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Full Discussion: Change directory error
Top Forums Shell Programming and Scripting Change directory error Post 302924557 by junior-helper on Monday 10th of November 2014 02:27:52 PM
Old 11-10-2014
Your code is relatively hard to read, I had real difficulties to decipher the program flow.
I wrote a script which utilizes functions for better understanding.

It assumes following program flow and to me it seems to make more sense than
match -> additional -> additional -> convert (repeated manual input of ids)

Code:
menu -> match -> convert? -> NO -> additional? -> NO -> menu
        ^               |          |         |
        |               +--> YES --+         +--> YES +
        |                                             |
        +---------------------------------------------+

Feel free to comment out the "DEBUG INFO" lines if all works as expected; I put them there to see if the variables still contained the values provided in the match function.

Hope this helps.
Code:
#!/bin/bash

menu() {
    clear
    printf "\n MENU \n
    ==================================\n\n
    \t 1  Match patient\n
    \t 2  Exit\n\n
    ==================================\n\n"

    printf "\t Your choice: "; read menu_choice

    case "$menu_choice" in
        1) match ;;
        2) printf "\n Bye! \n\n"; exit ;;
        *) printf "\n Invalid choice."; sleep 2; menu ;;
    esac
}


match() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
    printf "What is the id of the patient to be matched  : "; read id
    printf "What panel: "; read panel

    [ -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:\Users\cmccabe\Desktop\annovar'
    OMR=Output_Mutation_Report
    $( perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})' ${id}_${panel}_${OMR}.txt < ${id}_${panel}_${OMR}_Filtered.vcf > ${id}_matched.vcf )
    convert
}

convert() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
    printf "Does the file need to be converted? Y/N "; read convert_choice
    
    case "$convert_choice" in
        [yY]) $( perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput )
        additional ;;
        [nN]) additional ;;  
        *) convert ;;
    esac
}

additional() {
    printf "\n\n"
    printf "Are there additonal patients to be matched?  Y/N "; read match_choice

    case "$match_choice" in
        [yY]) id=""; panel=""; match ;;
        [nN]) id=""; panel=""; menu ;;  
        *) additional ;;
    esac
}

# actual start of this program
menu # run menu function

 

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LEARN ABOUT BSD

learn

LEARN(1)						      General Commands Manual							  LEARN(1)

NAME

       learn - computer aided instruction about UNIX

SYNOPSIS

       learn [ -directory ] [ subject [ lesson ] ]

DESCRIPTION

       Learn gives Computer Aided Instruction courses and practice in the use of UNIX, the C Shell, and the Berkeley text editors.  To get started
       simply type learn.  If you had used learn before and left your last session without completing a subject, the program will use  information
       in  $HOME/.learnrc  to start you up in the same place you left off.  Your first time through, learn will ask questions to find out what you
       want to do.  Some questions may be bypassed by naming a subject, and more yet by naming a lesson.  You may enter the  lesson  as  a  number
       that  learn  gave you in a previous session.  If you do not know the lesson number, you may enter the lesson as a word, and learn will look
       for the first lesson containing it.  If the lesson is `-', learn prompts for each lesson; this is useful for debugging.

       The subject's presently handled are

	    files
	    editor
	    vi
	    morefiles
	    macros
	    eqn
	    C

       There are a few special commands.  The command `bye' terminates a learn session and `where' tells you  of  your	progress,  with  `where m'
       telling	you  more.  The command `again' re-displays the text of the lesson and `again lesson' lets you review lesson.  There is no way for
       learn to tell you the answers it expects in English, however, the command `hint' prints the last part of the lesson script used to evaluate
       a  response, while `hint m' prints the whole lesson script.  This is useful for debugging lessons and might possibly give you an idea about
       what it expects.

       The -directory option allows one to exercise a script in a nonstandard place.

FILES

       /usr/share/learn    subtree for all dependent directories and files
       /usr/tmp/pl*   playpen directories
       $HOME/.learnrc startup information

SEE ALSO

       csh(1), ex(1)
       B. W. Kernighan and M. E. Lesk, LEARN - Computer-Aided Instruction on UNIX

BUGS

       The main strength of learn, that it asks the student to use the real UNIX, also makes possible baffling mistakes.   It  is  helpful,  espe-
       cially for nonprogrammers, to have a UNIX initiate near at hand during the first sessions.

       Occasionally lessons are incorrect, sometimes because the local version of a command operates in a non-standard way.  Occasionally a lesson
       script does not recognize all the different correct responses, in which case the `hint' command may be useful.  Such lessons may be skipped
       with the `skip' command, but it takes some sophistication to recognize the situation.

       To find a lesson given as a word, learn does a simple fgrep(1) through the lessons.  It is unclear whether this sort of subject indexing is
       better than none.

       Spawning a new shell is required for each of many user and internal functions.

       The `vi' lessons are provided separately from the others.  To use them see your system administrator.

7th Edition							 October 22, 1996							  LEARN(1)
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