Retrieve URL in perl get method because of its over length in a bioinformatics server

Question

I used perl program to make a bioinformatics server which takes only one sequence for finding motifs at a time, to take my sequences ($seq) simultaneously from a text file (example.txt) containing more than 6000 sequences with more than 10000bp. The problem is when my sequence exceeds 1408bp, I get the error that URL cannot be retrieved because of such a length. please help me to resolve this problem in perl..

#!usr/bin/perl
use LWP::Simple;
my $file = 'example.txt';
open my $fh, '<', $file or die;
$/ = undef;
$all=<$fh>;
@other=split(">",$all);

for($i=1;$i<=$#other;$i++)
{
  my ($first,@other)=split("\n",$other[$i]);
 $seq=join("\n",@other);
$len=length($seq);

my $link = "http://regrna2.mbc.nctu.edu.tw/detection_output.php?S1=%3E%0D%0A$seq&tfbs=ON&tfbs_species=rice%2C+Oryza+sativa&RadioGroup1=matrix&matchscore=1&rho=ON&SplicingSite=ON&GeneSplicer_species=Rice&SplicingMotif_species=Homo+sapiens&Polya=ON&RBSfinder=ON&UTRsite=ON&AUrich=ON&RNAediting=ON&RiboSW=ON&ERPIN=ON&Rfam=ON&LongStem=ON&LongStem_len=40&fRNAdb=ON&fRNAdb_similarity=0.9&fRNAdb_match_len=30&miRNA=ON&miRNA_species=Oryza+sativa&score=170&miRNA_FE=-25&ncRNA=ON&ncRNA_species=Oryza_sativa&ncRNA_length=20&ncRNA_FE=-20&S2=&GCratio=ON&GCratio_window_size=100&accessibility=ON&accessibility_window_size=100&unpair_size=6&StartCodon=1&draw_dotline=ON&position_line_interval_len=100&Size=950&B1=Submit";

$link =~m/.\/Results\/(\d+)\.all\.result/;


my $second = get("http://regrna2.mbc.nctu.edu.tw/Results/$1.all.result") or die "cannot retrieve code\n";


my $filename = "$first.txt";
open(my $fhh, '>', $filename) or die "Could not open file '$filename' $!";
print $fhh "$second";
close $fhh;

}

score 1 · Answer 1 · answered Apr 04 '17 at 15:10

URL length is dictated by both client and server. See:

What is the maximum length of a URL in different browsers?

It would appear that you may not be able to submit such as long sequence of chars via get() as the limit may be server-side. You likely need to use POST, which is described here:

http://lwp.interglacial.com/ch05_07.htm

Specifically:

But the file-upload part involves some doing. First off, you have to add a header line of 'Content_Type' => 'form-data' to mean that yes, you really mean this to be a "multipart/form-data" POSTing. And secondly, where you would have a string in 'saywhat'=>text, you instead have an array reference where the first array item is the path to the file you want to upload. So it ends up looking like this:

my $response = $browser->post(
  'http://pastel.int/feedback.pl',
  [ 'subject' => 'Demand for pie.',
    'saywhat' => ["./today/earth_pies1.dml"],
    'user'    => 'Adm. Kang',
  ],
  'Content_Type' => 'form-data',
  ...any other header lines...
);

Retrieve URL in perl get method because of its over length in a bioinformatics server

1 Answers1