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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: SeqFeatCollection.t,v 1.8 2003/02/26 15:59:26 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS);
my $error;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
$error = 0;
if( $@ ) {
use lib 't';
}
use Test;
$NUMTESTS = 432;
plan tests => $NUMTESTS;
eval { require DB_File; };
if( $@ ) {
print STDERR "DB_File not installed. This means the SeqFeatCollection wont work\n";
for( 1..$NUMTESTS ) {
skip("DB_File",1);
}
$error = 1;
}
}
if( $error == 1 ) {
exit(0);
}
my $testnum;
my $verbose = $ENV{'BIOPERLDEBUG'} || 0;
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
#First of all we need to create an flat db
require Bio::SeqFeature::Collection;
use Bio::Root::IO;
use Bio::Location::Simple;
use Bio::Tools::GFF;
use Bio::SeqIO;
my $simple = new Bio::SeqIO(-format => 'genbank',
-file => Bio::Root::IO->catfile
("t","data","AB077698.gb"));
my @features;
my $seq = $simple->next_seq();
@features = $seq->top_SeqFeatures();
ok(scalar @features, 11);
my $col = new Bio::SeqFeature::Collection(-verbose => $verbose);
ok($col);
ok($col->add_features( \@features), 11);
my @feat = $col->features_in_range(-range => ( new Bio::Location::Simple
(-start => 100,
-end => 300,
-strand => 1) ),
-contain => 0);
ok(scalar @feat, 5);
if( $verbose ) {
foreach my $f ( @feat ) {
print $f->location->to_FTstring(), "\n";
}
}
ok(scalar $col->features_in_range(-range => ( new Bio::Location::Simple
(-start => 100,
-end => 300,
-strand => -1) ),
-strandmatch => 'ignore',
-contain => 1), 2);
@feat = $col->features_in_range(-start => 79,
-end => 1145,
-strand => 1,
-strandmatch => 'strong',
-contain => 1);
ok(scalar @feat, 5);
if( $verbose ) {
foreach my $f ( sort { $a->start <=> $b->start} @feat ) {
print $f->primary_tag, " ", $f->location->to_FTstring(), "\n";
}
}
ok($feat[0]->primary_tag, 'CDS');
ok($feat[0]->has_tag('gene'));
$verbose = 0;
# specify input via -fh or -file
my $gffio = Bio::Tools::GFF->new(-file => Bio::Root::IO->catfile
("t","data","myco_sites.gff"),
-gff_version => 2);
@features = ();
# loop over the input stream
while(my $feature = $gffio->next_feature()) {
# do something with feature
push @features, $feature;
}
$gffio->close();
ok(scalar @features, 412);
$col = new Bio::SeqFeature::Collection(-verbose => $verbose,
-usefile => 1);
ok($col);
ok($col->add_features( \@features), 412);
my $r = new Bio::Location::Simple(-start => 67700,
-end => 150000,
-strand => 1);
@feat = $col->features_in_range(-range => $r,
-strandmatch => 'ignore',
-contain => 0);
ok(scalar @feat, 56);
ok($col->feature_count, 412);
my $count = $col->feature_count;
$col->remove_features( [$features[58], $features[60]]);
ok( $col->feature_count, 410);
@feat = $col->features_in_range(-range => $r,
-strandmatch => 'ignore',
-contain => 0);
ok( scalar @feat, 54);
# add the removed features back in in order to get the collection back to size
$col->add_features([$features[58], $features[60]]);
# let's randomize so we aren't removing and adding in the same order
# and hopefully randomly deal with a bin's expiration
fy_shuffle(\@features);
foreach my $f ( @features ) {
next unless defined $f;
$col->remove_features([$f]);
ok( $col->feature_count, --$count);
}
ok($col->feature_count, 0);
my $filename = 'featcol.idx';
my $newcollection = new Bio::SeqFeature::Collection(-verbose => $verbose,
-keep => 1,
-file => $filename);
$newcollection->add_features(\@feat);
ok($newcollection->feature_count, 54);
undef $newcollection;
ok(-e $filename);
$newcollection = new Bio::SeqFeature::Collection(-verbose => $verbose,
-file => $filename);
ok($newcollection->feature_count, 54);
undef $newcollection;
ok( ! -e $filename);
if( $verbose ) {
my @fts = sort { $a->start <=> $b->start}
grep { $r->overlaps($_,'ignore') } @features;
if( $verbose ) {
foreach my $f ( @fts ) {
print $f->primary_tag, " ", $f->location->to_FTstring(), "\n";
}
print "\n";
}
my %G = map { ($_,1) } @feat;
my $c = 0;
foreach my $A ( @fts ) {
if( ! $G{$A} ) {
print "missing ", $A->primary_tag, " ", $A->location->to_FTstring(), "\n";
} else {
$c++;
}
}
print "Number of features correctly retrieved $c\n";
foreach my $f ( sort { $a->start <=> $b->start} @feat ) {
print $f->primary_tag, " ", $f->location->to_FTstring(), "\n";
}
}
sub fy_shuffle {
my $array = shift;
my $i;
for( $i = @$array; $i--; ) {
my $j = int rand($i+1);
next if $i==$j;
@$array[$i,$j] = @$array[$j,$i];
}
}
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