in reply to Unique Variable names...

A few notes:
  1. Use strict, my, and pass your stuff into your functions. The way you're doing with, with all globals, is a recipe for a major headache. 
  2.       %hash={"$file"=>@final_data}; #this hash assignment +doesn't wor
+k
      close (FILE);
   }
   @values=values(%hash);

    [download]
    Yeah, no kidding that's not going to work. You create %hash every iteration through @filename. Try something like: 
          $hash{$file} = \@final_data;
      close (FILE);
   }
   @values=values(%hash);

    [download]
If I understand your code correctly, you're attempting to read all the files in a directory and grab all the values in the 4th column of each file, as defined by a tab delimiter. That's get_signal().

I'm not sure what you're doing with get_targets(), so I'll ignore it for now.

I would implement the subset of your script that doesn't deal with get_targets() as such: 

#!/usr/local/bin/perl
 
#Why do you need this?!?
#use Cwd qw(cdir);
use IO::Dir;
use IO::File;
 
print "Please enter the name and location of the directory to parse:\n
+";
chomp(my $directory = <STDIN>);
 
my $dh = IO::Dir->new($directory)
   || die "Cannot open directory '$directory': $!\n";
 
my @filenames;
push @filenames, $_ for map { "$directory/$_" } grep !/^\.\.?/, $dh->r
+ead;
 
$dh->close;
 
my %file_data;
foreach my $filename (@filenames)
{
   my @final_data;
 
   # Why do you need to do this?!?
   #chdir "./data";
 
   my $fh = IO::File->new($file)
      || die "Cannot open file '$file': $!\n";
 
   my $i = 0;
   while (<$fh>)
   {
      next while $i++ <= 14;
 
      push @{$file_data{$file}}, (split /\t/)[3];
   }
   $fh->close;
}
 
# Now, at this point, you have a hash called %file_data
# which is keyed by filename. Each filename points to an
# array reference contained the values in the 4th column,
# starting at the 15th line. What do you want to do with it?

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------
We are the carpenters and bricklayers of the Information Age.

Don't go borrowing trouble. For programmers, this means Worry only about what you need to implement.

Please remember that I'm crufty and crochety. All opinions are purely mine and all code is untested, unless otherwise specified.

Replies are listed 'Best First'.
Re: Re: Unique Variable names...
by BUU (Prior) on Jul 30, 2003 at 00:51 UTC
    Minor style/correctness whinge, but I believe $hash{$file} = \@final_data; should be $hash{$file}=[@final_data];. I suppose it wouldn't matter if you strictly used my @foo; every time the loop went around, but I think this way would be cleaner and less chance to bug up someplace..
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      Actually, it does matter, and potentially might matter a lot. $x{$y} = \@z; takes a reference to a data structure that already exists. $x{$y} = [@z]; creates a new reference and copies the existing data structure into it. This can be an expensive operation. My operation will always occur in the same amount of time, regardless of how many elements there are in @z.

      I suppose it wouldn't matter if you strictly used my @foo; every time the loop went around, but I think this way would be cleaner and less chance to bug up someplace..

      Always using my @foo; every time the loop went around is both cleaner and less bug-prone. I am having the language handle my memory management for me. The language will always do it right - I might not. The rule of thumb is that if you're doing $x{$y} = [@z]; and you don't have a compelling reason why, you probably are doing something that is bug-prone and should rewrite it.

      ------
      We are the carpenters and bricklayers of the Information Age.

      Don't go borrowing trouble. For programmers, this means Worry only about what you need to implement.

      Please remember that I'm crufty and crochety. All opinions are purely mine and all code is untested, unless otherwise specified.

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[d/l]
[select]
Re: Re: Unique Variable names...
by bioinformatics (Friar) on Jul 30, 2003 at 15:49 UTC
    The reason I used the Cwd module is because I needed to change the current directory in order for the program to function. Hence, when I use your program, I have the same issue: it will be unable to open the files until the working directory is changed within the program.
    Bioinformatics
[reply]
      bioinformatics,
      Why do you need to use Cwd when chdir will work just fine?

      Why do you put the chdir inside the foreach loop? Would not changing the directory at the top of the foreach loop once be sufficient.

      As a final note - dragonchild's code provides the directory and file name in the file list, so the chdir really is not required.

      Cheers - L~R

[reply]
Re: Re: Unique Variable names...
by bioinformatics (Friar) on Jul 30, 2003 at 19:50 UTC
    Thank you for your suggestions. I have incorporated a number of them into my program, as well as made it more streamlined. However, my problem still remains. I need to print the data from @signal into consecutive columns, as shown in my post at the end of the thread. The only way I know how to make this managable is to take the data pushed into @signal, grep it, and then shove it into 5 separate arrays (there are 5 input files CURRENTLY). This is all well and good, except that I need to somehow make this program capable of handling different numbers of files each time it is run. Do I need to manually assign, say 30, arrays in which to put the data, placing a limit on the program? I'm sure there are better ways to do this, but I don't know how.
    NOTE: please be patient with me, as I'm only a beginning programmer, perl being my first language. Having only been working with it for a month now, I suppose I could be doing worse...:-)
    My latest code:
    #! usr/local/bin/perl -w

use Cwd; 
use IO::Dir;
use IO::File;

print STDOUT "Please enter the name and location of the directory to p
+arse\:\n";

chomp (my $directory=<STDIN>);

open (OUTPUTFILE,">junk.txt"); 

my $dh = IO::Dir->new($directory) || die "Cannot open directory '$dire
+ctory': $!\n"; 

my @filenames; 
push @filenames, $_ for map { "$directory/$_" } grep !/^\.\.?/, $dh->r
+ead; 

$dh->close;

@output=get_signal;
for (@output){
@{$signal[0-4]};
@{$rprobe};}

print OUTPUTFILE "@signal";
close OUTPUTFILE;
exit;

sub get_signal {
   while (@filename) {
       $file=shift @filename;
      use Cwd 'chdir';
      chdir "./data";
      open (FILE, "$file") or die;
       @data=<FILE>;
       my $i=0;
      foreach (@data) {
         next while $i++ <=14;
         push @signal, (split(/\t/))[3];}
      my $g=0;
      foreach (@data) {
         next while $g++ <=14;
         @probe=(split(/\t/))[0];}
      $hash{$file}=\@signal;
      close (FILE);
   }
   @values=values(%hash);
   $rprobe=\@probe;
   return @values;
   return $rprobe;
}

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    Bioinformatics
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[d/l]

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