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# -*-Perl-*- mode (to keep my emacs happy)
# $Id: Unflattener2.t,v 1.6 2003/12/12 20:39:16 cjm Exp $
use strict;
use vars qw($DEBUG $TESTCOUNT);
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
$TESTCOUNT = 11;
plan tests => $TESTCOUNT;
}
use Bio::Seq;
use Bio::SeqIO;
use Bio::Root::IO;
use Bio::SeqFeature::Tools::Unflattener;
ok(1);
my $verbosity = 0; # Set to -1 for release version, so warnings aren't printed
#$verbosity = 1;
my ($seq, @sfs);
my $unflattener = Bio::SeqFeature::Tools::Unflattener->new;
$unflattener->verbose($verbosity);
if (1) {
# this is an arabidopsise gbk record. it has no mRNA features.
# it has explicit exon/intron records
my @path = ("t","data","ATF14F8.gbk");
$seq = getseq(@path);
ok ($seq->accession_number, 'AL391144');
my @topsfs = $seq->get_SeqFeatures;
my @cdss = grep {$_->primary_tag eq 'CDS'} @topsfs;
my $n = scalar(@topsfs);
printf "TOP:%d\n", scalar(@topsfs);
# write_hier(@topsfs);
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq=>$seq,
-use_magic=>1,
);
print "\n\nPOST PROCESSING:\n";
@sfs = $seq->get_SeqFeatures;
write_hier(@sfs);
printf "PROCESSED/TOP:%d\n", scalar(@sfs);
ok(@sfs == 28);
my @allsfs = $seq->get_all_SeqFeatures;
printf "ALL:%d\n", scalar(@allsfs);
ok(@allsfs == 202);
my @mrnas = grep {$_->primary_tag eq 'mRNA'} @allsfs;
printf "mRNAs:%d\n", scalar(@mrnas);
# relationship between mRNA and CDS should be one-one
ok(@mrnas == @cdss);
}
if (1) {
# this is a record from FlyBase
# it has mRNA features, and explicit exon/intron records
my @path = ("t","data","AnnIX-v003.gbk");
$seq = getseq(@path);
my @topsfs = $seq->get_SeqFeatures;
printf "TOP:%d\n", scalar(@topsfs);
# write_hier(@topsfs);
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq=>$seq,
-use_magic=>1,
);
print "\n\nPOST PROCESSING:\n";
@sfs = $seq->get_SeqFeatures;
write_hier(@sfs);
printf "PROCESSED/TOP:%d\n", scalar(@sfs);
ok(@sfs == 1);
my @exons = grep {$_->primary_tag eq 'exon'} $seq->get_all_SeqFeatures;
ok(@exons == 10); # total number of exons per splice
my %numberh = map {$_->get_tag_values("number") => 1} @exons;
my @numbers = keys %numberh;
printf "DISTINCT EXONS: %d [@numbers]\n", scalar(@numbers);
ok(@numbers == 6); # distinct exons
}
if (1) {
# example of a BAD genbank entry
my @path = ("t","data","dmel_2Lchunk.gb");
$seq = getseq(@path);
my @topsfs = $seq->get_SeqFeatures;
printf "TOP:%d\n", scalar(@topsfs);
# write_hier(@topsfs);
# UNFLATTEN
#
# we EXPECT problems with this erroneous record
$unflattener->error_threshold(2);
@sfs = $unflattener->unflatten_seq(-seq=>$seq,
-use_magic=>1,
);
my @probs = $unflattener->get_problems;
$unflattener->report_problems(\*STDOUT);
$unflattener->clear_problems;
print "\n\nPOST PROCESSING:\n";
@sfs = $seq->get_SeqFeatures;
write_hier(@sfs);
printf "PROCESSED/TOP:%d\n", scalar(@sfs);
ok(@sfs == 2);
my @exons = grep {$_->primary_tag eq 'exon'} $seq->get_all_SeqFeatures;
ok(@exons == 6); # total number of exons per splice
printf "PROBLEMS ENCOUNTERED: %d (EXPECTED: 6)\n", scalar(@probs);
ok(@probs == 6);
}
sub write_hier {
my @sfs = @_;
_write_hier(0, @sfs);
}
sub _write_hier {
my $indent = shift;
my @sfs = @_;
foreach my $sf (@sfs) {
my $label = '?';
if ($sf->has_tag('gene')) {
($label) = $sf->get_tag_values('gene');
}
if ($sf->has_tag('product')) {
($label) = $sf->get_tag_values('product');
}
if ($sf->has_tag('number')) {
$label = join("; ", $sf->get_tag_values('number'));
}
printf "%s%s $label\n", ' ' x $indent, $sf->primary_tag;
my @sub_sfs = $sf->sub_SeqFeature;
_write_hier($indent+1, @sub_sfs);
}
}
sub getseq {
my @path = @_;
my $seqio =
Bio::SeqIO->new('-file'=> Bio::Root::IO->catfile(
@path
),
'-format' => 'GenBank');
$seqio->verbose($verbosity);
my $seq = $seqio->next_seq();
return $seq;
}
# 1 2,3
# 2 1,2
# 3 4,5
# 4 1,4,5,6
# 5 1,4,5,6
# 6 1,4,5,6
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