my_ep_phasing.py

#!/usr/bin/python
# -*- coding: utf-8 -*-

#now going forward to do phasing after running xia2
# don't forget to do: module load big_ep



import os
from os import listdir
from os.path import isfile, join 
import argparse
import subprocess
#from libtbx import easy_mp
import datetime

#defining some directories and input/output paths

output_path = '/dls/tmp'
input_path = '/dls/tmp/ghp45345/xia2_stresstest/'

proc_dirs = sorted(os.listdir(input_path))
latest_proc_dir = proc_dirs[-1]

date = datetime.datetime.today().strftime('%Y%m%d')

if not os.path.exists('/dls/tmp/ghp45345/EP_phasing/%s' %(date)):
    os.makedirs(os.path.join(output_path, 'ghp45345', 'EP_phasing',
    date))

output_dir = '/dls/tmp/ghp45345/EP_phasing/%s' % date


#changing into output directory and create the job lists
#and directory structure

os.chdir(output_dir)

phasing_job_list = os.path.join(output_dir, 'pdb_id_phasing.txt')
fh = open(phasing_job_list, 'w')
phasing_pdb_list = listdir('/dls/tmp/ghp45345/xia2_stresstest/%s'
%latest_proc_dir)
phasing_pdb_id = []
for pdb in phasing_pdb_list:
  if len(pdb) == 4:
    phasing_pdb_id.append(pdb)
  else:
    pass
for pdb in phasing_pdb_id:
  fh.write(pdb)
  fh.write('\n')
fh.close()


number_phasing_pdb = len(phasing_pdb_id)
with open(os.path.join(output_dir,'EP_phasing.txt'), 'w') as text_file:
  text_file.write('Total number of data sets is %s \n'
  %(number_phasing_pdb))
text_file.close()

#running Big_EP

ep_phasing_jobs = open('pdb_id_phasing.txt', 'r+')
for line in ep_phasing_jobs:
  line = line.strip()
  pdb_id = line
  with open(os.path.join(output_dir, 'EP_phasing.txt'), 'a') as text_file:
    text_file.write('Run experimental phasing for %s using Big_EP \n' %(pdb_id))
  os.mkdir(os.path.join(output_dir,pdb_id))
  os.chdir(os.path.join(output_dir,pdb_id)) #this changes into the directory
  MTZ_dir = '/dls/tmp/ghp45345/xia2_stresstest/%s/%s' %(latest_proc_dir, pdb_id)
  #MTZ_dir = '/dls/tmp/ghp45345/xia2_stresstest/%s/%s' %date, pdb_id
  input_path = os.path.join(MTZ_dir, 'DataFiles', 'AUTOMATIC_DEFAULT_free.mtz')
  
  #p = subprocess.Popen(
  #  'big_ep',
  #  'data = %s' %(input_path), 
  #  'seq_file = /dls/mx-scratch/jcsg-data/sequence/%s.fasta' %(pdb_id), 
  #  'atom_type = Se',
  #  'sites = 10')

  #this is wher the Big_EP execution line goes in
  fh = open('dummy.txt', 'w')
  fh.close()
  #create an if statement here to test whether Big_EP produced any results
  #at all;
  with open(os.path.join(output_dir, 'EP_phasing.txt'), 'a') as text_file:
    text_file.write('Finished experimental phasing for %s  \n' %(pdb_id))
  text_file.close()
  os.chdir(output_dir)

with open(os.path.join(output_dir, 'EP_phasing.txt'), 'a') as text_file:
  text_file.write('Finished experimental phasing for %s  PDB IDs\n'
  %(number_phasing_pdb))
text_file.close()

  





#parser = argparse.ArgumentParser(description='commnad line argument')
#parser.add_argument(
#  '--phasing_directory',
#  type=str,
#  dest = 'phasing_directory',
#  default = '/dls/tmp/ghp45345/EP_phasing/%s' %(date),
#  help = 'phasing_data_directory')
#parser.add_argument(
#  '--data_directory',
#  type=str,
#  dest = 'data_directory',
#  default = 'latest_subdir/%s' %(pdb_id),
#  help='xia2_processing_directory')
#args = parser.parse_args()