+#define BOOST_AUTO_TEST_MAIN
#include <boost/test/auto_unit_test.hpp>
#include <boost/filesystem/path.hpp>
#include <boost/filesystem/operations.hpp>
using namespace std;
+BOOST_AUTO_TEST_CASE( sequence_copy_constructor )
+{
+ SequenceRef s(new Sequence("AAAAGGGG"));
+ s->set_species("foo");
+ BOOST_CHECK_EQUAL(s->get_species(), "foo");
+
+ SequenceRef c(new Sequence(s));
+ BOOST_CHECK_EQUAL(c->get_species(), "foo");
+
+ c->set_species("bar");
+ BOOST_CHECK_EQUAL(s->get_species(), "foo");
+ BOOST_CHECK_EQUAL(c->get_species(), "bar");
+}
BOOST_AUTO_TEST_CASE( sequence_get_sequence )
{
Sequence s;
BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
}
+BOOST_AUTO_TEST_CASE( sequence_from_string )
+{
+ std::string str1("AAAT");
+ Sequence seq1(str1);
+ BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
+}
+
+BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
+{
+ std::string str1("AAAAT");
+ Sequence seq1(str1);
+ BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
+
+ std::string str2("AATTGGCC");
+ Sequence seq2(str2);
+ BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
+}
+
//! when we try to load a missing file, do we get an error?
BOOST_AUTO_TEST_CASE( sequence_load_exception )
{
BOOST_AUTO_TEST_CASE( sequence_filter )
{
const char *core_seq = "AATTGGCC";
- Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
+ Sequence s1(core_seq, reduced_dna_alphabet);
BOOST_CHECK_EQUAL(s1, core_seq);
- Sequence s2("aattggcc", Sequence::reduced_dna_alphabet);
+ Sequence s2("aattggcc", reduced_dna_alphabet);
BOOST_CHECK_EQUAL(s2, "AATTGGCC");
BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
//We're currently forcing sequences to uppercase
BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
- Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
+ Sequence s3("asdfg", reduced_dna_alphabet);
BOOST_CHECK_EQUAL(s3, "ANNNG");
BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
- s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2);
+ s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2);
BOOST_CHECK_EQUAL(s3, "AA");
- s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
+ s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
BOOST_CHECK_EQUAL( s3, "GG");
- s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
+ s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
BOOST_CHECK_EQUAL( s3, "CCTT");
s3 = "AAGGFF";
BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
{
std::string agct("AGCT");
- Sequence seq(agct, Sequence::nucleic_alphabet);
+ Sequence seq(agct, nucleic_alphabet);
BOOST_CHECK_EQUAL(seq.size(), agct.size());
BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
std::string bdv("BDv");
- Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
+ Sequence seq_bdv(bdv, nucleic_alphabet);
BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
// forcing sequence to upper case
BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
BOOST_AUTO_TEST_CASE( subseq_names )
{
- Sequence s1("AAGGCCTT", Sequence::reduced_dna_alphabet);
+ Sequence s1("AAGGCCTT", reduced_dna_alphabet);
s1.set_species("species");
s1.set_fasta_header("a fasta header");
Sequence s2 = s1.subseq(2,2);
BOOST_CHECK_EQUAL( s1.stop(), 0 );
std::string seq_string("AAGGCCTT");
- Sequence s2(seq_string, Sequence::reduced_dna_alphabet);
+ Sequence s2(seq_string, reduced_dna_alphabet);
BOOST_CHECK_EQUAL( s2.start(), 0 );
BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
seq_path /= "human_mck_pro.fa";
Sequence s;
- s.load_fasta(seq_path, Sequence::reduced_dna_alphabet);
+ s.load_fasta(seq_path, reduced_dna_alphabet);
BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
"5' flank");
}
+BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
+{
+ fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
+ seq_path /= "broken.fa";
+ bool exception_thrown = false;
+ std::string exception_filename;
+ Sequence s;
+ try {
+ s.load_fasta(seq_path);
+ } catch(sequence_invalid_load_error e) {
+ exception_thrown = true;
+ size_t native_string_size = seq_path.native_file_string().size();
+ std:string estr(e.what());
+ BOOST_REQUIRE(estr.size() > native_string_size);
+ std::copy(estr.begin(), estr.begin()+native_string_size,
+ std::back_inserter(exception_filename));
+ }
+ BOOST_CHECK_EQUAL(exception_thrown, true);
+ BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
+}
+
+BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
+{
+ fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
+ seq_path /= "mouse_mck_pro.fa";
+ fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
+ annot_path /= "broken.annot";
+ bool exception_thrown = false;
+ Sequence s;
