#!/bin/bash
set -e

# Metadata files edited:
# rpob: remove positions above 1151
# embb: remove positions above 1054
#=======================================================================
#https://www.biostars.org/p/336891/
#python Mutate.py -v -o /path/to/output.fasta mutation_map_file.csv input.fasta
#=======================================================================
DATA_DIR="/home/tanu/git/Data"

echo "Processing Mutation Files"
echo "-------------------------"
echo

while read -r gene drug; do
  echo "vvvvvvvvvvvvvvvvvvvvv"
  echo "gene: $gene drug: $drug"; 
  echo "Source File: ${DATA_DIR}/${drug}/output/${gene}_metadata.csv"
  MSA_MAP=${DATA_DIR}/${drug}/output/${gene}_msa_map.csv
  wc -l ${DATA_DIR}/${drug}/output/${gene}_metadata.csv
  cat  ${DATA_DIR}/${drug}/output/${gene}_metadata.csv | rev| cut -d, -f1 |rev | tail -n +2 |sort | uniq -c  > ${DATA_DIR}/${drug}/output/${gene}_metadata_mut_count.csv
  cat  ${DATA_DIR}/${drug}/output/${gene}_metadata.csv | rev| cut -d, -f1 |rev | tail -n +2 |sort | sed -e 's/"//g' > $MSA_MAP
  echo "Output to: $MSA_MAP"
  sed -i "s/^/${gene},/" $MSA_MAP
  wc -l $MSA_MAP
  echo "^^^^^^^^^^^^^^^^^^^^^"
  echo
  echo "Running mutate.py on data file $MSA_MAP"
  python3 mutate.py -v -o ${DATA_DIR}/${drug}/output/${gene}_msa_interim.csv $MSA_MAP $DATA_DIR/${drug}/input/${gene}_f2.fasta
  echo "mutate.py completed"
  echo

done < gene_targets_names.txt

# Stop here so we don't run the examples below :)
exit

# make sure there is no new line at the end of the mutation file (snps.csv)
# check
cat  output/gid_metadata.csv | rev| cut -d, -f1 |rev | tail -n +2 |sort | head

cat  output/gid_metadata.csv | rev| cut -d, -f1 |rev | tail -n +2 |sort | uniq -c  > output/gid_metadata_mut_count.csv


cat  output/gid_metadata.csv | rev| cut -d, -f1 |rev | tail -n +2 |sort > gid_msa_snp.csv
sed -i 's/^/gid,/' gid_msa_snp.csv 

#cp gid_msa_snp.csv gid_mut_map.csv
#%%
# Date: 16/01/22
# pre processing
sed 's/"//g' gene_msa_snp.csv > gid_mut_map.csv

# mut prefix for mutation map file MUST match fasta file header 
python3 mutate.py -v -o /home/tanu/git/Data/streptomycin/output/TEST2.csv /home/tanu/git/Data/streptomycin/output/gid_mut_map.csv /home/tanu/git/Data/streptomycin/input/gid2.fasta

wc -l TEST2.csv

# post processing
sed -E 's/>.*//g' TEST2.csv | sed '/^$/d' > TEST3.csv
wc -l TEST3.csv

#==============================================