I try to automate a download from a website. the link is http://www.pdb.org/pdb/explore/explore.do?structureId=2CU3

Where "2CU3" can be replaced by anything, in my code the variable for this is $input, and all the structureId's are contained within a text file named 'data.txt'.

After that, I want to get a link from that webpage. The link url is http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=FASTA&compression=NO&structureId=2CU3.

My problem is, when this link is downloaded, it's just junk if I open it in textedit. If I open it using TextWrangler, the content is fine. Any idea what is causing this and how to fix it?

My code is as follows: 

#!/usr/bin/perl 

use strict;
use WWW::Mechanize;

open (FILE, "data.txt");

my $input;
while ($input = <FILE>){
chomp $input;

#download PDB html page
my $url = "http://www.rcsb.org/pdb/explore.do?structureId="."$input";
my $mech = WWW::Mechanize->new( autocheck => 1 );
   $mech->get( $url );
   
#write extracted data to an output file (.html)
my $file = "$input".".html";
print "$file";
use Data::Dumper;
open (OUTFILE, "> $file");
print OUTFILE Dumper($mech);
close(OUTFILE);

  #download the link (FASTA sequence)
 my $linkname = "fileFormat=FASTA&compression=NO&structureId="."$input
+";
 my @links = $mech->find_all_links( url_regex => qr/$linkname/ );
  for my $link ( @links ) {
  my $url = $link->url_abs;
  my $filename = $url;
  $filename =~ s[^.+/][];
   
  print "Fetching $url";
  $mech->get( $url, ':content_file' => $filename );

  print "   ", -s $filename, " bytes\n";
}
}
close (FILE);

[download]
--------------------------------------------------------------------

Thanks for the replies. This isn't a TextEdit question, I can't manipulate the data that I get because they're junk. What I mean by junk is that instead of text, I get (*^%&&^(*&^(* sort of stuff. It perplexes me how this data can be seen properly on TextWrangler.

I'll try all your suggestions today. Thanks again!

In reply to using WWW::Mechanize to download a link, opened fine in TextWrangler but as junk in TextEdit by nurulnad

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