Shell Programming and Scripting

menu

while [ 1 ]
do  menu
done

 
#!/usr/bin/perl

use strict;
use warnings;
use Switch;

my $input = '';

while ($input ne '7')
{
    clear_screen();

    print "type 1 for mutation match\n".
          "type 2 for annovar conversion\n". 
          "type 3 for individual or sanger annotation\n". 
          "type 4 for batch or sanger annotation\n". 
          "type 5 for individual noonan syndrome anotation\n".
		  "type 6 for batch noonan syndrome annotation\n".
          "type 7 to end\n";
		  
		   print "Enter your choice: ";
    $input = <STDIN>;
    chomp($input);

    switch ($input)
    {
        case '1'
        {
            $input = '';

 
printf "Enter ID  : "; read id
	printf "What panel: "; read panel
		cd 'C:\Users\cmccabe\Desktop\annovar'
			[ -z "$id" ] && break
			OMR=Output_Mutation_Report
	perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$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

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

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

#!/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 );
}