added shell script to format muts for mcsm NA

dynamut/run_submit.py

@@ -26,7 +26,7 @@ outdir = datadir + '/' + drug + '/output'
 my_chain = 'A'
 my_email = 'tanushree.tunstall@lshtm.ac.uk'
 
-my_pdb_file = homedir + '/git/Data/streptomycin/input/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'

mcsm_na/examples.py

@@ -20,10 +20,10 @@ my_prediction_url = f"{my_host}/mcsm_na/run_prediction_list"
 print(my_prediction_url)
 
 my_outdir = homedir + '/git/LSHTM_analysis/mcsm_na'
-
+my_nuc_type = 'RNA'
 my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb'
 my_mutation_list = homedir + '/git/LSHTM_analysis/mcsm_na/test_snps_b1.csv'
-my_suffix = 'gid_test_b1'
+my_suffix = 'TEST'
 
 #----------------------------------------------
 # example 1: 2 snps in a file
@@ -31,7 +31,7 @@ my_suffix = 'gid_test_b1'
 submit_mcsm_na(host_url = my_host
 , pdb_file = my_pdb_file
 , mutation_list = my_mutation_list
-, nuc_type = 'RNA'
+, nuc_type = my_nuc_type
 , prediction_url = my_prediction_url
 , output_dir = my_outdir
 , outfile_suffix = my_suffix) 
@@ -53,4 +53,4 @@ my_suffix = 'single'
 get_results(url_file  = my_url_file_single
             , host_url = my_host
             , output_dir = my_outdir
-            , outfile_suffix = my_suffix)
+            , outfile_suffix = my_suffix)

mcsm_na/mcsm_na_temp/mcsm_na_result_url_gid_test_b1.txt

@@ -1 +0,0 @@
-http://biosig.unimelb.edu.au/mcsm_na/results_prediction/1613147445.16

mcsm_na/run_submit.py

@@ -5,36 +5,41 @@ Created on Fri Feb 12 12:15:26 2021
 
 @author: tanu
 """
+#%% load packages
 import os
 homedir = os.path.expanduser('~')
-os.chdir (homedir + '/git/LSHTM_analysis/mcsm_na')
-from submit import *
-
-#%%#####################################################################
-#EXAMPLE RUN for different stages
-#=====================
-# STAGE: submit.py
-#=====================
+os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
+from submit_mcsm_na import *
+########################################################################
+# variables
 my_host = 'http://biosig.unimelb.edu.au'
-my_prediction_url = f"{host}/mcsm_na/run_prediction"
+my_prediction_url = f"{my_host}/mcsm_na/run_prediction_list"
 print(my_prediction_url)
 
-my_outdir = homedir + '/git/LSHTM_analysis/mcsm_na'
+# TODO: add cmd line args
+#gene = 'gid'
+drug = 'streptomycin'
+datadir = homedir + '/git/Data'
+indir = datadir + '/' + drug + '/input'
+outdir = datadir + '/' + drug + '/output'
 
-my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb'
-my_mutation_list = homedir + '/git/LSHTM_analysis/mcsm_na/input_snp_test_b1.csv'
-my_suffix = 'gid_test1'
+my_nuc_type = 'RNA'
+my_pdb_file = indir + '/gid_complex.pdb'
 
-#----------------------------------------------
-# example 1: 2 snps in a file
-#----------------------------------------------
+# batch 1: 00.txt
+my_mutation_list = outdir + '/snp_batches/20/snp_batch_00.txt'
+my_suffix = 'gid_b1'
+#RAN: 11 Feb, ~17:37
+
+#==========================
+# CALL: submit_mcsm_na() 
+# Data: gid+streptomycin
+#==========================
 submit_mcsm_na(host_url = my_host
-, pdb_file = my_pdb_file
-, mutation_list = my_mutation_list
-, chain = my_chain
-, email_address = my_email
-, prediction_url = my_prediction_url
-, output_dir = my_outdir
-, outfile_suffix = my_suffix) 
-#%%###################################################################
-
+               , pdb_file = my_pdb_file
+               , mutation_list = my_mutation_list
+               , nuc_type = my_nuc_type
+               , prediction_url = my_prediction_url
+               , output_dir = outdir
+               , outfile_suffix = my_suffix) 
+#%%#####################################################################               

mcsm_na/split_format_csv.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# FIXME: This is written for expediency to kickstart running dynamut and mcsm-NA
+
+# Usage: ~/git/LSHTM_analysis/dynamut/split_csv.sh <input file> <output dir> <chunk size in lines>
+# copy your snp file to split into the mcsm_na dir
+
+INFILE=$1
+OUTDIR=$2
+CHUNK=$3
+
+mkdir -p ${OUTDIR}/${CHUNK}
+cd ${OUTDIR}/${CHUNK}
+
+split ../../${INFILE} -l ${CHUNK} -d snp_batch_
+for i in *; do mv $i $i.txt; done
+sed -i 's/^/A /g' *.txt
+
+