CODEWITHSUNDEEP
perlshell
user3781528
user3781528

Reputation: 639

Passing variable between scripts

I've created a variable $date in Main.pl script that I would like to pass to Annotator.pl script. I use shell script to execute Annotator.pl. I can't figure out how to pass $date to Annotator.pl. When I run my $date = $ARGV[0]; in Annotator.pl I get the name of the current directory, however, $date = $ARGV[1]; returns nothing.

Please see the code below. The date is important because it has to be exact and I can't figure out how to pass it to Annotator.pl. Thanks for your help.

Main.pl Script:

#!/usr/bin/perl -w
    use strict;
    use warnings;

    my $sec; my $min; my $hour; my $mday; my $mon; my $year; my $wday; my $yday;    my $isdst;
    ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime();
    $mon=$mon+1; $year = 1900+$year;
    if (length($mon)==1) {$mon="0".$mon;}
    if (length($mday)==1) {$mday="0".$mday;}
    if (length($hour)==1) {$hour="0".$hour;}
    if (length($min)==1) {$min="0".$min;}
    if (length($sec)==1) {$sec="0".$sec;}

    my $date = "$mon"."_"."$mday"."_"."$year"."-".$hour.$min.$sec;

    my $cmd5 = `perl MDL_unzip_annotate.sh /data/test_all_runs pVCF $date`;   print "$cmd5";

Shell script: MDL_unzip_annotate.sh that executes Annotator.pl

home="/data/test_all_runs" #location of the run directory from which the program is launched
   scripts="/data/test_scripts"  

     datapath=$1 #this is called in Main.pl as [test_all_runs]
     process=$2 #the process  

    if [[ "$process" == "pVCF" ]];then
            cd $datapath
            folders="$(ls)"
            cd $scripts
        for ff in $folders; do
            dname=$ff
                echo $dname
                if [  ! -f $dname ];then

                    cmd2="perl Annotator.pl $dname"
                    echo $cmd2

                    cmd2=`perl Annotator.pl $dname`
                    echo $cmd2
                fi
            done    
    done          

    fi

Annotator.pl script:

#!perl
    use strict;
    use warnings;

    my $date = $ARGV[1]; print "the date is######## ".$date."\n";

Upvotes: 0

Views: 86

Answers (1)

user3781528
user3781528

Reputation: 639

Instead of using shell script I will use the following code to capture the name of the folder in a specific directory:

opendir my $dir, "/data/test_all_runs" or die "Cannot open directory: $!";
my @run_folder = readdir $dir;
closedir $dir;
my $last_one = pop @run_folder; print "The folder is".$last_one."\n";

Thanks for your suggestions.

Upvotes: 1

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