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#-*-perl-*-
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(
-tests => 61,
-requires_modules => [qw(XML::LibXML XML::LibXML::Reader XML::Writer)]
);
use_ok('Bio::SeqIO');
}
use_ok('Bio::PrimarySeq');
my $verbose = test_debug();
SKIP: {
# XML library version checks
if ( 1000 * $] < 5008 ) {
skip( "Reader interface only supported in Perl >= 5.8", 96 );
}
elsif ( XML::LibXML::LIBXML_VERSION() <= 20620 ) {
skip( "Reader not supported for libxml2 <= 2.6.20", 96 );
}
if ($verbose) {
diag( "libxml version: ", XML::LibXML::LIBXML_VERSION() );
}
# checks that your module is there and loads ok
use_ok('Bio::SeqIO::seqxml');
# read data
ok(
my $seq_stream = Bio::SeqIO->new(
-file => test_input_file("seqxml.xml"),
-format => 'seqxml',
-verbose => $verbose,
),
'stream ok',
);
# check metadata
is( $seq_stream->seqXMLversion, '0.3', 'seqXML version' );
is( $seq_stream->source, 'Ensembl', 'source' );
is( $seq_stream->sourceVersion, '56', 'source version' );
# now get and check the sequence entry itself
my $seq_obj = $seq_stream->next_seq;
isa_ok( $seq_obj, 'Bio::Seq' );
is( $seq_obj->display_id, 'ENST00000308775', 'display id' );
is( $seq_obj->primary_id, 'ENST00000308775', 'primary id' );
is( $seq_obj->desc, 'dystroglycan 1', 'description' );
is( $seq_obj->seq, 'AAGGC----UGAUGUC.....ACAU', 'sequence' );
is( $seq_obj->length, 25, 'length' );
my ($source) = $seq_obj->get_Annotations('source');
if ($source) { is($source->value, 'Ensembl', 'entry source'); }
# species
isa_ok( $seq_obj->species, 'Bio::Species', 'species' );
is( $seq_obj->species->node_name, 'Homo sapiens', 'species name' );
is( $seq_obj->species->ncbi_taxid, '9606', 'NCBI tax id' );
# alternative IDs
my @dblinks = $seq_obj->get_Annotations('dblink');
my $dblink = shift @dblinks;
isa_ok( $dblink, 'Bio::Annotation::DBLink' );
is( $dblink->database, 'RefSeq', 'dblink source' );
is( $dblink->primary_id, 'NM_004393', 'dblink ID' );
# properties
my @annotations = $seq_obj->get_Annotations();
foreach my $annot_obj (@annotations) {
next if ( $annot_obj->tagname eq 'dblink' );
next if ( $annot_obj->tagname eq 'source' );
isa_ok( $annot_obj, 'Bio::Annotation::SimpleValue' );
if ( $annot_obj->tagname eq 'has_splice_variants' ) {
is( $annot_obj->value, undef, 'boolean property' );
}
elsif ( $annot_obj->tagname eq 'prediction_method' ) {
is( $annot_obj->value, 'manual curation', 'property with value' );
}
}
# write data
my $outfile = test_output_file();
ok(
my $seq_writer = Bio::SeqIO->new(
-file => ">$outfile",
-format => 'seqxml',
-verbose => $verbose,
-source => 'Ensembl',
-sourceVersion => '56',
-seqXMLversion => '0.3',
),
'writer ok',
);
$seq_writer->flush; # to make sure output is written to file
ok( -s $outfile, 'outfile is created' );
# check metadata
is( $seq_writer->seqXMLversion, '0.3', 'seqXML version' );
is( $seq_writer->source, 'Ensembl', 'source' );
is( $seq_writer->sourceVersion, '56', 'source version' );
is( $seq_writer->schemaLocation, 'http://www.seqxml.org/0.3/seqxml.xsd', 'schemaLocation' );
# write one sequence entry to file
$seq_writer->write_seq($seq_obj);
$seq_writer->close;
if ( $verbose > 0 ) {
diag("writing first seqXML outfile");
diag(`cat $outfile`);
}
# verify written data by roundtripping it
{
my $new_in = Bio::SeqIO->new(
-file => $outfile,
-format => 'seqxml'
