ankit
Novice
Jul 6, 2011, 12:06 AM
Post #1 of 4
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Unable to run perl-cgi script in webbrowser of Cent OS linux
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Hi,
I want run my perl-CGI programe in Cent Os but when i am running on browser it gives following error in Apache error log:
[Wed Jul 06 12:37:41 2011] [error] [client 172.16.237.128] (2)No such file or directory: exec of '/var/www/cgi-bin/webrebase101.cgi' failed
[Wed Jul 06 12:37:41 2011] [error] [client 172.16.237.128] Premature end of script headers: webrebase101.cgi
My perl script is given below:
#!/usr/bin/perl
use Restrictionmap;
use Rebase;
use SeqFileIO;
use CGI qw/:standard/;
use CGI::Carp qw(warningsToBrowser fatalsToBrowser);
use CGI qw/:standard start_table/;
use strict;
use warnings;
print header,
start_html('Restriction Map'),
'<body bgcolor="#FFFFFF" text="black" link="#1F86FF" vlink="#005DC9" alink="#62A9FF" ><!--msnavigation--><table border="0" cellpadding="0" cellspacing="0" width="100%"><tr><td><!--mstheme-->',
'<center><b><font size="8" face="Bauhaus 93">Restriction Site Mapping</font></center></b>',
'<LEFT><b><font size="8" face="Courier">[ REMAP ]</font></center></b><div align="right"><a href="rebase1.html"><img src="SSRIMG/home2.JPG" width="100" height="55" border="0" alt="Home" align="middle"></a><a href="cont.html"><img src="SSRIMG/contact2.BMP" width="150" height="55" border="0" alt="Feedback" align="middle"></a> </div>',
start_multipart_form,
i,b('<font size=3><center>'),
'<body background="images-2/final.jpg">' ,
'<body bgcolor=white>',
'<font color=black>',
h3,'<A HREF="http://localhost/myscript/webrebase101.cgi">For Multiple sequence Click here</a>',
h3(" Restriction enzyme(s) [case sencetive] "),
textfield('enzyme'),p,
h3(" Sequence filename (fasta or raw format): "),
filefield(-name=>'fileseq',
-default=>'starting value',
-size=>50,
-maxlength=>200,
), p,
strong(em("or")),
h3("Type sequence: "),
textarea(
-name=>'typedseq',
-rows=>10,
-columns=>60,
-maxlength=>1000,
), p,
h3,("View Format :"),
'<input type="RADIO" name="format" value="png">PNG', '<input type="RADIO" name="format" value="jpg">JPG',
'<input type="RADIO" name="format" value="text">TEXT[ For large sequence Only ]<br>',
,p,
h3,("View String Frequency:"),
'<input type="RADIO" name="frequency" value="base">Yes','<input type="RADIO" name="frequency" value="base">NO<br>',
,p,
h3(" Make restriction map:"),
submit , p,
'</font>',
'</body>',
hr,
end_form;
if (param( )) {
my $sequence = '';
# must have exactly one of the two sequence input methods specified
if(param('typedseq') and param('fileseq')) {
print "<font color=red>You have given a file AND typed in sequence: do only one!</font>", hr;
exit;
}elsif(not param('typedseq') and not param('fileseq')) {
print "<font color=red>You must give a sequence file OR type in sequence!</
font>", hr;
exit;
}elsif(param('typedseq')) {
$sequence = param('typedseq');
}elsif(param('fileseq')) {
my $fh = upload('fileseq');
while (<$fh>) {
/^\s*>/ and next; # handles fasta file headers
$sequence .= $_;
}
}
if(not param('format')){
print "<font color=red>You must give a Format name!</
font>", hr;
exit;
}
# strip out non-sequence characters
$sequence =~ s/\s//g;
$sequence = uc $sequence;
my $rebase = Rebase->new(
#omit "bionetfile" attribute to avoid recalculating the DBM file
dbmfile => 'BIONET',
mode => '0444',
);
my $restrict = Restrictionmap->new(
enzyme => param('enzyme'),
rebase => $rebase,
sequence => $sequence,
graphictype =>param('format'),
);
print "<p>Your requested enzyme(s): ",em(param('enzyme')),p, "</p>\n";
# table start
print "<table border='black'>\n";
# teable header
print "<tr>\n"; # header row start
foreach my $head ('Restriction Enzyme','Restriction Site','Total No. of Fragments'){
print "<th>$head</th>\n"; # header cell
}
print "</tr>\n"; # header row end
# table content
(my $paramenzyme = param('enzyme')) =~ s/,/ /g;
# printing table rows within the circle
foreach my $enzyme (split(" ", $paramenzyme)) {
# define the values for columns here as
# $seq_name, $restr_enzyme, $restr_site, $count
my $restr_enzyme =$enzyme;
my $restr_site = join( ' ', $restrict->get_enzyme_map($enzyme)),;
my $count = join(' ', $restrict->get_enzyme_map($enzyme)+1, "\n");
# then print the table row
print "<tr>\n"; # row start
foreach my $value ( $restr_enzyme, $restr_site, $count ){
print "<td>$value</td>\n"; # data cell
}
print "</tr>\n"; # row end
}
# finish the table
print "</table>\n";
if (param('frequency')) {
my @DNA = ( );
my $base = ' ';
my $count_of_A = ( );
my $count_of_C = ( );
my $count_of_G = ( );
my $count_of_T = ( );
my $errors = ( );
@DNA = split( '', $sequence);
# Initialize the counts.
# Notice that we can use scalar variables to hold numbers.
$count_of_A = 0;
$count_of_C = 0;
$count_of_G = 0;
$count_of_T = 0;
$errors = 0;
# In a loop, look at each base in turn, determine which of the
# four types of nucleotides it is, and increment the
# appropriate count.
foreach $base (@DNA) {
if ( $base eq 'A' ) {
++$count_of_A;
} elsif ( $base eq 'C' ) {
++$count_of_C;
} elsif ( $base eq 'G' ) {
++$count_of_G;
} elsif ( $base eq 'T' ) {
++$count_of_T;
} else {
print "!!!!!!!! Error - I don\'t recognize this
base: $base\n";
++$errors;
}
}
print "The Total No. of Frequency of Different Bases are \n ";
print "A = $count_of_A\n";
print "C = $count_of_C\n";
print "G = $count_of_G\n";
print "T = $count_of_T\n";
print "\n\n\n";
}
# lets store the image in the images subfolder
# (relating to the script location)
my $img_path = 'images/';
mkdir $img_path unless -d $img_path;
# lets create the image name using the extension
# taken from the object. the result should be 'images/tmp.png'
$img_path .= 'tmp.' . param('format');
# storing the image
my $img_binary = $restrict->get_graphic();
open my $img, '>', $img_path or die "can not write to $img_path: $!";
binmode $img;
print $img $img_binary;
close $img or die "failed to close <$img_path> $!";
print qq|<A HREF="http://localhost/myscript/images/"><input type=image src="images-2/download_file.jpg"/></A>|, ;
print "<center><img src=\"$img_path\"><br/>","\n\n\n\n\n";
exit;
}
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