PERL Beginners - about running unix command in perl script

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about running unix command in perl script

Bing Zhao

2005-10-28, 7:56 am

Hi,
Is there a way to run unix command in perl?
To be specific, for the ftp command:
1.ftp ftp.rcsb.org
2.cd /pub/pdb/data/structures/divided/pdb/
3.cd nx
4.get pdb1nxc.ent.Z
5.bye
I need to automate this process to ftp get the file pdb1nxc.ent.Z.
thank you.

bing

John W. Krahn

2005-10-28, 7:56 am

ZHAO, BING wrote:
> Hi,

Hello,

> Is there a way to run unix command in perl?
> To be specific, for the ftp command:
> 1.ftp ftp.rcsb.org
> 2.cd /pub/pdb/data/structures/divided/pdb/
> 3.cd nx
> 4.get pdb1nxc.ent.Z
> 5.bye
> I need to automate this process to ftp get the file pdb1nxc.ent.Z.

perldoc Net::FTP

John
--
use Perl;
program
fulfillment

Dermot Paikkos

2005-10-28, 7:56 am

Have a look at Net::FTP. It can do all that your asking.
I think it's part of the standard distribution.

perldoc Net::FTP

hth.
Dp.

On 28 Oct 2005 at 3:37, ZHAO, BING wrote:

> Hi,
> Is there a way to run unix command in perl?
> To be specific, for the ftp command:
> 1.ftp ftp.rcsb.org
> 2.cd /pub/pdb/data/structures/divided/pdb/
> 3.cd nx
> 4.get pdb1nxc.ent.Z
> 5.bye
> I need to automate this process to ftp get the file pdb1nxc.ent.Z.
> thank you.
>
> bing
>
> --
> To unsubscribe, e-mail: beginners-unsubscribe@perl.org
> For additional commands, e-mail: beginners-help@perl.org
> <http://learn.perl.org/> <http://learn.perl.org/first-response>
>
>
>

John Doe

2005-10-28, 7:56 am

ZHAO, BING am Freitag, 28. Oktober 2005 12.37:
> Hi,
> Is there a way to run unix command in perl?
> To be specific, for the ftp command:
> 1.ftp ftp.rcsb.org
> 2.cd /pub/pdb/data/structures/divided/pdb/
> 3.cd nx
> 4.get pdb1nxc.ent.Z
> 5.bye
> I need to automate this process to ftp get the file
> pdb1nxc.ent.Z. thank you.

yes,

perldoc system
perldoc perlop (backticks)
several IPC modules

....but you'll save a headache using the Net::FTP module, see
http://search.cpan.org/search?query...FTP&mode=module

hth,
joe

José Pedro Silva Pinto

2005-10-28, 7:56 am

Yes

Example:

system("ftp ftp.rcsb.org ; /pub/pdb/data/structures/divided/pdb/ ; cd nx =
; get pdb1nxc.ent.Z ");

By

Jos=E9 Pinto

-----Original Message-----
From: ZHAO, BING [mailto:littleshrimp@berkeley.edu]=20
Sent: sexta-feira, 28 de Outubro de 2005 11:37
Cc: beginners@perl.org
Subject: about running unix command in perl script

Hi,
Is there a way to run unix command in perl?
To be specific, for the ftp command:
1.ftp ftp.rcsb.org
2.cd /pub/pdb/data/structures/divided/pdb/
3.cd nx
4.get pdb1nxc.ent.Z
5.bye
I need to automate this process to ftp get the file =
pdb1nxc.ent.Z.
thank you.

bing

--=20
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For additional commands, e-mail: beginners-help@perl.org
<http://learn.perl.org/> <http://learn.perl.org/first-response>

Dan Klose

2005-10-28, 7:56 am

On Fri, 2005-10-28 at 03:37 -0700, ZHAO, BING wrote:
> Hi,
> Is there a way to run unix command in perl?
> To be specific, for the ftp command:
> 1.ftp ftp.rcsb.org
> 2.cd /pub/pdb/data/structures/divided/pdb/
> 3.cd nx
> 4.get pdb1nxc.ent.Z
> 5.bye
> I need to automate this process to ftp get the file pdb1nxc.ent.Z.
> thank you.
>
> bing

Hello,

To get PDBs from the PDB!

try this:

#!/usr/bin/perl

#THIS SCRIPT WAS WRITTEN BY JAIME PRILUSKY @ WEIZMANN INSTITUTE

use LWP::Simple;

my @ids = @ARGV;
die "\nUsage: $0 PDBid PDBid\n\n" if ($ARGV[0] =~ /^ *$/);

foreach $id (@ids) {
my $pdbfile = $id . "\.pdb";
my $status = mirror("http://bip.weizmann.ac.il/oca-bin/save-pdb?$id",
$pdbfile);
if (-z $pdbfile) {
print "Unable to retrieve $pdbfile\n";
unlink($pdbfile);
} else {
print "Retrieved $pdbfile\n";
}
}

Thanks to Jaime Prilusky. I find this script rather handy.

>
--
Daniel Klose
PhD Student - Taylor Group
Mathematical Biology
National Institute for Medical Research
The Ridgeway
Mill Hill
London
NW7 1AA

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