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]
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'
>>> get_complement('C')
'G'
>>> get_complement('G')
'C'
>>> get_complement('T')
'A'
>>> get_complement('L')
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))
import pickle
import sys
from distance import levenshtein
from gene_finder import *
from load import load_metagenome
metagenome = load_metagenome()
# pauls_seq = 'GCCCGGACATTCTACATCTCCGCGAAAACACACACTTTTTCGTCTCCGGCGAAGCTTGGCACGCTCGTTGCAAAACAGGGATCAGCAAGGCGAGGGATGGTTGGCCGAGCAGTTACTGCAAAGGGCAACGTCCGCATCTGAGCCGTGCGACGGTTTTGAACGGAAGAAGGCTGCGCCTCGGCGCAAATCGATCAAGCGGCATTAGGTCAACGGAGAGAAAACATGGCACTTCGGCAAATCGCATTCTACGGCAAGGGCGGCATCGGCAAGTCGACCACCTCGCAGAACACCCTCGCGGCGCTGGTTGAGATGGGTCAGAAGATCCTGATCGTCGGCTGCGACCCCAAGGCGGACTCCACCCGTCTGATCCTCAACACCAAGATGCAGGACACGGTGCTGAGCCTCGCCGCGGAAGCGGGTTCGGTGGAAGACCTCGAACTCGAAGACGTGATGAAGATCGGCTACAAGGGCATCAAGTGCACCGAAGCCGGTGGCCCGGAGCCGGGCGTCGGCTGCGCCGGCCGCGGCGTTATCACCGCGATCAACTTCCTCGAAGAAAACGGCGCCTATGAAGACGTCGACTACGTCTCCTACGACGTGCTCGGCGACGTGGTGTGCGGCGGCTTCGCGATGCCGATCCGTGAAAACAAGGCGCAGGAAATCTACATCGTCATGTCCGGCGAGATGATGGCGCTGTATGCCGCCAACAACATCTCCAAGGGCATTCTGAAGTACGCTTCGTCGGGCGGCGTCCGTCTCGGCGGCCTGATCTGCAACGAGCGCCAGACCGACCGCGAGCTCGACCTCGCCGAAGCGCTGGCCAAGAAGCTGAACTCGAAGCTGATCCACTTCGTGCCGCGCGACAATATCGTGCAGCACGCCGAGCTGCGCCGCCAGACCGTGATCCAGTACGCGCCCGACAGCCAGCAGGCTAAGGAATATCGCGCCCTGGCCAACAAGGTCCATGCCAACTGCGGCAACGGCACCATCCCGACCCCGATCACCATGGAAGAGCTGGAAGAGATGCTGCTCGACTTCGGCATCATGAAGACCGAGGAGCAGCAGCTCGCCGAGCTCGCCGCCAAGGAAGCCGCCAAGGCGGCCGCGTCCGCCTGATCGCATCAGCCAGGCCGGTCGCCTAGCGCGACCGGCCGCCATCCCGGCGGCCCCAGACACGAGGAACAACGATGAGCACCGCAGTCGCAGAATCCCCCGCGGACATCAAGGAACGTAACAAGAAGCTGATCGGCGAAGTCCTGGAGGCCTATCCGGACAAGTCGGCCAAGCGTCGCGCCAAGCATCTCAACACGTACGACGCCGAGAAGGCGGAGTGCTCGGTCAAGTCCAACATCAAGTCGATCCCGGGCGTGATGACGATCCGCGGTTGCGCCTACGCCGGCTCGAAGGGCGTGGTGTGGGGCCCGATCAAGGACATGGTCCACATCAGCCACGGCCCGGTCGGCTGCGGCCAGTATTCGTGGGGTTCGCGCCGCAACTATTACAAGGGAACCACCGGCGTCGACACTTTCGGCACGATGCAGTTCACCTCCGACTTCCAGGAGAAGGACATCGTTTTCGGCGGTGACAAGAAGCTCGGCAAGATCATCGACGAGATCCAGGAGCTGTTCCCGCTCTCCAAGGGCATCTCGGTGCAGTCGGAATGCCCGATCGGTCTGATCGGCGACGACATCGAGGCGGTCTCCAAGGCCAAGTCGAAGCAGTATGACGGCAAGCCGATCATCCCGGTCCGCTGCGAAGGCTTCCGCGGCGTGTCGCAGTCGCTCGGCCACCACATCGCCAACGACGTGATCCGTGACTGGGTGTTCGACAAGGCCGCCGAGAAGAACGCCGGCTTCCAGTCGACCCCCTACGACGTCGCGATCATCGGCGACTACAACATCGGCGGCGATGCCTGGGCCTCGCGCATCCTGCTCGAGGAAATGGGCCTCCGCGTGATCGCGCAGTGGTCCGGCGACGGCACCATCGCGGAGCTGGAGAACACCCCGAAGGCGAAGCTGAACATCCTGCACTGCTACCGCTCGATGAACTACATCACGCGGCACATGGAAGAGAAGTTCGGTATTCCGTGGGTTGAATACAACTTCTTCGGCCCGTCCAAGATCGA'
#Loading the nitrogenase
from load import load_nitrogenase_seq
nitrogenase = load_nitrogenase_seq()
sys.setrecursionlimit(20000)
if __name__ == "__main__":
i = 0
holder_dna = []
for a in metagenome[1:5]:
dna = a[1]
snippet = find_all_ORFs_both_strands(dna)
for item in snippet:
if len(item[0]) > .8 * len(nitrogenase):
holder_dna.append(item)
data_output = []
lengths = [len(item[0]) for item in holder_dna]
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))
from load import load_nitrogenase_seq
from load import load_metagenome
#import pypy
from gene_finder import *
nitrogenase = str(load_nitrogenase_seq())
metagenome = load_metagenome()
one_metagenome = metagenome[0] #a tuple
def longestSubstringMetagenomeSnippet(enzyme, metagenome_snippet):
m = [[0] * (1 + len(metagenome_snippet)) for i in range(1 + len(enzyme))] #creates a list of lists
longest, x_longest = 0, 0
for x in range(1, 1 + len(enzyme)): #x starts with 1, goes up to (1 + length of 1st string)
for y in range(1, 1 + len(metagenome_snippet)): #y starts with 1, goes up to (1 + length of 2nd string)
if enzyme[x - 1] == metagenome_snippet[y - 1]:
m[x][y] = m[x - 1][y - 1] + 1 #if the upper-left diagonal characters are equal,
if m[x][y] > longest:
longest = m[x][y]
x_longest = x
else:
m[x][y] = 0
return enzyme[x_longest - longest: x_longest]
def longestSubstringAllMetagenomeSnippets(enzyme, metagenome):
i = 0
ORF_lengths = []
genome_names = [] #I think that's what you call a part of a metagenome?
for name, metagenome_snippet in metagenome:
ORF = longestSubstringMetagenomeSnippet(enzyme, metagenome_snippet)
