def going_beyond(): from load import load_nitrogenase_seq nitrogenase = load_nitrogenase_seq() #print nitrogenase from load import load_metagenome metagenome = load_metagenome() longest_snippet = "" k = 0 while k < len(metagenome): i = 0 while i < len(nitrogenase): j = 0 while j < len(metagenome[k][1]): length = 0 while (i + length < len(nitrogenase)) and (j + length < len(metagenome[k][1])) and (nitrogenase[i + length] == metagenome[k][1][j + length]): length += 1 if length > len(longest_snippet): longest_snippet = nitrogenase[i:i+length] j += 1 + length #adding length here makes the program run a little faster i += 1 k += 1 return longest_snippet
def substring_checkc():
"""Returns the parts of the string that match"""
nitrogenase = load_nitrogenase_seq()
metagenome = load_metagenome()#So, this actually is a list of tubles with the name of a seqquence and then the sequence.
for i in metagenome:
print(i)
pass
def nitrogenase_substring():
""" finds the metagenome with the longest substring in common with
the nitrogenase sequence.
I have no idea if it works, but it spit out an answer with no errors after over an hour
of running, so i'm considering that success.
"""
import load
nit_seq = load.load_nitrogenase_seq()
metagenomes = load.load_metagenome()
subs = []
for meta in metagenomes:
subs.append((meta[0], longest_substring(meta[1], nit_seq)))
return max(subs, key=lambda s:s[1])[0]
# -*- coding: utf-8 -*-
"""
Last updated: April 11, 2016
Find Nitrogenase
@author: Erica Lee, Rebecca Gettys, Liv Kelley
"""
import random
from amino_acids import aa, codons, aa_table # you may find these useful
#Importing the metagenome
from load import load_metagenome
metagenome = load_metagenome()
# metagenome = 'ATGGGAAAACTCCGGCAGATCGCTTTCTACGGCAAGGGCGGGATCGGCAAGTCGACGACCTCGCAGAACACCCTCGCGGCACTGGTCGAGATGGGTCAGAAGATCCTCATCGTCGGCTGCGATCCCAAGGCCGACTCGACCCGCCTGATCCTGAACACCAAGCTGCAGGACACCGTGCTTCACCTCGCCGCCGAAGCGGGCTCCGTCGAGGATCTCGAACTCGAGGATGTGGTCAAGATCGGCTACAAGGGCATCAAATGCACCGAAGCCGGCGGGCCGGAGCCGGGCGTGGGCTGCGCGGGCCGCGGCGTCATCACCGCCATCAACTTCCTGGAAGAGAACGGCGCCTATGACGACGTCGACTACGTCTCCTACGACGTGCTGGGCGACGTGGTCTGCGGCGGCTTCGCCATGCCGATCCGCGAGAACAAGGCGCAGGAAATCTACATCGTCATGTCGGGCGAGATGATGGCGCTCTATGCGGCCAACAACATCGCCAAGGGCATCCTGAAATACGCGAACTCGGGCGGCGTGCGCCTCGGCGGCCTGATCTGCAACGAGCGCAAGACCGACCGCGAGCTGGAACTGGCCGAGGCCCTCGCCGCGCGTCTGGGCTGCAAGATGATCCACTTCGTTCCGCGCGACAATATCGTGCAGCACGCCGAGCTCCGCCGCGAGACGGTCATCCAGTATGCGCCCGAGAGCAAGCAGGCGCAGGAATATCGCGAACTGGCCCGCAAGATCCACGAGAACTCGGGCAAGGGCGTGATCCCGACCCCGATCACCATGGAAGAGCTGGAAGAGATGCTGATGGATTTCGGCATCATGCAGTCCGAGGAAGACCGGCTCGCCGCCATCGCCGCCGCCGAGGCCTGA'
#Loading the nitrogenase
from load import load_seq
from load import load_nitrogenase_seq
nitrogenase = load_nitrogenase_seq()
def get_complement(nucleotide):
""" Returns the complementary nucleotide
nucleotide: a nucleotide (A, C, G, or T) represented as a string
returns: the complementary nucleotide
>>> get_complement('A')
'T'
from load import load_nitrogenase_seq
from load import load_metagenome
def longestSubstrings(meta, nitrogen):
ans = []
for m in meta:
length = 0
longest = ''
for x in range(len(nitrogen)):
span = 1
while (nitrogen[x:x + span] in m[1] and x + span < len(nitrogen)):
if (span > length):
length = span
longest = nitrogen[x:x + span]
span += 1
if (length >= 20):
ans.append([m[0], length, longest])
return ans
if __name__ == '__main__':
nitrogen = load_nitrogenase_seq().replace('\n', '')
meta = load_metagenome()
print(longestSubstrings(meta, nitrogen))
def loading_dna():
metagenome = load_metagenome()#So, this actually is a list of tubles with the name of a seqquence and then the sequence.
pass
