After that, I may rewrite it into pure Perl, but that sounds too much like work - if it works as it, why bother?

But lose the redundant backslashes. That alone would remove more than half of the uglyness factor.

Oh, and for the next time, come up with a better title.

IO::Uncompress::Gunzip would allow you to access the data within your Perl program, you could then treat them as ordinary files and check they start with the correct marker and if they do extract the required data.

Hope that helps

#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

my $cmd = system("zcat -l /path/to/.gz/files");
print Dumper($cmd);
[download]

Second, "zcat *gz": What do you want it to do?

$ zcat foo.gz
bar
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you'll need to use perl's "system" command

He is using system. If anything, he shouldn't be using system as it's forcing him to use a temporary file (assuming he's simply creating VARIABLES in order to read it in).

First, you didn't declare $cmd. That should be my $cmd = .

Uhm, no. This is Perl, remember. You don't have to declare anything. Besides, the OP was showing a code snippet. He might as well have your precious "my $cmd" somewhere in the code he (rightfully so) did not post.

Second, "zcat *gz": What do you want it to do? Did you have an option in mind? More information there would be helpful.

First, you misquote. It's zcat *.gz. Second, it's quite obvious that he wants to run zcat on all the gzipped files in the current directory. No need to further explain that.

Third, since you're running system commands, you'll need to use perl's "system" command.

That's neither correct, nor is your remark useful. system is not the only way to run external commands (backticks, exec and open do as well), but the OP is using system.

The print command would come after that.

Really? The OP is just printing the command to be executed. There's no need to first execute the command, than to print it.

my $cmd = system("zcat -l /path/to/.gz/files");
print Dumper($cmd);
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Now, that's a program that does little useful. Unlike the code of the OP that actually does something with the content of the uncompressed file - yours just dumps it to the screen. And then you use Data::Dumper to print out the value of an integer.

I'd say all your suggestions are utterly rubbish and worthless.

Bows... Thanks for everyone help just to add a bit more information. I am downloading compressed files which has the format like this below and parsing each of those files like this below: Bows Thank alot again.

$cmd =
"zcat *.gz \| grep -P \'\\!dataset\' \| grep -P \'\\=\'  \| perl -pi -
+e s\'\/^\\!dataset\\_\|\\=\.*\/\/g\' | sort | uniq  >VARIABLES";
print "$cmd\n";
system($cmd);
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Contents of VARIABLES would be everything between "!dataset_" and " = .*"

Contents of compressed files:

