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|
# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 21);
use_ok('Bio::SeqIO');
use_ok('Bio::SeqFeature::Tools::Unflattener');
}
my $verbosity = test_debug();
my ($seq, @sfs);
my $unflattener = Bio::SeqFeature::Tools::Unflattener->new;
$unflattener->verbose($verbosity);
if (1) {
my @path = ("NC_000007-ribosomal-slippage.gb");
$seq = getseq(@path);
my @topsfs = $seq->get_SeqFeatures;
if( $verbosity > 0 ) {
warn sprintf "TOP:%d\n", scalar(@topsfs);
write_hier(@topsfs);
}
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq => $seq,
-use_magic => 1);
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
is(@sfs, 1995);
}
if (1) {
my @path = ("ribosome-slippage.gb");
$seq = getseq(@path);
my @topsfs = $seq->get_SeqFeatures;
if( $verbosity > 0 ) {
warn sprintf "TOP:%d\n", scalar(@topsfs);
write_hier(@topsfs);
}
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq => $seq,
-use_magic => 1);
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
is(@sfs, 3);
}
if (1) {
my @path = ("AE003644_Adh-genomic.gb");
$seq = getseq(@path);
is ($seq->accession_number, 'AE003644');
my @topsfs = $seq->get_SeqFeatures;
if( $verbosity > 0 ) {
warn sprintf "TOP:%d\n", scalar(@topsfs);
write_hier(@topsfs);
}
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq => $seq,
-group_tag => 'locus_tag');
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
is(@sfs, 21);
}
# now try again, using a custom subroutine to link together features
$seq = getseq("AE003644_Adh-genomic.gb");
@sfs = $unflattener->unflatten_seq
(-seq => $seq,
-group_tag => 'locus_tag',
-resolver_method =>
sub {
my $self = shift;
my ($sf, @candidate_container_sfs) = @_;
if ($sf->has_tag('note')) {
my @notes = $sf->get_tag_values('note');
my @trnames = map {/from transcript\s+(.*)/; $1;}
@notes;
@trnames = grep {$_} @trnames;
my $trname;
if (@trnames == 0) {
$self->throw("UNRESOLVABLE");
}
elsif (@trnames == 1) {
$trname = $trnames[0];
}
else {
$self->throw("AMBIGUOUS: @trnames");
}
my @container_sfs =
grep {
my ($product) =
$_->has_tag('product') ? $_->get_tag_values('product')
: ('');
$product eq $trname;
} @candidate_container_sfs;
if (@container_sfs == 0) {
$self->throw("UNRESOLVABLE");
}
elsif (@container_sfs == 1) {
# we got it!
return ($container_sfs[0]=>0);
}
else {
$self->throw("AMBIGUOUS");
}
}
});
$unflattener->feature_from_splitloc(-seq => $seq);
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED2:%d\n", scalar(@sfs);
}
is(@sfs, 21);
# try again; different sequence
# this is an E-Coli seq with no mRNA features;
# we just want to link all features directly with gene
$seq = getseq("D10483.gbk");
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq => $seq,
-partonomy => {'*'=>'gene'});
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
is(@sfs, 98);
# this sequence has no locus_tag or or gene tags
$seq = getseq("AY763288.gb");
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq => $seq,
-use_magic => 1);
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
is(@sfs, 3);
# try again; different sequence - dicistronic gene, mRNA record
$seq = getseq("X98338_Adh-mRNA.gb");
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq => $seq,
-partonomy => {'*'=>'gene'});
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
is(@sfs, 7);
# try again; this sequence has no CDSs but rRNA present
$seq = getseq("no_cds_example.gb");
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq => $seq,
-use_magic => 1);
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED:%d\n", scalar(@sfs);
}
my @all_sfs = $seq->get_all_SeqFeatures;
my @exons = grep { $_-> primary_tag eq 'exon' } @all_sfs ;
is(@exons, 2);
if (1) {
# this is an arabidopsise gbk record. it has no mRNA features.
# it has explicit exon/intron records
my @path = ("ATF14F8.gbk");
$seq = getseq(@path);
is ($seq->accession_number, 'AL391144');
my @topsfs = $seq->get_SeqFeatures;
my @cdss = grep {$_->primary_tag eq 'CDS'} @topsfs;
my $n = scalar(@topsfs);
if( $verbosity > 0 ) {
warn sprintf "TOP:%d\n", scalar(@topsfs);
write_hier(@topsfs);
}
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq => $seq,
-use_magic => 1);
@sfs = $seq->get_SeqFeatures;
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED/TOP:%d\n", scalar(@sfs);
}
is(@sfs,28);
my @allsfs = $seq->get_all_SeqFeatures;
is(@allsfs,202);
my @mrnas = grep {$_->primary_tag eq 'mRNA'} @allsfs;
if( $verbosity > 0 ) {
warn sprintf "ALL:%d\n", scalar(@allsfs);
warn sprintf "mRNAs:%d\n", scalar(@mrnas);
}
# relationship between mRNA and CDS should be one-one
is(@mrnas,@cdss);
}
if (1) {
# this is a record from FlyBase
# it has mRNA features, and explicit exon/intron records
my @path = ("AnnIX-v003.gbk");
$seq = getseq(@path);
my @topsfs = $seq->get_SeqFeatures;
if( $verbosity > 0 ) {
warn sprintf "TOP:%d\n", scalar(@topsfs);
write_hier(@topsfs);
}
# UNFLATTEN
@sfs = $unflattener->unflatten_seq(-seq => $seq,
-use_magic => 1);
@sfs = $seq->get_SeqFeatures;
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED/TOP:%d\n", scalar(@sfs);
}
is scalar(@sfs), 1;
my @exons = grep {$_->primary_tag eq 'exon'} $seq->get_all_SeqFeatures;
is scalar(@exons), 6; # total number of exons per splice
my %numberh = map {$_->get_tag_values("number") => 1} @exons;
my @numbers = keys %numberh;
if( $verbosity > 0 ) {
warn sprintf "DISTINCT EXONS: %d [@numbers]\n", scalar(@numbers);
}
is scalar(@numbers), 6; # distinct exons
}
if (1) {
# example of a BAD genbank entry
my @path = ("dmel_2Lchunk.gb");
$seq = getseq(@path);
my @topsfs = $seq->get_SeqFeatures;
if( $verbosity > 0 ) {
warn sprintf "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);
@sfs = $seq->get_SeqFeatures;
if( $verbosity > 0 ) {
warn "\n\nPOST PROCESSING:\n";
write_hier(@sfs);
warn sprintf "PROCESSED/TOP:%d\n", scalar(@sfs);
}
is scalar(@sfs), 2;
my @exons = grep {$_->primary_tag eq 'exon'} $seq->get_all_SeqFeatures;
is scalar(@exons), 2; # total number of exons per splice
my @probs = $unflattener->get_problems;
$unflattener->report_problems(\*STDERR) if $verbosity > 0;
$unflattener->clear_problems;
if( $verbosity > 0 ) {
warn sprintf "PROBLEMS ENCOUNTERED: %d (EXPECTED: 6)\n", scalar(@probs);
}
is scalar(@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) = $sf->get_tag_values('gene');
}
elsif ($sf->has_tag('product')) {
($label) = $sf->get_tag_values('product');
}
elsif ($sf->has_tag('number')) {
$label = join("; ", $sf->get_tag_values('number'));
}
warn sprintf "%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' => test_input_file(@path),
'-format' => 'GenBank');
$seqio->verbose($verbosity);
my $seq = $seqio->next_seq();
return $seq;
}
|
