Adapting script to use under CGI

[idorjee]

hi guys,
i've a perl script which does fine when i execute it as follows on unix environment:

bash-2.05$ perl <scriptname>

But, when i used CGI to output the result a browser, i see nothing. can anyone plz check the following to see what's going on. i would appreciate it.

!/usr/bin/perl

#use the CGI module
use CGI;

use Bio::Perl;
use Bio::SearchIO;
use Bio:B::GenPept;

####there are some more lines here

print STDOUT "<pre>";
print STDOUT "Performing BLAST....<br>may take few min.....\n";

system("blastall -p blastp -d nrpart -i $seq -o repo.bls");

my $in = new Bio::SearchIO(-format => 'blast', -file => 'repo.bls');
while( my $result = $in->next_result ) {
	while( my $hit = $result->next_hit ) {
		while( my $hsp = $hit->next_hsp ) {
			if ( $hsp->evalue <= 0.001 ) {
				print OUTFILE "Accession=",$hit->accession,"\tEvalue=",$hsp->evalue,"\tPercent_id=",$hsp->percent_identity, "\n";
				push(@1array, $hit->accession);
			}
		}
	}
}


my $genpeptdb = new Bio:B::GenPept();
my $seqio = Bio::SeqIO->new(-file => ">outputfilename", -format => 'fasta');

#### more lines follows

thanks

[miller]

Can you verify that blastall is being called via the system command when run under the web service?

Are you assuming that blastall is in the current working directory?
Does the web service run under a user/group that has execute and access permissions to the blastall?
Are there any other environmental issues that the webservice would introduce that you are not taking into account?

Is the OUTFILE location assuming a certain working directory?
Does the webservice have write permissions for that location?

Answer these questions and ones like it and you'll be able to get it to work eventually.

Good Luck,
- Miller

[idorjee]

thanks for your reply, Miller. but there's something that i don't understand. the blastall seems to be working fine when i change the input (-i) to a file in the same directory instead of $seq, which obviously comes from the html form input. however, i can print the $seq variable with print command. do you know what's going on?


#### part of the script ######

...
my $seq=$query->param("sequenc e");
print STDOUT "<br>$seq<b r>";

print STDOUT "<br>The contents of the uploaded file:\n<br></b>\n";

print STDOUT "<pre>";
print STDOUT "Performing BLAST....<br>ma y take few min.....\n";

system("blastal l -p blastp -d /export/home/dorjee/database/nrpart -i \$seq -o repo.bls");
......

[idorjee]

by the way, blastall is a database search program for protein and dna sequences which can be download (freely) from NCBI (http://www.ncbi.nlm.ni h.gov/). blastp for protein and blastn for nucleotide sequence search.

:) DJ

[idorjee]

thanks for your reply, Miller. but there's something that i don't understand. the blastall seems to be working fine when i change the input (-i) to a file in the same directory instead of $seq, which obviously comes from the html form input. however, i can print the $seq variable with print command. do you know what's going on?


#### part of the script ######

...
my $seq=$query->param("sequenc e");
print STDOUT "<br>$seq<b r>";

print STDOUT "<br>The contents of the uploaded file:\n<br></b>\n";

print STDOUT "<pre>";
print STDOUT "Performing BLAST....<br>ma y take few min.....\n";

system("blastal l -p blastp -d /export/home/dorjee/database/nrpart -i \$seq -o repo.bls");
......

by the way, blastall is a database search program for protein and dna sequences which can be download (freely) from NCBI (http://www.ncbi.nlm.nih.gov/). blastp for protein and blastn for nucleotide sequence search.

-DJ :)

Can you verify that blastall is being called via the system command when run under the web service?

Are you assuming that blastall is in the current working directory?
Does the web service run under a user/group that has execute and access permissions to the blastall?
Are there any other environmental issues that the webservice would introduce that you are not taking into account?

Is the OUTFILE location assuming a certain working directory?
Does the webservice have write permissions for that location?

Answer these questions and ones like it and you'll be able to get it to work eventually.

Good Luck,
- Miller