item[1]
] not in superstrings:
superstrings.append(inner_item + [item[1]])
if len(inner_item) == len(fasta_dict) - 1:
return superstrings
def build_superstring(fasta_dict, keys_list):
overlap_len = len(fasta_dict[keys_list[0]]) // 2
superstring = fasta_dict[keys_list[0]]
for index in range(1, len(keys_list)):
new_string = fasta_dict[keys_list[index]]
overlap_start = common.substring_positions(
new_string, superstring[-overlap_len:])[0]
superstring += new_string[overlap_start + overlap_len:]
return superstring
fasta_dict = common.fasta_parser('LONG.txt')
adj_list = list()
for key in fasta_dict.keys():
for inner_key in fasta_dict.keys():
if common.overlapping(fasta_dict[key],
fasta_dict[inner_key]) and key != inner_key:
adj_list.append((key, inner_key))
print(len(adj_list))
longest_path = sorted(get_superstrings(adj_list), key=len)[-1]
print(longest_path)
print(build_superstring(fasta_dict, longest_path))
import common
import math
'''
Assuming we have the same amount of occurences of A-U and G-C, all possible perfect matches is simply (AU)!*(GC)!
! - cause of number of permutations of size AU from AU list
* - cause of independent states of this pairs
'''
fasta_dict = common.fasta_parser('PMCH.txt')
sequence = fasta_dict[list(fasta_dict.keys())[0]]
AU = 0
GC = 0
AU, GC = (sequence.count(item) for item in ('A', 'G'))
matchings = math.factorial(AU) * math.factorial(GC)
print(matchings)
import common
fdict = common.fasta_parser('GC.txt')
gc_count = dict()
max_gc = 0
max_key = ''
for key in fdict.keys():
gc_count[key] = round((fdict[key].count('G') + fdict[key].count('C')) *
100 / len(fdict[key]), 6)
if gc_count[key] > max_gc:
max_gc = gc_count[key]
max_key = key
print(max_key)
print(max_gc)
import common
fasta_dict = common.fasta_parser('ORF.txt')
sequence = fasta_dict[list(fasta_dict.keys())[0]]
forward_orf = [
common.translate_dna(orf) for orf in common.find_orf_dna(sequence)
]
reverse_orf = [
common.translate_dna(orf)
for orf in common.find_orf_dna(common.reverse_comp(sequence))
]
print(forward_orf)
print(reverse_orf)
with open('ORF_result.txt', 'w') as f:
[print(orf, file=f) for orf in set(forward_orf) | set(reverse_orf)]
import common
adj_len = 3
fasta_dict = common.fasta_parser('GRPH.txt')
adj_list = []
for key in fasta_dict.keys():
for inner_key in fasta_dict.keys():
if fasta_dict[key][-adj_len:] == fasta_dict[
inner_key][:adj_len] and key != inner_key:
adj_list.append((key, inner_key))
with open('GRPH_result.txt', 'w') as output_file:
for adj in adj_list:
print(' '.join(map(str, [item for item in adj])), file=output_file)
import common
fasta_dict = common.fasta_parser('SSEQ.txt')
ref_seq = fasta_dict[list(fasta_dict.keys())[0]]
search_seq = fasta_dict[list(fasta_dict.keys())[1]]
print(ref_seq, search_seq)
indices_list = [common.substring_positions(ref_seq, letter) for letter in search_seq]
#print(indices_list)
spliced_motif = list()
for item in indices_list:
if spliced_motif == []:
spliced_motif.append(item[0])
continue
for index in item:
if spliced_motif[0] == index:
continue
elif index > spliced_motif[-1]:
spliced_motif.append(index)
break
print(' '.join(map(lambda x: str(x+1), spliced_motif)))
import common
def long_substr(data):
substr = ''
if len(data) > 1 and len(data[0]) > 0:
