Merge branch 'embb_dev'

mcsm_na/run_format_results_mcsm_na.py

@@ -52,15 +52,16 @@ if not outdir:
 outdir_na = outdir + 'mcsm_na_results/'
 
 # Input file
-infile_mcsm_na =  outdir_na +  gene + '_output_combined_clean.tsv'
+infile_mcsm_na =  outdir_na +  gene.lower() + '_output_combined_clean.tsv'
 
 # Formatted output file
-outfile_mcsm_na_f = outdir_na + gene + '_complex_mcsm_na_norm.csv'
+outfile_mcsm_na_f = outdir_na + gene.lower() + '_complex_mcsm_na_norm.csv'
 
-#==========================
+#===========================================
 # CALL: format_results_mcsm_na() 
 # Data: gid+streptomycin
-#==========================
+# Data: rpob+rifampicin, date: 18/11/2021
+#===========================================
 print('Formatting results for:', infile_mcsm_na)
 mcsm_na_df_f = format_mcsm_na_output(mcsm_na_output_tsv = infile_mcsm_na)
 

mcsm_na/run_submit_mcsm_na.py

@@ -18,14 +18,14 @@ print(my_prediction_url)
 
 # TODO: add cmd line args
 #gene = 'gid'
-drug = 'streptomycin'
-datadir = homedir + '/git/Data'
-indir = datadir + '/' + drug + '/input'
-outdir = datadir + '/' + drug + '/output'
-outdir_mcsm_na = outdir + 'mcsm_na_results'
+drug = ''
+datadir = homedir + '/git/Data/'
+indir = datadir + drug + 'input/'
+outdir = datadir + drug + 'output/'
+outdir_mcsm_na = outdir + 'mcsm_na_results/'
 
 my_nuc_type = 'RNA'
-my_pdb_file = indir + '/gid_complex.pdb'
+my_pdb_file = indir + gene.lower() + '_complex.pdb'
 
 #=============================================================================
 # batch 26: 25.txt # RAN: 16 Feb:

mcsm_na/split_csv.sh

@@ -0,0 +1,27 @@
+#!/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_
+
+# use case
+#~/git/LSHTM_analysis/mcsm_na/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50
+#~/git/LSHTM_analysis/mcsm_na/split_csv.sh embb_mcsm_formatted_snps.csv snp_batches 50
+
+
+#~/git/LSHTM_analysis/mcsm_na/split_csv.sh rpob_mcsm_formatted_snps_chain.csv snp_batches 20 # date: 17/11/2021
+
+
+#acccidently replaced file original rpob batches
+
+#~/git/LSHTM_analysis/mcsm_na/split_csv.sh 5uhc_mcsm_formatted_snps_chain.csv snp_batches_5uhc 20 # date: 17/11/2021