otu2pg

#!/bin/bash

set -euo pipefail

OLD_IFS=${IFS}

#IFS=','

file=myosd2015-1000-otu-table.csv
declare -gr OUT_FILE='myosd-otu-count.csv'
# takes also first out col header
declare -i COL_NUM=$(head -n 1 ${file} | tr ',' '\n' | wc -l)

#COL_NUM=3
header=''
silva_otu='';
myosd_id=shoot;



function colcut () {
    cut -d ',' -s -f 1,"$1" "$2"
}

function analyse_header () {   
    IFS=',' read id mid;
    #echo "mid=${mid}"
    myosd_id="${mid//_*a/}";
    myosd_id="${myosd_id//\"MYOSD/}";
    declare -gx myosd_id="${myosd_id//\"/}";
    echo "${myosd_id}"    
}

function cutheader() {
    head -n 1 $2 | colcut "${1}" '-' 
}

function cutcol () {
    #echo "i=$1"
    tail -n +2 "${2}"| colcut "$1" '-'
}


echo "Column count: ${COL_NUM}"
echo "myosd_id,silva_otu,num" > "${OUT_FILE}";
for i in $(seq 2 ${COL_NUM}); do
    echo "working on head"

    test=$(cutheader "${i}" "${file}" | analyse_header)

    echo "myosdid=${test}"


    echo "now rest"
    while IFS=',' read -r id num; do
	echo "${test},${id//\"/},$num" >> "${OUT_FILE}";
   done < <(cutcol "${i}" "${file}")

done;