AutoHomology/run_me.py at master · SysSynBio/AutoHomology · GitHub

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
39
40
41
42
43
44
45
46
47
48
49
import glob, os, sys, time
from datetime import datetime

starting_dir = os.getcwd()
util_path = starting_dir + "/util/"
sys.path.insert(0, util_path)
from util import *


def run_AutoHomology(target_fasta_file, retrievd_csv):
    current_dir = os.getcwd()

    command = "python ../prepare_to_hybridize/download_pdb_chain.py " + starting_dir + " " + retrievd_csv
    os.system(command)

    command = "python ../prepare_to_hybridize/make_grishin_files.py " + target_fasta_file
    os.system(command)

    command = "python ../prepare_to_hybridize/partial_thread.py " + target_fasta_file
    os.system(command)

########### end of def run_AutoHomology(fasta_file, retrievd_csv):


if (__name__ == "__main__") :
  total_start_time = time.time()
  args=sys.argv[1:]

  if len(args) < 2:
      print "\nPlease provide fasta file for homology modeling and psi-blasted.csv"
      print "Usage:         python run_me.py <fasta file> <csv file>"
      print "Example usage: python DGAT.fasta ZFHADRTG016-Alignment-HitTable.csv"

  else:
    fasta_file = os.path.join(starting_dir, args[0])
    retrievd_csv = os.path.join(starting_dir, args[1])

    today = datetime.now()
    working_folder = today.strftime('%Y%m%d') + "_" + str(today.hour) + str(today.minute) + str(today.second)
    os.mkdir(working_folder)
    os.chdir(working_folder)

    run_AutoHomology(fasta_file, retrievd_csv)

  total_end_time = time.time()
  process = "\nTotal AutoHomology run"
  print show_time(process, total_start_time, total_end_time)