batch modify command line

if you want to modify batch of command line,you need try below scripts.
#!/usr/bin/perl -w
#use strict;
use warnings;
use Cwd qw(abs_path getcwd);
use FindBin '$Bin';

open(IN,"$ARGV[0]") or die "$!";
open(SH,">$ARGV[1]");
my @array=();
while(<IN>){
        chomp;
        push @array,$_;
}
my @sortar=sort @array;
my $count=0;
for(my $i=0;$i<=$#sortar;$i+=2){
                #`mkdir "$Bin/Result/L$count"` unless -d "$Bin/Result/L$count";
        $sortar[$i] =~/(L\d+)/
                my $cmd="mkdir /home/data/Result/$1 && cd /home/data/Result/$1 && /home/data/hisat/2.0.4/hisat2 --dta -p 6 --rna-strandness RF -x /home/data/genome/Bactrocera_dorsalis.ASM78921v2.genome -1 $sortar[$i] -2 $sortar[$i+1] -S /home/data/Result/$1/$1.HISAT_aln.sam > /home/data/Result/$1/$1.log\n";
                print SH $cmd;
}

close IN;
close SH;

#simple commands

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

open(my $out,">command13-30bamSort.list_new.sh");
my @arrdata=`find /home/Result/ -name "*HISAT_aln.bam" |sort`; #get data absolute pathway 
print @arrdata;
while(my $line=<@arrdata>){
        chomp($line);
        $line =~/(L\d+)/;
        print $out "cd /home/Result/$1/ && /home/samtools/0.1.18/samtools sort /home/Result/$1/$1.HISAT_aln.bam /home/Result/$1/$1.HISAT_aln_sort\n";
}
close $out