^DATABASE = Geo
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/projects/geo
!Database_email = geo@ncbi.nlm.nih.gov
!Database_ref = Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6
^DATASET = GDS100
!dataset_title = UV exposure time course (ecoli_8.0)
!dataset_description = Time course of UV-responsive genes and their ro
+le in cellular recovery. lexA SOS-deficient strains analyzed.
!dataset_type = gene expression array-based
!dataset_pubmed_id = 11333217
!dataset_platform = GPL18
!dataset_platform_organism = Escherichia coli
!dataset_platform_technology_type = spotted DNA/cDNA
!dataset_feature_count = 5764
!dataset_sample_organism = Escherichia coli
!dataset_sample_type = RNA
!dataset_channel_count = 2
!dataset_sample_count = 8
!dataset_value_type = log ratio
!dataset_reference_series = GSE9
!dataset_order = none
!dataset_update_date = Apr 06 2003
^SUBSET = GDS100_1
!subset_dataset_id = GDS100
!subset_description = irradiated
!subset_sample_id = GSM544,GSM545,GSM546,GSM547,GSM548
!subset_type = protocol
^SUBSET = GDS100_2
!subset_dataset_id = GDS100
!subset_description = not irradiated
!subset_sample_id = GSM542,GSM543,GSM549
!subset_type = protocol
^SUBSET = GDS100_3
!subset_dataset_id = GDS100
!subset_description = 5 minute
!subset_sample_id = GSM547
!subset_type = time
^SUBSET = GDS100_4
!subset_dataset_id = GDS100
!subset_description = 10 minute
!subset_sample_id = GSM544
!subset_type = time
^SUBSET = GDS100_5
!subset_dataset_id = GDS100
!subset_description = 20 minute
!subset_sample_id = GSM545,GSM542
!subset_type = time
^SUBSET = GDS100_6
!subset_dataset_id = GDS100
!subset_description = 40 minute
!subset_sample_id = GSM546
!subset_type = time
^SUBSET = GDS100_7
!subset_dataset_id = GDS100
!subset_description = 60 minute
!subset_sample_id = GSM548,GSM543
!subset_type = time
^SUBSET = GDS100_8
!subset_dataset_id = GDS100
!subset_description = 0 minute
!subset_sample_id = GSM549
!subset_type = time
^DATASET = GDS100
#ID_REF = Platform reference identifier
#IDENTIFIER = identifier
#GSM549 = Value for GSM549: lexA vs. wt, before UV treatment, MG1655; 
+src: 0' wt, before UV treatment, 25 ug total RNA, 2 ug pdN6; src: 0' 
+lexA, before UV 25 ug total RNA, 2 ug pdN6
#GSM542 = Value for GSM542: lexA 20' after NOuv vs. 0', MG1655; src: 0
+', before UV treatment, 25 ug total RNA, 2 ug pdN6; src: lexA 20 min 
+after NOuv, 25 ug total RNA, 2 ug pdN6
#GSM543 = Value for GSM543: lexA 60' after NOuv vs. 0', MG1655; src: 0
+', before UV treatment, 25 ug total RNA, 2 ug pdN6; src: lexA 60 min 
+after NOuv, 25 ug total RNA, 2 ug pdN6
#GSM547 = Value for GSM547: lexA 5' after UV vs. 0', MG1655; src: 0', 
+before UV treatment, 25 ug total RNA, 2 ug pdN6; src: lexA 5 min afte
+r UV treatment, 25 ug total RNA, 2 ug pdN6
#GSM544 = Value for GSM544: lexA 10' after UV vs. 0', MG1655; src: 0',
+ before UV treatment, 25 ug total RNA, 2 ug pdN6; src: lexA 10 min af
+ter UV treatment, 25 ug total RNA, 2 ug pdN6
#GSM545 = Value for GSM545: lexA 20' after UV vs. 0', MG1655; src: 0',
+ before UV treatment, 25 ug total RNA, 2 ug pdN6; src: lexA 20 min af
+ter UV treatment, 25 ug total RNA, 2 ug pdN6
#GSM546 = Value for GSM546: lexA 40' after UV vs. 0', MG1655; src: 0',
+ before UV treatment, 25 ug total RNA, 2 ug pdN6; src: lexA 40 min af
+ter UV treatment, 25 ug total RNA, 2 ug pdN6
#GSM548 = Value for GSM548: lexA 60' after UV vs. 0', MG1655; src: 0',
+ before UV treatment, 25 ug total RNA, 2 ug pdN6; src: lexA 60 min af
+ter UV treatment, 25 ug total RNA, 2 ug pdN6
!dataset_table_begin
ID_REF    IDENTIFIER    GSM549    GSM542    GSM543    GSM547    GSM544
+    GSM545    GSM546    GSM548
1    EMPTY    0.211    0.240    0.306    0.098    0.101    0.208    0.
+167    0.190
2    EMPTY    0.045    0.097    0.142    0.107    0.074    0.202    0.
+019    0.266
3    EMPTY    0.191    0.243    0.312    0.023    0.158    0.261    0.
+255    0.128
4    EMPTY    -0.013    -0.041    0.112    -0.028    0.175    0.111   
+ 0.139    0.137
etc
[download]

Untested, but this might get you close:

#! perl -slw
use strict;

open ZCAT, '|-', 'zcat *.gz' or die;

my %uniq;

while( <ZCAT> ) {
    my( $varname ) = m[!dataset_([^=]+)=] or next;
    $uniq{ $varname } = 1;
}

close ZCAT;

print "uniq names sorted";
print for sort keys %uniq;
[download]

---

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

RIP an inspiration; A true Folk's Guy

Thanks BrowserUk The parsing works nicely...thanks. Only 1 issue how to I stop this line from spiting out the contents of the files to the terminal or it is something in my setup? It doesnt pass the data to ZCAT it just spits it out to the terminal.

open ZCAT, '|-', 'zcat *.gz' or die;
[download]

Thanks once again