Perl script for batch file processing - perl

Question

I have a relatively simple question for you experts. I have 300 files in a directory that I want to process with my perl script (shown below). I was wondering if there is a way to use a variable and process in a batch of files in perl. I have a file containing a list of file name if this helps.
Your feedback will be appreciated.
====================================
#!/usr/bin/perl
use strict;
use warnings;
open (FILE1, "001.txt") or die ("Can't open file $!");
while(<FILE1>){
my $line = $_;
chomp $line;
if ( $line =~ m/^chr/ ) {
open OUT, '>>', '001_tmp.txt';
print OUT "$line\n";
}
}
close(OUT);
close(FILE1);
======================================
Clarification:
Basically I want the perl script that is equivalent to the following shell script where I can accommodate all files using the variable.
#!/bin/bash
if [[ $# != 1 ]]
then
echo "Usage: error <input>"
else
echo $# $1
export input=$1
grep "^chr" $1 > ${input}_tmp.vcf

Answer 1

So you want your while loop to read through each file in some given directory..
I would do something like this:
Use opendir and readdir so you can get the file names to operate on.
I would also look at grep to filter out the files you don't care about, in my example I filter out directories...
opendir(my $dh, $dir) or die "$dir: $!";
my #files = grep { !-d $_ } readdir $dh;
closedir $dh;
Now you will have a list of files to do work on...
for my $file (#files) {
open my $fh, "<", $file or die "$!";
while( my $line = <$fh> ) {
#TODO: stuff
}
close $fh;
}

Answer 2

Edit: Your tags indicated batch-file, meaning Windows batch file. If that's not what you mean, disregard this. :-)
Perhaps something like this:
From a batch file:
for /f %%x in (listoffilenames.txt) do (
perl myperlscript.pl %%x
)
And then your Perl script can be modified like this:
#!/usr/bin/perl
use strict;
use warnings;
# You may want to add a little more error handling
# around getting the filename, etc.
my $filename = shift or die "No filename specified.";
open (FILE1, "<", $filename) or die ("Can't open file $!");
while(<FILE1>){
my $line = $_;
chomp $line;
if ( $line =~ m/^chr/ ) {
open OUT, '>>', "temp-$filename";
print OUT "$line\n";
}
}
close(OUT);
close(FILE1);