);
my $new_seqobj = $new_in->next_seq;
isa_ok( $new_seqobj, 'Bio::Seq' );
is( $new_seqobj->display_id, 'ENST00000308775', 'display id' );
is( $new_seqobj->primary_id, 'ENST00000308775', 'primary id' );
is( $new_seqobj->desc, 'dystroglycan 1', 'description' );
is( $new_seqobj->seq, 'AAGGC----UGAUGUC.....ACAU', 'sequence' );
is( $new_seqobj->length, 25, 'length' );
my ($new_source) = $new_seqobj->get_Annotations('source');
if ($new_source) { is($new_source->value, 'Ensembl', 'entry source'); }
# species
isa_ok( $new_seqobj->species, 'Bio::Species', 'species' );
is( $new_seqobj->species->node_name, 'Homo sapiens', 'species name' );
is( $new_seqobj->species->ncbi_taxid, '9606', 'NCBI tax id' );
# alternative IDs
my @dblinks = $new_seqobj->get_Annotations('dblink');
my $dblink = shift @dblinks;
isa_ok( $dblink, 'Bio::Annotation::DBLink' );
is( $dblink->database, 'RefSeq', 'dblink source' );
is( $dblink->primary_id, 'NM_004393', 'dblink ID' );
# properties
my @annotations = $new_seqobj->get_Annotations();
foreach my $annot_obj (@annotations) {
next if ( $annot_obj->tagname eq 'dblink' );
next if ( $annot_obj->tagname eq 'source' );
isa_ok( $annot_obj, 'Bio::Annotation::SimpleValue' );
if ( $annot_obj->tagname eq 'has_splice_variants' ) {
is( $annot_obj->value, undef, 'boolean property' );
}
elsif ( $annot_obj->tagname eq 'prediction_method' ) {
is(
$annot_obj->value,
'manual curation',
'property with value'
);
}
}
}
# write data from a Seq object created from a fasta file
{
# forcing a Bio::Seq to be created
# due to SeqIO::fasta creating a PrimarySeq by default
# as of r16838
my $factory = Bio::Seq::SeqFactory->new(-type => 'Bio::Seq');
my $seq_stream = Bio::SeqIO->new(
-file => test_input_file("test.fasta"),
-format => 'fasta',
-seqfactory => $factory,
);
my $outfile = test_output_file();
my $writer = Bio::SeqIO->new(
-file => ">$outfile",
-format => 'seqxml'
);
$writer->flush;
ok( -s $outfile, 'outfile is created' );
while ( my $seq_obj = $seq_stream->next_seq ) {
$writer->write_seq($seq_obj);
}
$writer->close;
if ( $verbose > 0 ) {
diag(`cat $outfile`);
}
# now read that newly made seqxml back in
my $in = Bio::SeqIO->new(
-file => $outfile,
-format => 'seqxml'
);
# check header
is( $in->seqXMLversion, '0.3', 'seqXML version' );
is( $in->source, undef, 'source' );
is( $in->sourceVersion, undef, 'source version' );
# check first sequence entry
my $seqxml_obj = $in->next_seq;
is( $seqxml_obj->display_id, 'roa1_drome', 'display id' );
is( $seqxml_obj->primary_id, 'roa1_drome', 'primary id' );
is( $seqxml_obj->desc, 'Rea guano receptor type III >> 0.1',
'description' );
is(
$seqxml_obj->seq,
'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY',
'sequence'
);
is( $seqxml_obj->length, 358, 'length' );
# check second sequence entry
my $seqxml_obj2 = $in->next_seq;
is( $seqxml_obj2->display_id, 'roa2_drome', 'display id' );
is( $seqxml_obj2->primary_id, 'roa2_drome', 'primary id' );
is( $seqxml_obj2->desc, 'Rea guano ligand', 'description' );
is(
$seqxml_obj2->seq,
'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVVVMKDPTSTSTSTSTSTSTSTSTMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHLLLLLLLDLLLLDLLLLDLLLFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY',
'sequence'
);
is( $seqxml_obj2->length, 358, 'length' );
}
}
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