Promen

while(read($fh, $buffer, BUFFER_SIZE)) #Write content to OUTPUT file ##

##


#!/usr/bin/perl -w

use strict;
use CGI;
use Fcntl qw(:DEFAULT :flock);

#SUB error needs to be completed

print "Content-type:text/html\n\n";

#Declaring constants
use constant UPLOAD_DIR     => "/tmp/";
use constant MAX_FILE_SIZE  => 1_048_576; #Limit each upload to 1MB
use constant MAX_OPEN_TRIES => 100;
use constant BUFFER_SIZE    => 16_384;
# New object
$CGI::POSTMAX   = MAX_FILE_SIZE;
my $query = new CGI;
$query->cgi_error and error($query, "Error transferring file: " . $query->cgi_error );

my $file        = $query->param('fname')|| error ($query, "No file received.");
my $fh          = $query->upload("$file");
my $buffer      = "";
my $filename    = "";
my @annotation  = "";
my @list        = "";

$query->header();
$query->start_html();
$query->startform();

################# IF file has been uploaded #############################
if($file)
{
 $file =~ s/[^\w.-]/_/g;    #Rectifying the string for name of the file
 if($file=~ /^(\w[\w.-]*)/)
 {
  $file = $1;
 }
 else
 {
  error($query, "Invalid file name; file must start with a letter or number.");
 }
until (sysopen OUTPUT, UPLOAD_DIR . $file,O_CREAT|O_EXCL )

 {
  $file =~ s/(\d*)(\.\w+)$/($1||0)+1 .$2/e;
  $1 >= MAX_OPEN_TRIES and error ($query, "Unable to save your file");
 }

 while(read($fh, $buffer, BUFFER_SIZE))  #Write content to OUTPUT file
 {
  print OUTPUT $buffer;
 }
 close OUTPUT;

# $filename = $file.'.'.'fasta';
 $filename = $file;

# if($format eq "embl")
# {
#embl_fasta();
# }
# elsif($format eq "genbank")
# {
#genbank_fasta();
# }
open(IN,"UPLOAD_DIR/$filename")||die error($query, "cant open from UPLOAD dir");
my $one = 0;
my $header;
my $prevhead;
my $sequence;
#reading the genome sequence
my $x=1;
while()
{
  my $seqline = $_;
  $seqline =~ s/\n//g;
  if($seqline =~ /^>/g)
  {
    if($one == 0)
    {
        $header = $seqline;
        $prevhead = $header;
        $sequence = '';
        $one++;
      next;
    }
    else
    {
        $header = $seqline;
        $annotation[$x]=$prevhead;
        $list[$x]=$sequence;
        $x++;
        $prevhead = $header;
        $sequence = '';
        next;
    }
  }#end if $seqline
  $sequence = $sequence.$seqline;
  $sequence =~ s/\s//g;
}#end while
close(IN);
$annotation[$x]=$prevhead;
$list[$x]=$sequence;
} # If Sequence has been uploaded

################# Opening of each sequence ###############################
my $z=0;

for my $name(@annotation)
{
  my $sequence="";
  $sequence = $list[$z];
  print "$name\t$sequence\n";
  $z++;

print $query->p("$sequence");
print " PROMOTER PREDICTION AT A SENSITIVITY LEVEL 

";

print " ";

print " Sequence ID :   $sequence
";
print "
RESULTS

 ";
print "";
print "FORWARD STRAND

";
print "";
}
   $query->endform();
$query->end_html();

sub error
{
  my ($q, $reason)=@_;
  print $q -> header ("text/html"),
   $q -> start_html ("Error"),
 $q -> h1 ("Error"),
 $q->p("following err::"),
 $q->p($q->i($reason)),
 $q-> end_html;

exit;
}

 
##

##



Promen





PromEn: Promoter prediction using energy differences

Upload the sequence file #### >EMBOSS_001 gagccggaacaaattgaacaatcctacgccagctgccaaccgtggccggagcaggtggta ttagatggggaacgtgaaacgttaggcctgtacctgaccggacaccctatcaaccagtat ttaaaagagattgagcgttatgtcggaggcgtaaggctgaaagacatgcacccgacagaa cgtggtaaagtcatcacggctgcggggctcgttgttgccgcgcgggttatggtcaccaag cgcggcaatcgtatcggtatctgcacgctggatgaccgttccgggcggctggaagtgatg ttgtttactgacgccctggataaataccagcaattgctggaaaaagaccgcatacttatc gtcagcggacaggtcagctttgatgacttcagcggtgggcttaaaatgaccgctcgcgaa gtgatggatattgacgaagcccgggaaaaatatgctcgcgggcttgctatctcgctgacg gacaggcaaattgatgaccagcttttaaaccgactccgtcagtctctggaaccccaccgc tctgggacaattccagtacatctctactatcagagggcggatgcacgcgcgcggttgcgt tttggcgcgacgtggcgtgtctctccgagcgatcgtttattaaacgatctccgtggcctc attggttcggagcaggtggaactggagtttgactaatacaggaatactatgagtctgaat ttccttgattttgaacagccgattgcagagctggaagcgaaaatcgattctctgactgcg gttagccgtcaggatgagaaactggatattaacatcgatgaagaagtgcatcgtctgcgt gaaaaaagcgtagaactgacacgtaaaatcttcgccgatctcggtgcatggcagattgcg caactggcacgccatccacagcgtccttataccctggattacgttcgcctggcatttgat gaatttgacgaactggctggcgaccgcgcgtatgcagacgataaagctatcgtcggtggt atcgcccgtctcgatggtcgtccggtgatgatcattggtcatcaaaaaggtcgtgaaacc aaagaaaaaattcgccgtaactttggtatgccagcgccagaaggttaccgcaaagcactg cgtctgatgcaaatggctgaacgctttaagatgcctatcatcacctttatcgacaccccg ggggcttatcctggcgtgggcgcagaagagcgtggtcagtctgaagccattgcacgcaac ctgcgtgaaatgtctcgcctcggcgtaccggtagtttgtacggttatcggtgaaggtggt