I figured out a solution. I installed the "WMCTRL" package, a linux windows manager, using "sudo apt-get install wmctrl". Now I use the "wmctrl -c "title of window"" system command in my perl script to close only the browser window with that title. See the 2 new lines of code below.

#!/usr/bin/perl 
use strict;
use warnings;
use WWW::Mechanize::Firefox;

my $mech = WWW::Mechanize::Firefox->new();
$mech->get("http://david.abcc.ncifcrf.gov/summary.jsp");
$mech->click({ xpath => ('//*[@href="Upload a Gene List or Population"
+]', single => 1), synchronize => 0 });
$mech->form_name('frmManager');
$mech->set_fields( 
    'pasteBox' =>     "RRI1, YLR149C, FUN19, YBR285W, ALD3, CUE5, RTC3
+, AIM3, YDL199C, FMP45, AST2, GIP2,
            YKL091C, YKL133C, GLG2, SYM1, VHS3, YJR124C, MCH1, MHO1, I
+KS1, RKM1, STF2, SAC1, ATG7, YAK1",    
    'Identifier' => "OFFICIAL_GENE_SYMBOL",
);
$mech->click ({ xpath => ('//input[@name="rbUploadType" and @value="li
+st"]', single => 1), synchronize => 0 }); 
$mech->click({xpath => ('//*[@value="Submit List"]', single => 1), syn
+chronize => 0});
$mech->back;
my $retries = 100;
while ($retries-- and ! $mech->is_visible( xpath => '//*[@value="Funct
+ional Annotation Clustering"]' )) {
    sleep 1;
};
die "Timeout" unless $retries;
$mech->click({xpath => ('//*[@value="Functional Annotation Clustering"
+]', single => 1), synchronize => 0});
$mech->get("http://david.abcc.ncifcrf.gov/term2term.jsp?annot=52,9,79,
+85,25,32,39,3,47,45,63,76&currentList=1");
my $title = 'DAVID: Database for Annotation, Visualization, and Integr
+ated Discovery (Laboratory of Immunopathogenesis and Bioinformatics (
+LIB); National Institute of Allergies and Infectious Diseases (NIAID)
+; Science Applications International Corporation (SAIC)';
system("wmctrl -c \"$title\"");

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In reply to Re: WWW::Mechanize::Firefox -- how to close firefox browser window by jbernest
in thread WWW::Mechanize::Firefox -- how to close firefox browser window by jbernest

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