+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 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, reduced_dna_alphabet);
+ BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
+ reduced_dna_alphabet),
+ sequence_invalid_load_error);
+ BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
+ reduced_dna_alphabet),
+ sequence_invalid_load_error);
+ BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
+ 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, reduced_rna_alphabet);
+ BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
+ reduced_rna_alphabet),
+ sequence_invalid_load_error);
+ BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
+ reduced_rna_alphabet),
+ sequence_invalid_load_error);
+ BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
+ 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, reduced_nucleic_alphabet);
+ BOOST_CHECK_EQUAL(s, specific);
+
+ s.load_fasta(reduced_dna_fasta1);
+ specific.load_fasta(reduced_dna_fasta2, 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_load_multiple_sequences_one_fasta )
+{
+ std::string fasta_file(
+ ">gi|10129974|gb|AF188002.1|AF188002\n"
+ "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
+ ">gi|180579|gb|M21487.1|HUMCKMM1\n"
+ "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
+ ">gi|1621|emb|X55146.1|OCMCK1\n"
+ "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
+ );
+ istringstream seq1_file(fasta_file);
+ Sequence seq1;
+ seq1.load_fasta(seq1_file, 1, 0, 0);
+ BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
+
+ istringstream seq2_file(fasta_file);
+ Sequence seq2;
+ seq2.load_fasta(seq2_file, 2, 0, 0);
+ BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
+
+ istringstream seq3_file(fasta_file);
+ Sequence seq3;
+ seq3.load_fasta(seq3_file, 3, 0, 0);
+ BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
+}
+
+BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
+{
+ std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
+ Sequence seq(iupac_symbols, nucleic_alphabet);
+ Sequence seqr = seq.rev_comp();
+
+ BOOST_CHECK( seq != seqr );
+ BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
+ // forcing sequence to upper case
+ BOOST_CHECK_EQUAL( seq.get_sequence(),
+ boost::algorithm::to_upper_copy(iupac_symbols) );
+}
+
+BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
+{
+ std::string dna_str("AGCTN");
+ 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, 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, reduced_dna_alphabet);
+ Sequence subseq = seq.subseq(8,4);
+ BOOST_CHECK_EQUAL( subseq, "AAGG");
+ Sequence rev_subseq = subseq.rev_comp();
+ BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
+ BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
+}
+
+BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
+{
+ std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
+ std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
+ Sequence seq(dna_str);
+ std::string seq_reversed(seq.rbegin(), seq.rend());
+ BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
+
+ std::string substr = dna_str.substr(8,4);
+ Sequence subseq = seq.subseq(8,4);
+ BOOST_CHECK_EQUAL(substr, subseq);
+
+ std::string substr_reversed(substr.rbegin(), substr.rend());
+ std::string subseq_reversed(subseq.rbegin(), subseq.rend());
+ BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
+}
+
+BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
+{
+ // so what happens with reverse interators when we have no sequence?
+ Sequence seq1;
+ Sequence seq2;
+ Sequence seq3("AGCT");
+
+ // all the empty sequences should have equal iterators
+ BOOST_CHECK(seq1.rbegin() == seq1.rend());
+ BOOST_CHECK(seq1.rbegin() == seq2.rend());
+
+ // none of the seq1 iterators should equal any of the seq3 iterators
+ BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
+ BOOST_CHECK(seq1.rbegin() != seq3.rend());
+ BOOST_CHECK(seq1.rend() != seq3.rbegin());
+ BOOST_CHECK(seq1.rend() != seq3.rend());
+
+ // seq3 iterators should work
+ BOOST_CHECK(seq3.rbegin() != seq3.rend());
+
+}
+
+BOOST_AUTO_TEST_CASE( annotation_load )
+{
+ string annot_data = "human\n"
+ "0 10 name type\n" //0
+ "10 20 myf7\n" //1
+ "20 30 myod\n" //2
+ "50\t55 anothername\n" //3
+ "60 50 backward\n" //4
+ ">ident3 asdf\n" //7 (as these are added last)
+ "GCT\n"
+ "gCTn\n"
+ "75\t90\tname2\ttype2\n" //5
+ "100 120 name-asdf type!@#$%\n" //6
+ ;
+ string s(100, 'A');
+ s += "GCTGCTAATT";
+ Sequence seq(s, reduced_dna_alphabet);
+
+ //istringstream annot_stream(annot_data);
+ seq.parse_annot(annot_data, 0, 0);
