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Could you check this script? Keeps churning out files that are 0kb

effc
Novice

Nov 1, 2012, 5:39 AM

Post #1 of 4 (984 views)

Could you check this script? Keeps churning out files that are 0kb	Can't Post

Hi I'm searching through a directory of files that are about 700kb a piece for the string ^ASSAY=BLAH_BLAH_BLAH, I need to replace the BLAH_BLAH_BLAH with CHA21 (and add.manual, which is working properly). The files that I come up with are 0kb.

#!/usr/bin/perl

opendir(FILES, ".") || die; #open current directory

foreach (readdir(FILES))

{

{

$next_file = $_;

chomp($next_file);

print "$nextfile.$suffix\n";

if ($next_file =~ m/.sift/)

{

open (IN, "<$next_file" || die);

print "$next_file\t";

$next_file=~ s/\.sift//;

print "$next_file.manual.sift\n";

open (OUT, ">$next_file.manual.sift" || die);

while ($line = <IN>)

{

if($line =~ /^ASSAY=BLAH_BLAH_BLAH/){

$line =~ s/BLAH_BLAH_BLAH/CHA21/gi;

}

}

}

close OUT;

close IN;

} # close OUT;

# close IN;

}

Thanks in advance!

BillKSmith
Veteran

Nov 1, 2012, 7:07 AM

Post #2 of 4 (981 views)

Re: [effc] Could you check this script? Keeps churning out files that are 0kb [In reply to]	Can't Post

You must print every line (whether you changed it or not) to the OUT file.

Code

        while ( $line = <IN> ) { 
            if ( $line =~ /^ASSAY=BLAH_BLAH_BLAH/ ) { 
                $line =~ s/BLAH_BLAH_BLAH/CHA21/gi; 
            } 
            print OUT $line; 
        }

I recommend several other improvements.

always use

Code

use strict; 
use warnings;

Fix all the errors that they reveal.

The variable $suffix does not do anything useful and should be removed completely.

Use the three argument form of open. (refer: perldoc -f open)

Use lexical filehandles.

Your test for the success of open is an excelent practice. You should supply a message with die to tell the user what happened.

You may not want the program to abort because one open fails. Consider the block form of eval to trap the error. (Refer: perldoc -f eval)

Close the directory at the end of your program.
Good Luck,
Bill

effc
Novice

Nov 1, 2012, 7:38 AM

Post #3 of 4 (978 views)

Re: [BillKSmith] Could you check this script? Keeps churning out files that are 0kb [In reply to]	Can't Post

Thank you so much that was incredibly helpful! Perl script ran perfectly.

Laurent_R
Enthusiast / Moderator

Nov 1, 2012, 8:24 AM

Post #4 of 4 (976 views)

Re: [effc] Could you check this script? Keeps churning out files that are 0kb [In reply to]	Can't Post

You could simplify your check and avoid using two regexes:

Code

       while ( $line = <IN> ) {  
           $line =~ s/^ASSAY=BLAH_BLAH_BLAH/ASSAY=CHA21/i) ; 
           print OUT $line;  
       }

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