# *%) $Id: test.pl,v 1.1.1.1 2004/05/25 01:34:52 scottz Exp $
use lib './lib';
use Bio::SAGE::Comparison;
use strict;
print "Creating new Bio::SAGE::Comparison instance...\n";
my $sage = Bio::SAGE::Comparison->new();
print " ...complete.\n";
print "Creating a fake tag data files...\n";
# create a fake FASTA sequence file
open( SCRIPT, $0 ) || die( "Couldn't open this script: $0" );
open( TAG1, '>fakelib1.tags' ) || die( "Could create file fakelib1.tags" );
my $bParsing = 0;
while( my $line = <SCRIPT> ) {
chomp( $line ); $line =~ s/\r//g;
if( $line =~ /^\/\/ START_LIBRARY$/ ) {
$bParsing = 1; next;
}
if( $line =~ /^\/\/ END_LIBRARY$/ ) {
$bParsing = 0; last;
}
if( $bParsing == 1 ) {
print TAG1 $line . "\n";
}
}
close( TAG1 );
open( TAG2, '>fakelib2.tags' ) || die( "Could create file fakelib2.tags" );
$bParsing = 0;
while( my $line = <SCRIPT> ) {
chomp( $line ); $line =~ s/\r//g;
if( $line =~ /^\/\/ START_LIBRARY$/ ) {
$bParsing = 1; next;
}
if( $line =~ /^\/\/ END_LIBRARY$/ ) {
$bParsing = 0; last;
}
if( $bParsing == 1 ) {
print TAG2 $line . "\n";
}
}
close( TAG2 );
close( SCRIPT );
print " ...complete.\n";
print "Inputting fake tag files...\n";
# read the fake file in
open( FAKETAGS1, 'fakelib1.tags' ) || die( "Could not open file fakelib1.tags" );
$sage->add_library( 'LIB1', $sage->load_library( *FAKETAGS1 ) );
close( FAKETAGS1 );
unlink( 'fakelib1.tags' );
open( FAKETAGS2, 'fakelib2.tags' ) || die( "Could not open file fakelib2.tags" );
$sage->add_library( 'LIB2', $sage->load_library( *FAKETAGS2 ) );
close( FAKETAGS2 );
unlink( 'fakelib2.tags' );
print "Getting library labels...\n";
foreach my $l ( $sage->get_library_labels() ) {
print " " . $l . "\n";
}
print " ...complete.\n";
print "Getting library sizes...\n";
print " LIB1 = " . $sage->get_library_size( 'LIB1' ) . "\n";
print " LIB2 = " . $sage->get_library_size( 'LIB2' ) . "\n";
print " ...complete.\n";
print "Calculating and printing comparison...\n";
print $sage->print_library_comparison( $sage->get_library_comparison( 'LIB1', 'LIB2' ) );
print " ...complete.\n";
print "Tests completed successfully.\n";
exit( 0 );
=pod
=for comment
// START_LIBRARY
AAAAAAAAAAA 100
AAACAGAGTAA 50
GATACAGATAA 10
CCAGATAGGCC 2
// END_LIBRARY
// START_LIBRARY
AAAAAAAAAAA 80
AAACAGAGTAA 60
GATACAGATAA 9
CCAGATAGGCC 2
TAGAGACCAAA 5
// END_LIBRARY
=cut