+ SeqSpanRefList annots_list(seq.annotations());
+ std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
+ BOOST_REQUIRE_EQUAL( annots.size(), 8);
+ BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
+ BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
+ BOOST_REQUIRE( annots[0]->annotations() );
+ BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
+ BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "name");
+ BOOST_REQUIRE( annots[1]->annotations() );
+ BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "myf7");
+ BOOST_REQUIRE( annots[2]->annotations() );
+ BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "myod");
+ BOOST_REQUIRE( annots[3]->annotations() );
+ BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "anothername");
+ BOOST_REQUIRE( annots[4]->annotations() );
+ BOOST_CHECK_EQUAL( annots[4]->annotations()->name(), "backward");
+ BOOST_REQUIRE( annots[5]->annotations() );
+ BOOST_CHECK_EQUAL( annots[5]->annotations()->name(), "name2");
+ BOOST_CHECK_EQUAL( annots[5]->start(), 75);
+ BOOST_CHECK_EQUAL( annots[5]->stop(), 90);
+ BOOST_CHECK_EQUAL( annots[6]->start(), 100);
+ BOOST_CHECK_EQUAL( annots[6]->stop(), 110);
+ BOOST_REQUIRE( annots[6]->annotations() );
+ BOOST_CHECK_EQUAL( annots[6]->annotations()->name(), "name-asdf");
+ BOOST_CHECK_EQUAL( annots[6]->annotations()->get("type"), "type!@#$%");
+ // sequence defined annotations will always be after the
+ // absolute positions
+ BOOST_REQUIRE( annots[7]->annotations() );
+ BOOST_CHECK_EQUAL( annots[7]->annotations()->name(), "ident3 asdf");
+ BOOST_CHECK_EQUAL( annots[7]->start(), 100);
+ BOOST_CHECK_EQUAL( annots[7]->stop(), 107);
+
+ //BOOST_CHECK_EQUAL( annots
+}
+
+BOOST_AUTO_TEST_CASE( annotation_broken_load )
+{
+ string annot_data = "human\n"
+ "0 10 name type\n"
+ "blah60 50 backward\n"
+ ">ident3 asdf\n"
+ "GCT\n"
+ "gCTn\n"
+ ;
+ string s(100, 'A');
+ s += "GCTGCTAATT";
+ 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);
+ }
+
+BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
+{
+ // this actually is basically what's returned by UCSC
+ // (well actually with some of the sequence and copies of fasta blocks
+ // removed to make the example shorter
+ string annot_data = "\n"
+ "<PRE>\n"
+ ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
+ "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
+ ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
+ "GGTGGAGACGACCTGGACCCTAACTACGT\n"
+ "</PRE>\n"
+ "\n"
+ "</BODY>\n"
+ "</HTML>\n"
+ ;
+
+ string s =
+ "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
+ "AAAAA"
+ "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
+ Sequence seq(s, reduced_dna_alphabet);
+ seq.parse_annot(annot_data);
+ SeqSpanRefList annots(seq.annotations());
+ BOOST_CHECK_EQUAL( annots.size(), 2);
+}
+
+BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
+{
+ string annot_data = "0 10 name type\n"
+ "10 20 myf7\n"
+ "20 30 myod\n"
+ "50\t55 anothername\n"
+ "60 50 backward\n"
+ ">ident3 asdf\n"
+ "GCT\n"
+ "gCTn\n"
+ "75\t90\tname2\ttype2\n"
+ "100 120 name-asdf type!@#$%\n"
+ ;
+ string s(100, 'A');
+ s += "GCTGCTAATT";
+ Sequence seq(s, reduced_dna_alphabet);
+
+ //istringstream annot_stream(annot_data);
+ seq.parse_annot(annot_data, 0, 0);
+ SeqSpanRefList annots_list(seq.annotations());
+ std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
+ BOOST_REQUIRE_EQUAL( annots.size(), 8);
+ BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
+ BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
+ BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
+}
+
+// when we do a subsequence (or something that calls copy_children)
+// the annotations need to be updated to have the right parent
+BOOST_AUTO_TEST_CASE( update_annotations_seqref )
+{
+ Sequence s1("AAAAGGGG");
+ s1.add_annotation("A", "A", 0, 4);
+ BOOST_CHECK_EQUAL(s1.annotations().size(), 1);
+ BOOST_CHECK_EQUAL(s1.seqspan(), s1.annotations().front()->parent() );
+
+ Sequence subseq1(s1.subseq(2,4));
+ BOOST_CHECK_EQUAL(subseq1.annotations().size(), 1);
+ BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStart(), 0 );
+ BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStop(), 2 );
+ BOOST_CHECK_EQUAL(subseq1.seqspan(), subseq1.annotations().front()->parent() );
+}
+
+// ticket:83 when you try to load a sequence from a file that doesn't
+// have fasta headers it crashes.
+BOOST_AUTO_TEST_CASE( sequence_past_end )
+{
+ fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
+ seq_path /= "misformated_seq.fa";
+ Sequence s;
+ BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
+}
+