Re: about running unix command in perl script

[Dan Klose]

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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