+ s.load_fasta(seq_path);
+
+ std::string exception_filename;
+ try {
+ s.load_annot(annot_path, 0, 0);
+ } catch(annotation_load_error e) {
+ exception_thrown = true;
+ std:string estr(e.what());
+ size_t native_string_size = annot_path.native_file_string().size();
+ BOOST_REQUIRE(estr.size() > native_string_size);
+ std::copy(estr.begin(), estr.begin()+native_string_size,
+ std::back_inserter(exception_filename));
+ }
+ BOOST_CHECK_EQUAL(exception_thrown, true);
+ BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
+}
+
BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
{
std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
std::stringstream garbage_fasta(garbage_string);
Sequence s;
- s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
+ s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
- Sequence::reduced_dna_alphabet),
+ reduced_dna_alphabet),
sequence_invalid_load_error);
BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
- Sequence::reduced_dna_alphabet),
+ reduced_dna_alphabet),
sequence_invalid_load_error);
BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
- Sequence::reduced_dna_alphabet),
+ reduced_dna_alphabet),
sequence_invalid_load_error);
}
std::stringstream garbage_fasta(garbage_string);
Sequence s;
- s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
+ s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
- Sequence::reduced_rna_alphabet),
+ reduced_rna_alphabet),
sequence_invalid_load_error);
BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
- Sequence::reduced_rna_alphabet),
+ reduced_rna_alphabet),
sequence_invalid_load_error);
BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
- Sequence::reduced_rna_alphabet),
+ reduced_rna_alphabet),
sequence_invalid_load_error);
}
// there's two copies of reduced_rna_fasta because i didn't feel like
// figuring out how to properly reset the read pointer in a stringstream
s.load_fasta(reduced_rna_fasta1);
- specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
+ specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
BOOST_CHECK_EQUAL(s, specific);
s.load_fasta(reduced_dna_fasta1);
- specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
+ specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
BOOST_CHECK_EQUAL(s, specific);
BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
{
std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
- Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
+ Sequence seq(iupac_symbols, nucleic_alphabet);
Sequence seqr = seq.rev_comp();
BOOST_CHECK( seq != seqr );
BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
{
std::string dna_str("AGCTN");
- Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
+ Sequence dna_seq(dna_str, reduced_dna_alphabet);
BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
}
BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
{
std::string rna_str("AGCUN");
- Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
- BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
- BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
+ Sequence rna_seq(rna_str, reduced_rna_alphabet);
+ BOOST_CHECK_EQUAL(rna_seq.rev_comp().get_sequence(), "NAGCU");
+ BOOST_CHECK_EQUAL(rna_seq.get_sequence(),
+ rna_seq.rev_comp().rev_comp().get_sequence());
}
BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
{
std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
- Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
+ Sequence seq(dna_str, reduced_dna_alphabet);
Sequence subseq = seq.subseq(8,4);
BOOST_CHECK_EQUAL( subseq, "AAGG");
Sequence rev_subseq = subseq.rev_comp();
;
string s(100, 'A');
s += "GCTGCTAATT";
- Sequence seq(s, Sequence::reduced_dna_alphabet);
+ Sequence seq(s, reduced_dna_alphabet);
//istringstream annot_stream(annot_data);
seq.parse_annot(annot_data, 0, 0);
;
string s(100, 'A');
s += "GCTGCTAATT";
- Sequence seq(s, Sequence::reduced_dna_alphabet);
+ Sequence seq(s, reduced_dna_alphabet);
BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
"TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
"AAAAA"
"GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
- Sequence seq(s, Sequence::reduced_dna_alphabet);
+ Sequence seq(s, reduced_dna_alphabet);
seq.parse_annot(annot_data);
std::list<annot> annots = seq.annotations();
BOOST_CHECK_EQUAL( annots.size(), 2);
;
string s(100, 'A');
s += "GCTGCTAATT";
- Sequence seq(s, Sequence::reduced_dna_alphabet);
+ Sequence seq(s, reduced_dna_alphabet);
//istringstream annot_stream(annot_data);
seq.parse_annot(annot_data, 0, 0);
BOOST_AUTO_TEST_CASE( sequence_empty_equality )
{
- Sequence szero("", Sequence::reduced_dna_alphabet);
