instances(sample, query):
    
    locations= []

    substring = query
    string = sample
    string_length = len(string)
    substring_length = len(substring)
    cursor = 0
    
    if (DEBUG): 
        print "substring:", substring 
        print "string:", string 

  
    while cursor < string_length:
        current_chunk = string[cursor:(cursor+substring_length)]
        if current_chunk == substring:
                if (DEBUG): 
                    print "I found: ", current_chunk, " at position: ", cursor+1
                locations.append(cursor+1)
        cursor += 1


    return locations


sample= 'AGGGAGGTCCATAAGTCGTCGTGCGTCGTCGCTGTGACATCAACGTCGTCGGTCGTCGGTTTGAATAGTCGTCGCGTCGTCGGTCGTCGCGTCGTCGGTCGTCGTGTCGTCGACGTCGTCGATGTCGTCGGCCCATAACTCCGTCGTCGGTCGTCGGTCGTCGGGTCGTCGGTCGTCGTATTCGTCGTCGCTTGTCGTCGTGTCGTCGAGCGTCGTCGGTCGTCGTCTAGGTCGTCGGTCGTCGGCTATGTCGTCGGTCGTCGTTTGACGTCGTCGTGTCGTCGGTCGTCGTGTCGTCGCGTCGTCGGTCGTCGGTCGTCGGTCGTCGCAAACGTCGTCGTCCGTCGTCGTGTTGTCGTCGGTCGTCGGTCGTCGGTCGTCGCAGTCGTCGCTGTCGTCGTGTCGTCGATCGTCGTCGGTCGTCGCCGTCGTCGGTCGTCGTCCTCGTCGTCGATGTCGTCGTAAAGTCGTCGTAAAACTTGTCGTCGGTCGTCGGGCGTCGTCGGATAGGTCGTCGGTCGTCGGTCGTCGGTCGTCGGAAGTGTCGTCGAGTTGCGTCGTCGTTCGTCGTCGAGGGTCGTCGGTCGTCGTTGGTCGTCGGATCGTCGTCGTGGTCGTCGACGTCGTCGCGTCGTCGGGTCGTCGAAGTCGTCGCGTCGTCGCCTGTCGTCGGTCGTCGGTCGTCGTGTGTGTCGTCGAGTCGTCGTAGGTCGTCGGTCGTCGGTCGTCGGTCGTCGGCACATTGTCGTCGCACCCTGTCGTCGGGTGACCAGTCGTCGAGTCGTCGGTCGTCGCATGTTCGTCGTCGGTCGTCGTGCCAAGAGGTCGTCGGGTCGTCGGGTCGTCGGTCGTCGTGTCGTCGGTCGTCGCGTCGTCGCATGTCGTCGATTCTTCGATGCCCGTCGTCGTGAACGGAATGGGTCGTCGGTCGTCGTGTCGTCGGTCGTCGATCAAGAGTCGTCGCGTCGTCGTG'
query='GTCGTCGGT'

print find_instances(sample, query)