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running dynamut in batches

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Tanushree Tunstall 2021-02-18 11:27:20 +00:00
parent cfdd18086a
commit 69b62e54a5
2 changed files with 13 additions and 19 deletions
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11
dynamut/run_get_results_dynamut.py
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@ -9,7 +9,7 @@ Created on Wed Aug 19 14:33:51 2020
import os import os
homedir = os.path.expanduser('~') homedir = os.path.expanduser('~')
os.chdir (homedir + '/git/LSHTM_analysis/dynamut') os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
from get_results import * from get_results_dynamut import *
######################################################################## ########################################################################
# variables # variables
my_host = 'http://biosig.unimelb.edu.au' my_host = 'http://biosig.unimelb.edu.au'
@ -23,9 +23,12 @@ datadir = homedir + '/git/Data'
indir = datadir + '/' + drug + '/input' indir = datadir + '/' + drug + '/input'
outdir = datadir + '/' + drug + '/output' outdir = datadir + '/' + drug + '/output'
# batch 1: 00.txt #==============================================================================
my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b1.txt' # batch 3: 02.txt, # RETRIEVED 18 Feb
my_suffix = 'gid_b1' my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b3.txt'
my_suffix = 'gid_b3'
#==============================================================================
#========================== #==========================
# CALL: get_results() # CALL: get_results()

21
dynamut/run_submit_dynamut.py
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@ -9,7 +9,7 @@ Created on Wed Aug 19 14:33:51 2020
import os import os
homedir = os.path.expanduser('~') homedir = os.path.expanduser('~')
os.chdir (homedir + '/git/LSHTM_analysis/dynamut') os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
from submit import * from submit_dynamut import *
######################################################################## ########################################################################
# variables # variables
my_host = 'http://biosig.unimelb.edu.au' my_host = 'http://biosig.unimelb.edu.au'
@ -28,20 +28,11 @@ my_email = 'tanushree.tunstall@lshtm.ac.uk'
my_pdb_file = indir + '/gid_complex.pdb' my_pdb_file = indir + '/gid_complex.pdb'
# batch 1: 00.txt #==============================================================================
#my_mutation_list =outdir + '/snp_batches/50/snp_batch_00.txt' # batch 5: 04.txt, # RAN: 18 Feb, ~11:21
#my_suffix = 'gid_b1' my_mutation_list = outdir + '/snp_batches/50/snp_batch_04.txt'
#RAN: 11 Feb, ~14:00 pm * RETRIEVED my_suffix = 'gid_b5'
#==============================================================================
# batch 2: 01.txt
#my_mutation_list = outdir + '/snp_batches/50/snp_batch_01.txt'
#my_suffix = 'gid_b2'
#RAN: 12 Feb, ~10:00 am, AWAITING
# batch 3: 02.txt
my_mutation_list = outdir + '/snp_batches/50/snp_batch_02.txt'
my_suffix = 'gid_b3'
#RAN: 12 Feb, ~12:40 pm, AWAITING
#========================== #==========================
# CALL: submit_dynamut() # CALL: submit_dynamut()