SAM-preprocessor

#!/usr/bin/perl
#
# Edgar Berdahl, Jan 21 2012
# Updated February 2012
#
# First argument is input filename for MDL file
# Second argument is output filename for MDX file
#
# For example: ./SAM-preprocessor examplelinks.mdl examplelinks.mdx
#
# ALL NUMBERS IN MDL FILES SHOULD BE FLOATING-POINT NUMBERS (NOT INTEGERS)


# Here we include the regular expression definitions necessary for parsing model specification files.
require 'SAM-reg-ex';


use v5.10;

use warnings;
$filename = $ARGV[0];      # e.g. "examplelinks.mdl";
$filenameout = $ARGV[1];   # e.g. "examplelinks.mdx";
my $indx = 0;              # index variable used over and over again



#say "Starting SAM-preprocessor...";


# First remove all of the comments and write the result into $tmp_filename
$tmp_filename = "tempSAM3981.tmp";
open my $fh_tmp_out, '>', $tmp_filename
    or die "Cannot write '$tmp_filename'";
open $filehandle, '<', $filename
    or die "Cannot read '$filename': $!\n";
#my $beforeComment = qr/(\A[^\n\r#]*)/;   # Contains anything except newlines, returns, and pound symbols (#)
#my $afterComment = qr/([^\n\r]*)/;       # Contains anything except newlines and returns
my $beforeComment = qr/([^#]*)/;   # Contains anything except pound symbols (#)
my $afterComment = qr/(.*)/;       # Contains anything
my $filterOutComments = qr/\A${beforeComment}#${afterComment}$/;
while (<$filehandle>)
{
    chomp;
    $theline = $_;
    
    # Each line out is simply the line in up until the point where a pound symbol (#) is reached
    if ($theline =~ qr/$filterOutComments/) {
	#say "1=" . $1 . ",   2=" . $2;
        say $fh_tmp_out $1;
    } else {
	say $fh_tmp_out $theline;     # If there are no comments in the line
    }
}
close $fh_tmp_out;
$filename = $tmp_filename;    # Starting now we read out of the temporary file




# Open MDX file for output and prepare to write into it
open my $fh_out, '>', $filenameout
    or die "Cannot write '$filenameout': $!\n";








# For now just copy over all lines
open $filehandle, '<', $filename
    or die "Cannot read '$filename': $!\n";
while (<$filehandle>)
{
    chomp;
    $theline = $_;

    say $fh_out $theline;	    
}









# Delete the temporary file if it still exists
close $filehandle;
if (-e $tmp_filename)
{
    unlink($tmp_filename);
}




#say "SAM-preprocessor finished.";