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long.py
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long.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# @File : long.py
# @Date : 2019-02-18
# @Author : luyang(luyang@novogene.com)
import networkx as nx
from module.readfasta import readfasta
def compare_reads(r1, r2):
for i in range(len(r1)):
length = len(r1) - i
if r1[i:length + i] == r2[:length]:
if length > len(r2) / 2:
return length
else:
continue
return 0
def main():
file = 'input/rosalind_long.txt'
reads = readfasta(file)
G = nx.DiGraph()
for name in reads:
G.add_node(name)
for i in reads:
for j in reads:
if i == j:
continue
else:
w = compare_reads(reads[i], reads[j])
if w:
G.add_edge(i, j, weight=w)
seq = []
node_list = nx.dag_longest_path(G)
seq.append(reads[node_list[0]])
for i in range(1, len(node_list)):
src = node_list[i - 1]
dst = node_list[i]
w = G.get_edge_data(src, dst)['weight']
seq.append(reads[dst][w:])
print(seq)
print(''.join(seq))
if __name__ == "__main__":
main()