How can I create a new output file for each subfolder under a main folder using perl? - perl

Question

I have 100 subfolder in a main folder. They have difference names. Each subfolder includes a .txt file, which has 10 column. I want to get a new .txt file for each subfolder. Each new .txt file must be in its own folder. That is I will have 2 .txt files (old and new) in each subfolder. I am trying to select the lines starting "ATOM" and some columns 2,6,7 and 8 from each .txt file. My code is the following. It doesn't work correctly. It doesnt create a new .txt file. How can i figure out this problem?
#!/usr/bin/perl
$search_text = "ATOM";
#files = <*/*.txt>;
foreach $file (#files) {
print $file . "\n";
open(DATA, $file);
open(OUT_FILE, ">$file a.txt");
while ($line = <DATA>)
{
#fields = split /\s+/, $line;
if ($line =~ m/$search_text/)
{
print OUT_FILE "$fields[2]\t$fields[6]\t$fields[7]\t$fields[8]\n";
}
}
}
close(OUT_FILE);

Answer 1

To put the output file a.txt into the same directory as the input file, you need to extract the directory name from the input file name, and prepend it to the output file name (a.txt). There are a couple of ways you can do that; probably the simplest is to use dirname() from the standard module File::Basename:
use File::Basename;
my $dir = dirname($file);
open(OUT_FILE, ">", "$dir/a.txt") or die "Failed to open $dir/a.txt: $!";
or you could use File::Spec directly:
use File::Spec;
my ($volume, $dir) = File::Spec->splitpath($file);
my $outname = File::Spec->catpath($volume, $dir, 'a.txt');
open(OUT_FILE, ">", $outname) or die "Failed to open $outname: $!";
or you could just use a regexp substitution:
my $outname = ( $file =~ s![^/]+$!a.txt!r );
open(OUT_FILE, ">", $outname) or die "Failed to open $outname: $!";
Ps. In any case, I'd recommend adopting several good habits that will help you write better Perl scripts:
Always start your scripts with use strict; and use warnings;. Fix any errors and warnings they produce. In particular, declare all your local variables with my to make them lexically scoped.
Check the return value of functions like open(), and abort the script if they fail. (I've done this in my examples above.)
Use the three-argument form of open(), as I also did in my examples above. It's a lot less likely to break if your filenames contain funny characters.
Consider using lexically scoped file handles (open my $out_file, ...) instead of global file handles (open OUT_FILE, ...). I didn't do that in my code snippets above, because I wanted to keep them compatible with the rest of your code, but it would be good practice.
If you're pre-declaring a regular expression, like your $search_text, use qr// instead of a plain string, like this:
my $search_text = qr/ATOM/;
It's slightly more efficient, and the quoting rules for special characters are much saner.
For printing multiple columns from an array, consider using join() and a list slice, as in:
print OUT_FILE join("\t", #fields[2,6,7,8]), "\n";
Finally, if I were you, I'd reconsider my file naming scheme: the output file name a.txt matches your input file name glob *.txt, so your script will likely break if you run it twice in a row.