[Bioperl-l] Bio::Tools::Genscan

[Hilmar Lapp]

"Pan, Youlian" wrote:
> 
> Hello,
> 
> I am new to Bioperl and writing-up a parser using some of Bioperl modules
> for my thesis work at Canadian Bioinformatics Resource in Halifax.  I have
> used Bio::Tools::Genscan, it worked fine when I invoke my perl script on
> command line in Unix, but when I try to print to a web browser (IE or
> netscape), I am not able to see anything after I use Bio::Tools::Genscan.
> 
> Follow are part of my code:
> 
> ##########################################################
> 
> ..............
> 
> print "Content-type: text/html\n\n";
> print "this is a test\n";
> @exons =  get_exons();
> 
> ........................
> 
> sub get_exons {
>     print "<br>I am in the get exons\n";
>     $genscan = Bio::Tools::Genscan->new(-file => 'result.genscan');
>     print "<br> I am after Genscan<br>\n";
> ..................
> 
>     return @exons;
> }
> 
> Print out on browser:
>            this is a test
>            I am in the get exons
> 
> Print out at UNIX:
>             Content-type: text/html
> 
>             this is a test
>             I am in the get exons
>             I am after Genscan
>             ..................
> 
> ############################################################
> 
> Could anyone explain this discrepancy?

The cgi-script probably cannot find or cannot access the
'result.genscan' file. Note that a cgi-script usually will run under
another user, usually 'nobody'. It may also need directory information
in order to find it.

I guess what happens is that the Genscan->new() call fails with an
exception because the file cannot be found or not opened. The
exception message is printed to STDERR, which why you don't see it in
the browser (depending on the server's settings, you should still find
it in the httpd error-log), and after that the script terminates.

You can enclose the call in an eval {} and examine $@ after the eval
(eval will catch the exception). You can also test for existence and
readability like in

	if(-r 'somefile') {
		print "file is readable (and therefore also exists)\n";
	} else {
		print "file is not readable, open with Genscan will fail\n";
	}

Hilmar
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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