-
Notifications
You must be signed in to change notification settings - Fork 1
/
concatenation.py
41 lines (33 loc) · 1.08 KB
/
concatenation.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
import os
import io
import sys
import argparse
import Bio.SeqIO as SeqIO
import gzip
import numpy as np
import pandas as pd
def get_no_hidden_folder_list(wd):
folder_list = []
for each_folder in os.listdir(wd):
if not each_folder.startswith('.'):
folder_list.append(each_folder)
folder_list_sorte = sorted(folder_list)
return folder_list_sorte
def main(path , output_file):
file_list = get_no_hidden_folder_list(path)
bin_num = len(file_list)
for k in range(bin_num):
seq_file = '%s/%s' % (path , file_list[k])
if k==0:
op1 = 'echo ' + '\">BIN_' + str(k) + '\" ' + '> ' + output_file
else:
op1 = 'echo ' + '\">BIN_' + str(k) + '\" ' + '>> ' + output_file
os.system(op1)
op2 = 'grep ' + '-v ' + '\'>\' ' + seq_file + ' >> ' + output_file
os.system(op2)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("-p",help="path")
parser.add_argument("-o",help="output_file")
args=parser.parse_args()
main(args.p,args.o)