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cons.py
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cons.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# @File : cons.py
# @Date : 2019-02-18
# @Author : luyang([email protected])
import numpy as np
from Bio import SeqIO
def main():
file = 'input/rosalind_cons.txt'
with open(file) as f:
seqs = []
cons = []
records = list(SeqIO.parse(f, "fasta"))
for i in range(len(records)):
seqs.append(' '.join(str(records[i].seq)).split())
array_seqs = np.array(seqs)
position_count = np.zeros(shape=(4, array_seqs.shape[1]), dtype=int)
for i in range(array_seqs.shape[1]):
array = array_seqs[:, i]
unique, counts = np.unique(array, return_counts=True)
base_count = dict(zip(unique, counts))
j = 0
cons.append(max(base_count.items(), key=lambda x: x[1])[0])
for key in ['A', 'C', 'G', 'T']:
if key in base_count:
position_count[j, i] = base_count[key]
j += 1
else:
j += 1
print(''.join(cons))
j = 0
for i in ['A', 'C', 'G', 'T']:
print(i + ': ' + ' '.join(str(e) for e in position_count[j]))
j += 1
if __name__ == "__main__":
main()