Shell Programming and Scripting

execute() {
    while true
    do
# oldest folder stored as variable for analysis, version log created, and quality indicators matched to run
dir=/home/cmccabe/Desktop/NGS/API

find "$dir" -maxdepth 1 -mindepth 1 -type d -printf '%T+\t%P\0' | sort -rz |
while read -r -d $'\t' time && read -r -d '' filename
do
    printf "The oldest folder is $filename, created on $time and analysis done using v1.7 by $USER at $(date "+%D %r")\n" >> /home/cmccabe/medex.logs/folder.log
    awk -v FL="$filename" '
         FNR == 1 {filenum++}
         filenum==1 && index($0, FL) { 
              match($0, "_0*([0-9]+)/")
              FNUM=substr($0,RSTART+1,RLENGTH-2)
              gsub(/^0+/,"", FNUM)
          }
          #filenum==2 && $0 ~ FNUM".pdf$"' /home/cmccabe/s5_files/downloads/list /home/cmccabe/s5_files/pdf/pdf > /home/cmccabe/s5_files/pdf/output
    break
done
...
...
...
...
panel
done
}

menu() {
    while true
    do
        printf "\n please make a selection from the MENU \n
        ==================================
        \t 1  gene
        \t 2  test
        ==================================\n\n"
        printf "\t Your choice: "; read menu_choice
        echo "$menu_coice panel selected"

        case "$menu_choice" in
        1) gene ;;
        2) test ;;
        *) printf "\n Invalid choice."; sleep 2 ;;
        esac
    done
}


while true; do
    read -p "Do you want to start the me?" yn
    case $yn in
        [Yy]* ) execute; break ;;
        [Nn]* ) exit ;;
        * ) echo "Please answer yes or no.";;
    esac
done

panel() {
    printf "Do you want to get coverage of a specific gene, genes, or panel?"; read yn
    case $yn in
        [Yy]* ) menu ;;
        [Nn]* ) move ;;
        * ) echo "Please answer yes or no.";;
    esac
}

#!/usr/bin/env bash

# @(#) s1       Demonstrate placement of function definitions.

LC_ALL=C ; LANG=C ; export LC_ALL LANG
pe() { for _i;do printf "%s" "$_i";done; printf "\n"; }
pl() { pe;pe "-----" ;pe "$*"; }
em() { pe "$*" >&2 ; }
db() { ( printf " db, ";for _i;do printf "%s" "$_i";done;printf "\n" ) >&2 ; }
db() { : ; }
C=$HOME/bin/context && [ -f $C ] && $C

a() {
  printf " Hello, inside function a\n"
}

pl " Executing function a:"
a

pl " Executing function b before definition:"
b

b() {
  printf " Hello, inside function b\n"
}


pl " Executing function b after definition:"
b

exit 0

$ ./s1

Environment: LC_ALL = C, LANG = C
(Versions displayed with local utility "version")
OS, ker|rel, machine: Linux, 3.16.0-4-amd64, x86_64
Distribution        : Debian 8.7 (jessie) 
bash GNU bash 4.3.30

-----
 Executing function a:
 Hello, inside function a

-----
 Executing function b before definition:
./s1: line 21: b: command not found

-----
 Executing function b after definition:
 Hello, inside function b