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from pyensembl import Locus, cached_release
from .common import eq_, neq_, gt_, run_multiple_genomes
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
@run_multiple_genomes(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
gt_(len(full_sequence), 0)
utr5 = transcript.five_prime_utr_sequence
gt_(len(utr5), 0)
cds = transcript.coding_sequence
gt_(len(cds), 0)
utr3 = transcript.three_prime_utr_sequence
gt_(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)
@run_multiple_genomes()
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))
@run_multiple_genomes()
def test_not_equal_transcripts(genome):
t1 = genome.genes_by_name("MUC1")[0].transcripts[0]
t2 = genome.genes_by_name("BRCA1")[0].transcripts[0]
neq_(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)
@run_multiple_genomes()
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")
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