loop issue...

lomSpace has asked for the wisdom of the Perl Monks concerning the following question:

Hello, I am trying to resolve a looping issue which causes my script
to append the files 4x instead of once.

#!/usr/bin/perl
use strict;
use Data::Dumper;
use File::Glob ':glob';
    
my @dirs = glob("C:/Documents and Settings/mydir/Desktop/KOMP/*");
foreach my $maid_dir(@dirs){
    if (-d $maid_dir){ # directory check
        if ($maid_dir=~m%\d+\s[A-Z]%){ # match the dir name
            my $seq_dir = $maid_dir."/sequencing/";
            chdir ($maid_dir);
            #next if (-M $seq_dir > 1.0);
            chdir ($seq_dir);
            #print Dumper ($maid_dir, $seq_dir);
            opendir my $dh, "$seq_dir";
            if(-d $seq_dir){
                my @files = readdir $dh;
                for my $f(@files){
                    if($f=~ m%^(\d*)(HU.fa|HD.fa|Ltvec_small.FA|_fasta
+)$%){
                        my ($fa, $hu, $hd, $lt)= ($1."_fasta", $1."HU.
+fa", $1."HD.fa", $1."Ltvec_small.FA");
                        if(-e $fa){
                            open (my $out, ">>".$seq_dir."/".$fa) or d
+ie "Can't open $seq_dir/$fa for append: $!\n";
                            # Append the contents of the three files t
+o $fa
                            open my $hu_file, '<', $hu or die "Can't o
+pen $hu: $!\n";
                            while (my $line = <$hu_file>) {
                                print $out $line;
                            }
                            open my $hd_file, '<', $hd or die "Can't o
+pen $hd: $!\n";
                            while (my $line = <$hd_file>) {
                                print $out $line;
                            }
                            open my $lt_file, '<', $lt or die "Can't o
+pen $lt: $!\n";
                            while (my $line = <$lt_file>) {
                                print $out $line;
                            }
                            print $out, "\n";
                            #print Dumper($f);
                            close($out);
                            close($hu_file);
                            close($hd_file);
                            close($lt_file);
                        }
                    }
                }            
            }        
        }    
    }    
}
[download]

Any ideas?

Comment on loop issue... Download Code

Replies are listed 'Best First'.
Re: loop issue... by bellaire (Hermit) on Mar 20, 2009 at 14:40 UTC
Well, here you check whether this particular file is one of the four you want: `for my $f(@files){ if($f=~ m%^(\d*)(HU.fa\|HD.fa\|Ltvec_small.FA\|_fasta)$%) {` [download] But on the very next line, you decide to process all of them: `my ($fa, $hu, $hd, $lt)= ($1."_fasta", $1."HU.fa", $1."HD.fa", $1."Ltv +ec_small.FA");` [download] So each time your code hits `HU.fa`, it'll process all the files. Then when it hits `HD.fa`, it'll process them all again. Same for the other two. That's why you see the output 4x.	[reply] [d/l] [select]
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Re: loop issue... by kennethk (Abbot) on Mar 20, 2009 at 14:44 UTC
As a side note, you may want to add `or die` clauses after your `chdir`, `opendir` etc. And you should probably swap open $out to a three-argument form like you have for your other open statements.	[reply] [d/l] [select]
Re^2: loop issue... by Fletch (Bishop) on Mar 20, 2009 at 15:22 UTC
Sounds like awfully familiar advice, doesn't it OP? :) He's at least checking your open calls which is good, but he'll be kicking himself n months hence when he has to spend time chasing down why things don't work that a simple `opendir( FOO, $dir ) or die "opendir '$dir': $!"` would have caught. The cake is a lie. The cake is a lie. The cake is a lie.	[reply] [d/l]
Re^3: loop issue... by Nkuvu (Priest) on Mar 20, 2009 at 16:52 UTC
The OP copied the lines for the `open` calls that I provided -- but skipped the rest of the script. Granted I missed the check on the `readdir`, but I also noted that (and at least failure there would just mean that `@files` would be empty, rather than trying to alter files in the wrong directory). I had hoped that the OP would see what was intended with the advice given, but I think that's too much to ask. I was toying with the idea of completely revising the script (I have a current script that's taking a very long time to execute, so have some downtime while I wait for it) but I think it would be rather pointless.	[reply] [d/l] [select]
Re^3: loop issue... by lomSpace (Scribe) on Mar 20, 2009 at 16:35 UTC
I got the right output. Thanks!	[reply]
Re^2: loop issue... by Bloodnok (Vicar) on Mar 20, 2009 at 14:54 UTC
...or, alternatively, ~~`use autoload;`~~ `autodie;` - which would have the effect of `die()`ing if a built-in fails, thus not unduly cluttering the code. Update: Thanx to Fletch, I did in fact mean `autodie` A user level that continues to overstate my experience :-))	[reply] [d/l] [select]
Re^2: loop issue... by lomSpace (Scribe) on Mar 20, 2009 at 16:34 UTC
Thanks for the help. I got the right output!	[reply]


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