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Full Discussion: Change directory error
Top Forums Shell Programming and Scripting Change directory error Post 302924889 by Aia on Thursday 13th of November 2014 12:39:42 AM
Old 11-13-2014
@cmccabe

If you are serious about it, you are going to have to learn and figure out what this line does first and how to converted from a command line invocation to a Perl code script. Calling Perl inside Perl would be a bit silly.

Code:
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

Since it is very ugly and hard to read, I separated them in sections to facilitate understanding for you.

Code:
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

Also, you'll need to figure out how to deal with all those shell variables, like ${id}, ${panel}, etc. Perl would not inherit those from the shell automatically.

Once, you do that, you might be ready for a menu.
There are many ways of doing it, depending on the design. Here's just a guide:

Code:
#!/usr/bin/perl

use strict;
use warnings;

sub run {
    print "I am running...\n";
}

sub walk {
    print "I am walking...\n";
}

sub dance {
    print "I am dancing...\n";
}

sub stop {
    print "See you!\n";
    exit;
}


sub menu {
    my $items  = shift;
    my $number = 1;

    print "\nWhat would you like me to do:\n";
    for my $item ( @{$items} ) {
        printf "%d: %s\n", $number++, $item->{'message'};
    }
    print "\nEnter option number: ";

    while (my $input = <STDIN>) {
        chomp $input;
        if ($input =~ m/\d+/
                and $input <= @{$items}
                and $input > 0) {
            return &{$items->[$input -1]->{$input}};
        }

        print "\nInvalid option, please try again: ";
    }
}

my @choice = (
    { 'message' =>     'running', '1' =>   \&run, },
    { 'message' =>     'dancing', '2' => \&dance, },
    { 'message' =>     'walking', '3' =>  \&walk, },
    { 'message' => 'end program', '4' =>  \&stop, },
);

while (1) {
    menu( \@choice );
}

There are no substitute for practicing and practicing some more.

After practice for some time, you could take a look at CPAN and search for menus. There are some modules to build some menus, like Term::Menus
Last edited by Aia; 11-13-2014 at 01:43 AM.. Reason: Missing last braquet
 

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LEARN ABOUT SUNOS

helpitem

ckitem(1)							   User Commands							 ckitem(1)

NAME

       ckitem, erritem, helpitem - build a menu; prompt for and return a menu item

SYNOPSIS

       ckitem  [-Q]  [-W width]  [-uno]  [-f filename]	[-l label]  [ [-i invis] [,...]] [-m max] [-d default] [-h help] [-e  error] [-p prompt] [
       -k pid [-s signal]] [ choice [...]]

       /usr/sadm/bin/erritem [-W width] [-e error] [ choice [..]]

       /usr/sadm/bin/helpitem [-W width] [-h help] [ choice [..]]

DESCRIPTION

       The ckitem utility builds a menu and prompts the user to choose one item from a menu of items. It then  verifies the response. Options  for
       this  command  define,  among  other  things,  a prompt message whose response will be a menu item, text for help and error messages, and a
       default value (which will be returned if the user responds with a carriage return).

       By default, the menu is formatted so that each item is prepended by a number and is printed in columns across the terminal.  Column  length
       is determined by the longest choice. Items are alphabetized.

       All messages are limited in length to 70 characters and are formatted automatically. Any white space used in the definition (including new-
       line) is stripped. The -W option cancels the automatic formatting. When a tilde is placed at the beginning or end of a message  definition,
       the default text will be inserted at that point, allowing both custom text and the default text to be displayed.

       If the prompt, help or error message is not defined, the default message (as defined under NOTES) will be displayed.

       Two  visual  tool  modules  are	linked	to the ckitem command. They are erritem (which formats and displays an error message) and helpitem
       (which formats and displays a help message). These modules should be used in conjunction with FML objects. In this instance, the FML object
       defines the prompt. When choice is defined in these modules, the messages will describe the available menu choice (or choices).

OPTIONS

       The following options are supported:

       -d default      Define the default value as default.  The default is not validated and so does not have to meet any criteria.

       -e error        Define the error message as  error.

       -f filename     Define  a  file,  filename,  which  contains  a	list  of  menu	items  to  be  displayed.   (The  format  of this file is:
		       token<tab>description. Lines beginning with a pound sign (#) are designated as comments and ignored.)

       -h help	       Define the help messages as  help.

       -i invis        Define invisible menu choices (those which will not be printed in the menu). (For example, ``all''  used  as  an  invisible
		       choice  would  mean  it is a legal option but does not appear in the menu. Any number of invisible choices may be defined.)
		       Invisible choices should be made known to a user either in the prompt or in a help message.

       -k pid	       Specify that the process ID pid is to be sent a signal if the user chooses to abort.

       -l label        Define a label, label, to print above the menu.

       -m max	       Define the maximum number of menu choices that the user can choose. The default is 1.

       -n	       Specify that menu items should not be displayed in alphabetical order.

       -o	       Specify that only one menu token will be returned.

       -p prompt       Define the prompt message as prompt.

       -Q	       Specify that quit will not be allowed as a valid response.

       -s signal       Specify that process ID pid defined with the -k option is to be sent signal  signal when quit is chosen. If  no	signal	is
		       specified, SIGTERM is used.

       -u	       Specify that menu items should be displayed as an unnumbered list.

       -W width        Specify that prompt, help and error messages will be formatted to a line length of width.

OPERANDS

       The following operand is supported:

       choice	       Define menu items. Items should be separated by white space or newline.

EXIT STATUS

       The following exit values are returned:

       0	Successful execution.

       1	EOF on input, or negative width on -W option, or inability to open file on -f option, or usage error.

       3	User termination (quit).

       4	No choices from which to choose.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWcsu			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       attributes(5)

NOTES

       The user may input the number of the menu item if choices are numbered or as much of the string required for a unique identification of the
       item. Long menus are paged with 10 items per page.

       When menu entries are defined both in a file (by using the -f option) and also on the command line, they are  usually  combined	alphabeti-
       cally. However, if the -n option is used to suppress  alphabetical ordering, then the entries defined in the file are shown first, followed
       by the options defined on the command line.

       The default prompt for ckitem is:

       Enter selection [?,??,q]:

       One question mark will give a help message and then redisplay the prompt. Two question marks will give a help message  and  then  redisplay
       the menu label, the menu and the prompt.

       The default error message if you typed a number is:

       ERROR: Bad numeric choice specification

       The default error message if you typed a string is:

       ERROR: Entry does not match available menu selection. Enter the number
       of the menu item you wish to select, the token which is associated
       with the menu item, or a partial string which uniquely identifies the
       token for the menu item. Enter ?? to reprint the menu.

       The default help message is:

       Enter the number of the menu item you wish to select, the token
       which is associated with the menu item, or a partial string which
       uniquely identifies the token for the menu item. Enter ? to
       reprint the menu.

       When the quit option is chosen (and allowed), q is returned along with the return code 3.

SunOS 5.10							    14 Sep 1992 							 ckitem(1)
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