Shell Programming and Scripting

printf "Enter variant: "; read variant

 #!/bin/bash

menu() {
    printf "\n Welcome to annovar, please make a selection from the MENU \n
    ==================================\n\n
    \t 1  GJB2 analysis\n
    \t 2  MECP2 analysis\n
    \t 3  Phox2B analysis\n
    \t 4  Exit\n\n
    ==================================\n\n"

    printf "\t Your choice: "; read menu_choice

    case "$menu_choice" in
        1) gjb2 ;;
	2) mecp2 ;;
	3) phox2b ;;
	4) printf "\n Bye! \n\n"; exit ;;
        *) printf "\n Invalid choice."; sleep 2; menu ;;
    esac
}

gjb2() {
    printf "\n\n"
    printf "What is the id of the patient getting GJB2 analysis  : "; read id
    printf "Enter variant: "; read variant

    [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
    [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu

    cd 'C:'
    C:\Users\cmccabe\Desktop\Python27\python.exe C:\Users\cmccabe\Desktop\Python27\run_batch_job.py C:\Users\cmccabe\Desktop\Python27\${variant}.txt
    C:\Users\cmccabe\Desktop\annovar\${id}.txt PositionConverter
    parse
}

#!/bin/bash

menu() {
    while true
    do
        printf "\n Welcome to annovar, please make a selection from the MENU \n
        ==================================\n\n
        \t 1  GJB2 analysis\n
        \t 2  MECP2 analysis\n
        \t 3  Phox2B analysis\n
        \t 4  Exit\n\n
        ==================================\n\n"

        printf "\t Your choice: "; read menu_choice

        case "$menu_choice" in
            1) gjb2 ;;
        2) mecp2 ;;
        3) phox2b ;;
        4) printf "\n Bye! \n\n"; exit ;;
        *) printf "\n Invalid choice."; sleep 2 ;;
        esac
    done
}

gjb2() {
    printf "\n\n"
    printf "What is the id of the patient getting GJB2 analysis  : "; read id
    printf "Enter variant: "; read variant

    printf "%s\n" "$variant" > c:/Users/cmccabe/Desktop/NM_004004.4

    [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && return
    [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && return

    cd 'C:'
    C:/Users/cmccabe/Desktop/Python27/python.exe C:/Users/cmccabe/Desktop/Python27/run_batch_job.py C:/Users/cmccabe/Desktop/Python27/${variant}.txt
    C:/Users/cmccabe/Desktop/annovar/${id}.txt PositionConverter
    parse
}

 @echo off
set PATH=C:\cygwin\bin\;%PATH%@
    c:\cygwin\bin\bash.exe c:\cygwin\home\cmccabe\bashparse.sh

 
Welcome to annovar, please make a selection from the MENU

        ==================================


                 1  GJB2 analysis

                 2  MECP2 analysis

                 3  Phox2B analysis

                 4  Exit


        ==================================

         Your choice: 1


What is the id of the patient getting GJB2 analysis  : GJB-1
Enter variant: c.203G>A
usage: run_batch_job.py [-h] [-v] [-b BUILD] INPUT OUTPUT TYPE
run_batch_job.py: error: argument INPUT: can't open 'C:/Users/cmccabe/Desktop/Py
thon27/c.203G>A.txt': [Errno 22] invalid mode ('r') or filename: 'C:/Users/cmcca
be/Desktop/Python27/c.203G>A.txt'
c:\cygwin\home\cmccabe\bashparse.sh: line 38: C:/Users/cmccabe/Desktop/annovar/G
JB-1.txt: No such file or directory

 c:/Users/cmccabe/Desktop/Python27

 printf "%s\n" "$variant" > c:/Users/cmccabe/Desktop/NM_004004.4

 sed -i '$a NM_004004.4' $id.txt

 printf "%s\n" "$variant" > c:/Users/cmccabe/Desktop/Python27/$id.txt

 What is the id of the patient getting GJB2 analysis  : GJB-2
Enter variant: c.204G>A
sed: can't read GJB-2.txt: No such file or directory

 printf "%s\n" "$variant" > c:/Users/cmccabe/Desktop/Python27/$id.txt

 sed -i '$a NM_004004.4:' c:/Users/cmccabe/Desktop/Python27/$id.txt