+ Sequence szero("", reduced_dna_alphabet);
BOOST_CHECK_EQUAL(szero.empty(), true);
BOOST_CHECK_EQUAL(szero, szero);
BOOST_CHECK_EQUAL(szero, "");
- Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
+ Sequence sclear("AGCT", reduced_dna_alphabet);
sclear.clear();
BOOST_CHECK_EQUAL(sclear.empty(), true);
BOOST_CHECK_EQUAL(sclear, sclear);
BOOST_AUTO_TEST_CASE ( sequence_iterators )
{
std::string seq_string = "AAGGCCTTNNTATA";
- Sequence s(seq_string, Sequence::reduced_dna_alphabet);
+ Sequence s(seq_string, reduced_dna_alphabet);
const Sequence cs(s);
std::string::size_type count = 0;
{
string m("AAAA");
string bogus("AATTGGAA");
- Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
+ Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
list<motif>::const_iterator motif_i = s1.motifs().begin();
list<motif>::const_iterator motif_end = s1.motifs().end();
*/
}
+BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
+{
+ // when searching for a motif on a subsequence we should
+ // only search the subsequence ticket:199
+ string aaaa("AAAA");
+ string cccc("CCCC");
+ Sequence s1("AAAANCCCC", reduced_dna_alphabet);
+
+ // this shouldn't show up
+ s1.add_motif(cccc);
+ BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
+
+ s1.add_motif(aaaa);
+ BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
+
+ Sequence subseq1 = s1.subseq(4,5);
+ BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
+ subseq1.clear_motifs();
+ BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
+ // this is outside of our subsequence, and so shouldn't be found
+ subseq1.add_motif(aaaa);
+ BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
+
+ subseq1.add_motif(cccc);
+ BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
+ std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
+ BOOST_REQUIRE(motif_i != subseq1.motifs().end());
+ BOOST_CHECK_EQUAL(motif_i->begin, 1);
+ BOOST_CHECK_EQUAL(motif_i->end, 5);
+}
+
BOOST_AUTO_TEST_CASE( annot_test )
{
annot a(0, 10, "test", "thing");
"AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
string gc("GCCCCC");
string gga("GGACACCTC");
- Sequence seq(s, Sequence::reduced_dna_alphabet);
+ Sequence seq(s, reduced_dna_alphabet);
std::list<Sequence> query_list;
std::list<string> string_list;
"GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
"CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
"AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
- Sequence seq(s, Sequence::reduced_dna_alphabet);
+ Sequence seq(s, reduced_dna_alphabet);
seq.add_annotation(annot(0, 10, "0-10", "0-10"));
"GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
"CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
"AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
- Sequence seq(s, Sequence::reduced_dna_alphabet);
+ Sequence seq(s, reduced_dna_alphabet);
// starting conditions
BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
BOOST_AUTO_TEST_CASE( out_operator )
{
string s("AAGGCCTT");
- Sequence seq(s, Sequence::reduced_dna_alphabet);
+ Sequence seq(s, reduced_dna_alphabet);
ostringstream buf;
buf << s;
BOOST_AUTO_TEST_CASE( get_name )
{
- Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
+ Sequence seq("AAGGCCTT", reduced_dna_alphabet);
BOOST_CHECK_EQUAL( seq.get_name(), "" );
seq.set_species("hooman"); // anyone remember tradewars?
BOOST_AUTO_TEST_CASE( serialize_simple )
{
std::string seq_string = "AAGGCCTT";
- Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
+ Sequence seq(seq_string, reduced_dna_alphabet);
seq.set_species("ribbet");
std::ostringstream oss;
// allocate/deallocate serialization components
BOOST_AUTO_TEST_CASE( serialize_tree )
{
std::string seq_string = "AAGGCCTT";
- Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
+ Sequence seq(seq_string, reduced_dna_alphabet);
seq.set_species("ribbet");
seq.add_motif("AA");
seq.add_motif("GC");
BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
{
std::string seq_string = "AAGGCCTT";
- Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
+ Sequence seq(seq_string, reduced_dna_alphabet);
seq.set_species("ribbet");
seq.add_motif("AA");
seq.add_motif("GC");
BOOST_AUTO_TEST_CASE( serialize_xml_two )
{
std::string seq_string = "AAGGCCTT";
- Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
+ Sequence seq1(seq_string, reduced_dna_alphabet);
Sequence seq2(seq1);
std::ostringstream oss;
BOOST_CHECK_EQUAL(seq1_loaded, seq1);
BOOST_CHECK_EQUAL(seq2_loaded, seq2);
// test if our pointers are the same
- BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());
+ BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());
}
projects / mussa.git / blobdiff