BOOST_AUTO_TEST_CASE( sequence_filter )
{
const char *core_seq = "AATTGGCC";
- Sequence s1(core_seq);
+ Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
BOOST_CHECK_EQUAL(s1, core_seq);
- Sequence s2("aattggcc");
+ Sequence s2("aattggcc", Sequence::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
BOOST_CHECK_EQUAL(s2.size(), s2.size());
- BOOST_CHECK_EQUAL(s2.get_sequence(), core_seq);
+ BOOST_CHECK_EQUAL(s2.get_sequence(), "aattggcc");
- Sequence s3("asdfg");
+ Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
BOOST_CHECK_EQUAL(s3, "ANNNG");
BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
- s3.set_filtered_sequence("AAGGCCTT", 0, 2);
+ s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2);
BOOST_CHECK_EQUAL(s3, "AA");
- s3.set_filtered_sequence("AAGGCCTT", 2, 2);
+ s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
BOOST_CHECK_EQUAL( s3, "GG");
- s3.set_filtered_sequence("AAGGCCTT", 4);
+ s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
BOOST_CHECK_EQUAL( s3, "CCTT");
s3 = "AAGGFF";
BOOST_CHECK_EQUAL(s3, "AAGGNN");
}
+BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
+{
+ std::string agct("AGCT");
+ Sequence seq(agct, Sequence::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);
+ BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
+ BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), bdv);
+
+}
+
+BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
+{
+ std::string agct("AGCT");
+ Sequence seq(agct);
+ BOOST_CHECK_EQUAL(seq.size(), agct.size());
+ BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
+ BOOST_CHECK_EQUAL(seq[0], agct[0]);
+ BOOST_CHECK_EQUAL(seq[1], agct[1]);
+ BOOST_CHECK_EQUAL(seq[2], agct[2]);
+ BOOST_CHECK_EQUAL(seq[3], agct[3]);
+
+ std::string bdv("BDv");
+ Sequence seq_bdv(bdv);
+ BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
+ // default alphabet only allows AGCTUN
+ BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
+}
+
BOOST_AUTO_TEST_CASE( subseq_names )
{
- Sequence s1("AAGGCCTT");
+ Sequence s1("AAGGCCTT", Sequence::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 s2(seq_string, Sequence::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);
+ s.load_fasta(seq_path, Sequence::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_dna_reduced )
+{
+ std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
+ std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
+ std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
+ std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
+ std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
+ std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
+ std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
+ std::stringstream garbage_fasta(garbage_string);
+
+ Sequence s;
+ s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
+ BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
+ Sequence::reduced_dna_alphabet),
+ sequence_invalid_load_error);
+ BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
+ Sequence::reduced_dna_alphabet),
+ sequence_invalid_load_error);
+ BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
+ Sequence::reduced_dna_alphabet),
+ sequence_invalid_load_error);
+
+}
+
+BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
+{
+ std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
+ std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
+ std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
+ std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
+ std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
+ std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
+ std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
+ std::stringstream garbage_fasta(garbage_string);
+
+ Sequence s;
+ s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
+ BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
+ Sequence::reduced_rna_alphabet),
+ sequence_invalid_load_error);
+ BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
+ Sequence::reduced_rna_alphabet),
+ sequence_invalid_load_error);
+ BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
+ Sequence::reduced_rna_alphabet),
+ sequence_invalid_load_error);
+}
+
+BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
+{
+ std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
+ std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
+ std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
+ std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
+ std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
+ std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
+ std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
+ std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
+ std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
+ std::stringstream garbage_fasta(garbage_string);
+
+ Sequence s;
+ Sequence specific;
+ // 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);
+ BOOST_CHECK_EQUAL(s, specific);
+
+ s.load_fasta(reduced_dna_fasta1);
+ specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
+ BOOST_CHECK_EQUAL(s, specific);
+
+ BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
+ sequence_invalid_load_error);
+ BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
+ sequence_invalid_load_error);
+}
+
+BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
+{
+ std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
+ Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
+ Sequence seqr = seq.rev_comp();
+
+ BOOST_CHECK( seq != seqr );
+ BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
+ BOOST_CHECK_EQUAL( seq.get_sequence(), iupac_symbols );
+}
+
+BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
+{
+ std::string dna_str("AGCTN");
+ Sequence dna_seq(dna_str, Sequence::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());
+}
+
BOOST_AUTO_TEST_CASE( annotation_load )
{
string annot_data = "human\n"
;
string s(100, 'A');
s += "GCTGCTAATT";
- Sequence seq(s);
+ Sequence seq(s, Sequence::reduced_dna_alphabet);
//istringstream annot_stream(annot_data);
seq.parse_annot(annot_data, 0, 0);
"TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
"AAAAA"
"GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
- Sequence seq(s);
+ Sequence seq(s, Sequence::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 seq(s, Sequence::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 szero("", Sequence::reduced_dna_alphabet);
BOOST_CHECK_EQUAL(szero.empty(), true);
BOOST_CHECK_EQUAL(szero, szero);
BOOST_CHECK_EQUAL(szero, "");
- Sequence sclear("AGCT");
+ Sequence sclear("AGCT", Sequence::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 s(seq_string, Sequence::reduced_dna_alphabet);
const Sequence cs(s);
std::string::size_type count = 0;
{
string m("AAAA");
string bogus("AATTGGAA");
- Sequence s1("AAAAGGGGCCCCTTTT");
+ Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
list<motif>::const_iterator motif_i = s1.motifs().begin();
list<motif>::const_iterator motif_end = s1.motifs().end();
"AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
string gc("GCCCCC");
string gga("GGACACCTC");
- Sequence seq(s);
+ Sequence seq(s, Sequence::reduced_dna_alphabet);
std::list<Sequence> query_list;
std::list<string> string_list;
}
}
BOOST_CHECK_EQUAL(seq.annotations().size(), count);
+ const std::list<annot> &a = seq.annotations();
+ for (std::list<annot>::const_iterator annot_i = a.begin();
+ annot_i != a.end();
+ ++annot_i)
+ {
+ int count = annot_i->end - annot_i->begin ;
+ }
}
BOOST_AUTO_TEST_CASE( subseq_annotation_test )
"GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
"CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
"AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
- Sequence seq(s);
+ Sequence seq(s, Sequence::reduced_dna_alphabet);
seq.add_annotation(annot(0, 10, "0-10", "0-10"));
"GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
"CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
"AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
- Sequence seq(s);
+ Sequence seq(s, Sequence::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 seq(s, Sequence::reduced_dna_alphabet);
ostringstream buf;
buf << s;
BOOST_AUTO_TEST_CASE( get_name )
{
- Sequence seq("AAGGCCTT");
+ Sequence seq("AAGGCCTT", Sequence::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 seq(seq_string, Sequence::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 seq(seq_string, Sequence::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 seq(seq_string, Sequence::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 seq1(seq_string, Sequence::reduced_dna_alphabet);
Sequence seq2(seq1);
std::ostringstream oss;
projects / mussa.git / blobdiff