CGI and Perl Script in one single file
#!/usr/bin/perl -wT
use strict;
use warnings;
use LWP::Simple;
use CGI::Carp qw(warningsToBrowser fatalsToBrowser);
################### Environmental Variables ###################
my ($buffer, @pairs, $pair, $name, $value, %FORM);
# Read in text
$ENV{'REQUEST_METHOD'} =~ tr/a-z/A-Z/;
if ($ENV{'REQUEST_METHOD'} eq "POST")
{
read(STDIN, $buffer, $ENV{'CONTENT_LENGTH'});
} else {
$buffer = $ENV{'QUERY_STRING'};
}
#print "$buffer\n";
# Split information into name/value pairs
@pairs = split(/&/, $buffer);
foreach $pair (@pairs) {
($name, $value) = split(/=/, $pair);
$value =~ tr/+/ /;
# $value =~ s/%(..)/pack("C", hex($1))/eg;
$FORM{$name} = $value;
}
my $access = $FORM{accession};
if ($access =~ m{\A(\w+\d+)\z}) {
$access = $1;
}
print "Content-type:text/html\r\n\r\n";
print "";
print "";
print " CGI Program";
print "";
print "";
if ($access eq "") {
print " Please check the accession number
";
exit;
}
print "$access
";
print "";
print "";
print <
Output result of the program
Summary result
| S.No. |
Fragment |
Position |
Region |
GC% |
HEADING
;
######################## INPUT PARAMETERS #####################
my $utils = "http://www.ncbi.nlm.nih.gov/entrez/eutils";
my $db = "nuccore";
my $query = $access; #"$ARGV[0]" or die "Please provide input for the accession number. $!";
############### END OF INPUT PARAMETERS ######################
############### FILE DOWNLOAD FROM NCBI ######################
my $report = "gb"; # downloads the summary text file
open (IN,">", $query.".summary");
my $esearch = "$utils/esearch.fcgi?" . "db=$db&retmax=1&usehistory=y&term=";
my $esearch_result = get($esearch . $query);
$esearch_result =~ m|(\d+).*(\d+).*(\S+)|s;
my $Count = $1; my $QueryKey = $2; my $WebEnv = $3;
my $retstart; my $retmax=3;
for($retstart = 0; $retstart < $Count; $retstart += $retmax) {
my $efetch = "$utils/efetch.fcgi?" .
"rettype=$report&retmode=text&retstart=$retstart&retmax=$retmax&" .
"db=$db&query_key=$QueryKey&WebEnv=$WebEnv";
my $efetch_result = get($efetch);
print IN $efetch_result, "\n";
}
close (IN);
####
HTML form: