from pyensembl import Locus, cached_release from nose.tools import eq_, assert_not_equal, assert_greater from .common import test_ensembl_releases from .data import ( FOXP3_001_transcript_id, CTNNBIP1_004_transcript_id, CTNNBIP1_004_UTR5, CTNNBIP1_004_UTR3, CTNNBIP1_004_CDS, CTNNBIP1_004_locus, CTTNNIP1_004_exon_lengths, CTTNNIP1_004_exon_ids, EGFR_001_protein_sequence, TP53_gene_id, ) ensembl77 = cached_release(77) def test_transcript_start_codon(): """ test_transcript_start_codon : Check that fields Transcript (for transcript named CTNNBIP1-004) matches known values. """ CTNNBIP1_004_transcript = ensembl77.transcript_by_id( CTNNBIP1_004_transcript_id) assert Locus.__eq__(CTNNBIP1_004_transcript, CTNNBIP1_004_locus), \ "Expected locus %s but got %s" % ( CTNNBIP1_004_locus, Locus.__str__(CTNNBIP1_004_transcript)) start_offsets = CTNNBIP1_004_transcript.start_codon_spliced_offsets assert len(start_offsets) == 3, \ "Wrong length for start codon: %d (%s)" % ( len(start_offsets), start_offsets) assert all(isinstance(i, int) for i in start_offsets), \ "Wrong type %s for beginning start codon offset" % ( [type(i) for i in start_offsets],) expected_start_codon_offset = len(CTNNBIP1_004_UTR5) start_codon_offset = min(start_offsets) assert start_codon_offset == expected_start_codon_offset, \ "Incorrect start codon offset, expected %d but got %d" % ( expected_start_codon_offset, start_codon_offset) def test_transcript_exons(): """ test_transcript_exons : Ensure that properties of CTTNBIP1-004's Exon objects match known values. """ transcript = ensembl77.transcript_by_id(CTNNBIP1_004_transcript_id) exons = transcript.exons assert isinstance(exons, list), \ "Expected list of Exon objects, got %s : %s" % (exons, type(exons)) # CTTNBIP1-004 has 5 exons assert len(exons) == len(CTTNNIP1_004_exon_lengths), \ "Expected %d exons but got %d" % ( len(CTTNNIP1_004_exon_lengths), len(exons)) for i, exon in enumerate(exons): expected_id = CTTNNIP1_004_exon_ids[i] assert exon.id == expected_id, \ "Expected exon #%d of %s to have ID %s but got %s" % ( i + 1, transcript, expected_id, exon.id) expected_length = CTTNNIP1_004_exon_lengths[i] assert len(exon) == expected_length, \ "Expected exon #%d of %s (%s) to have length %d but got %d" % ( i + 1, transcript, exon, expected_length, len(exon)) # not testing NCBI/Release 54 since I just discovered that ensembl54 # feature='transcript' entries don't have a gene ID. # TODO: Add gene_id patching to gtf_parsing, add ensembl54 to the list # below @test_ensembl_releases(75, 77) def test_sequence_parts(genome): # Ensure that the UTRs and coding sequence can be # combined to make the full transcript. transcript = genome.transcript_by_id(FOXP3_001_transcript_id) # The combined lengths of the upstream untranslated region, # coding sequence, and downstream untranslated region full_sequence = transcript.sequence assert_greater(len(full_sequence), 0) utr5 = transcript.five_prime_utr_sequence assert_greater(len(utr5), 0) cds = transcript.coding_sequence assert_greater(len(cds), 0) utr3 = transcript.three_prime_utr_sequence assert_greater(len(utr3), 0) # need to use `seq` property of Sequence objects to get underlying # strings which can be concatenated and compared combined_string = utr5 + cds + utr3 combined_sequence_length = len(combined_string) # make sure length property of transcript matches the sequence length eq_( combined_sequence_length, len(transcript), "Length 5' UTR(%dnt) + CDS(%dnt) + 3' UTR(%d) = %d, expected %d" % ( len(utr5), len(cds), len(utr3), combined_sequence_length, len(transcript))) eq_( combined_string, full_sequence, "Expected FOXP3-001 sequence:\n%s\n\n5' UTR + CDS + 3' UTR:\n%s" % ( full_sequence, combined_string)) def test_transcript_utr5_sequence_CTNNIP1_004(): transcript = ensembl77.transcript_by_id(CTNNBIP1_004_transcript_id) utr5 = transcript.five_prime_utr_sequence expected_utr5_length = len(CTNNBIP1_004_UTR5) eq_(len(utr5), expected_utr5_length, "Expected 5' UTR length %d, got %d" % ( expected_utr5_length, len(utr5))) eq_(utr5, CTNNBIP1_004_UTR5) def test_transcript_utr3_sequence_CTNNIP1_004(): transcript = ensembl77.transcript_by_id(CTNNBIP1_004_transcript_id) utr3 = transcript.three_prime_utr_sequence expected_utr3_length = len(CTNNBIP1_004_UTR3) eq_(len(utr3), expected_utr3_length, "Expected 3' UTR length %d, got %d" % ( expected_utr3_length, len(utr3))) eq_(utr3, CTNNBIP1_004_UTR3) def test_transcript_cds_CTNNIP1_004(): transcript = ensembl77.transcript_by_id(CTNNBIP1_004_transcript_id) cds = transcript.coding_sequence expected_cds_length = len(CTNNBIP1_004_CDS) eq_( len(cds), expected_cds_length, "Expected CDS length %d, got %d" % (expected_cds_length, len(cds))) eq_(cds, CTNNBIP1_004_CDS) @test_ensembl_releases() def test_equal_transcripts(genome): t1 = genome.genes_by_name("TP53")[0].transcripts[0] # get an identical gene t2 = genome.transcript_by_id(t1.id) eq_(t1, t2) eq_(hash(t1), hash(t2)) @test_ensembl_releases() def test_not_equal_transcripts(genome): t1 = genome.genes_by_name("MUC1")[0].transcripts[0] t2 = genome.genes_by_name("BRCA1")[0].transcripts[0] assert_not_equal(t1, t2) def test_protein_id(): transcript = ensembl77.transcripts_by_name("EGFR-001")[0] eq_(transcript.protein_id, "ENSP00000275493") def test_protein_protein_sequence(): transcript = ensembl77.transcripts_by_name("EGFR-001")[0] eq_(transcript.protein_sequence, EGFR_001_protein_sequence) def test_transcript_gene_should_match_parent_gene(): gene = ensembl77.gene_by_id(TP53_gene_id) for transcript in gene.transcripts: eq_(transcript.gene, gene) @test_ensembl_releases() def test_BRCA1_201_has_protein_coding_biotype(genome): transcript = genome.transcripts_by_name("BRCA1-201")[0] assert transcript.is_protein_coding, \ "Expected BRCA1-201 transcript %s to have a protein coding biotype in %s" % ( transcript, genome) eq_(transcript.biotype, "protein_coding")