for i in range(len(data[0])):
for j in range(len(data[0]) - i + 1):
if j > len(substr) and all(data[0][i:i + j] in x
for x in data):
substr = data[0][i:i + j]
return substr
fasta_dict = common.fasta_parser('LCSM.txt')
data = [fasta_dict[key] for key in fasta_dict.keys()]
print(long_substr(data))
import numpy as np
from level4.HAMM import hamming_distance
import common
def get_dist_table(fasta_dict):
fasta_list = [fasta_dict[item] for item in fasta_dict.keys()]
d = np.zeros((len(fasta_list), len(fasta_list)))
for i in range(len(fasta_list)):
for j in range(len(fasta_list)):
d[i][j] = round(
hamming_distance(fasta_list[i], fasta_list[j]) /
len(fasta_list[i]), 4)
return d
if __name__ == '__main__':
input_fasta_dict = common.fasta_parser('PDST.txt')
dist_matrix = get_dist_table(input_fasta_dict)
with open('PDST_result.txt', 'w') as outfile:
for i in dist_matrix:
print(' '.join(map(str, i)), file=outfile)
import common
import numpy as np
fasta_dict = common.fasta_parser('CONS.txt')
letter_dict = dict()
base_list = ['A', 'C', 'G', 'T']
for base in base_list:
letter_dict[base] = [0] * len(fasta_dict[list(fasta_dict.keys())[0]])
for key in fasta_dict.keys():
count = 0
for letter in fasta_dict[key]:
letter_dict[letter][count] += 1
count += 1
cons_seq = ''
counter = 0
for _ in range(len(fasta_dict[list(fasta_dict.keys())[0]])):
value_list = [letter_dict[base][counter] for base in letter_dict.keys()]
cons_seq += base_list[np.argmax(value_list)]
counter += 1
print(cons_seq)
with open('CONS_result.txt', 'w') as f:
print(cons_seq, file=f)
for key in letter_dict.keys():
print('{}: {}'.format(key, ' '.join(map(str, [item for item in letter_dict[key]]))), file=f)
import common
fasta_dict = common.fasta_parser('SPLC.txt')
raw_seq = fasta_dict[list(fasta_dict.keys())[0]]
for key in fasta_dict.keys():
if fasta_dict[key] != raw_seq:
start_position = raw_seq.index(fasta_dict[key])
raw_seq = raw_seq[:start_position] + raw_seq[start_position +
len(fasta_dict[key]):]
print(common.translate_rna(raw_seq.replace('T', 'U')))
import common
fasta_dict = common.fasta_parser('TRAN.txt')
seq1, seq2 = (fasta_dict[key] for key in fasta_dict.keys())
transitions = [set(['A', 'G']), set(['C', 'T'])]
transitions_num, transfections_num = 0, 0
for index in range(len(seq1)):
if seq1[index] != seq2[index]:
if set([seq1[index], seq2[index]]) in transitions:
transitions_num += 1
else:
transfections_num += 1
print(round(transitions_num / transfections_num, 3))
import common
fasta_dict = common.fasta_parser('REVP.txt')
sequence = fasta_dict[list(fasta_dict.keys())[0]]
output_file = open('REVP_result.txt', 'w')
for half_pal_len in [2, 3, 4, 5, 6]:
for position in range(len(sequence) - half_pal_len):
if sequence[position:position + half_pal_len] == common.reverse_comp(
sequence[position + half_pal_len:position + 2 * half_pal_len]):
print(position + 1, 2 * half_pal_len, file=output_file)
output_file.close()
import common
kmer_len = 4
def get_kmer_count(string, kmer):
return len(common.substring_positions(string, kmer))
fasta_dict = common.fasta_parser('KMER.txt')
sequence = fasta_dict[list(fasta_dict.keys())[0]]
all_kmers = common.get_kmers(["A", "T", "G", "C"], kmer_len)
print(' '.join(map(str,
[get_kmer_count(sequence, kmer) for kmer in all_kmers])))