def test_transcript_fasta_only():
genome = Genome(
reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
transcript_fasta_path_or_url=MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH)
genome.index()
eq_(2, len(genome.transcript_sequences.fasta_dictionary))
with assert_raises(ValueError) as cm:
genome.genes()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.gene_ids()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.gene_ids_of_gene_name("test")
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.transcript_names()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.protein_sequence("test")
no_protein_(cm)
def test_transcript_fasta_only():
genome = Genome(reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
transcript_fasta_paths_or_urls=[
MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH
])
genome.index()
eq_(2, len(genome.transcript_sequences.fasta_dictionary))
with assert_raises(ValueError) as cm:
genome.genes()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.gene_ids()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.gene_ids_of_gene_name("test")
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.transcript_names()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.protein_sequence("test")
no_protein_(cm)
def test_protein_fasta_only():
genome = Genome(
reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
protein_fasta_path_or_url=MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH)
genome.index()
eq_(4, len(genome.protein_sequences.fasta_dictionary))
with assert_raises(ValueError) as cm:
genome.genes()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome.transcript_sequence("test")
no_transcript_(cm)
def test_ucsc_refseq_genome():
"""
Test Genome object with a small RefSeq GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
with TemporaryDirectory() as tmpdir:
genome = Genome(reference_name="GRCh38",
annotation_name="ucsc_test",
gtf_path_or_url=UCSC_REFSEQ_PATH,
cache_directory_path=tmpdir)
genome.index()
genes = genome.genes()
for gene in genes:
assert gene.id, \
"Gene with missing ID in %s" % (genome.gtf.dataframe(),)
assert len(genes) == 2, \
"Expected 2 genes, got %d: %s" % (
len(genes), genes)
transcripts = genome.transcripts()
for transcript in transcripts:
assert transcript.id, \
"Transcript with missing ID in %s" % (genome.gtf.dataframe(),)
assert len(transcripts) == 2, \
"Expected 2 transcripts, got %d: %s" % (
len(transcripts), transcripts)
genes_at_locus = genome.genes_at_locus(1, 67092176)
assert len(genes_at_locus) == 2, \
"Expected 2 genes at locus chr1:67092176, got %d: %s" % (
len(genes_at_locus), genes_at_locus)
ids = set([gene.id for gene in genes_at_locus])
eq_(set(["NM_001276352", "NR_075077"]), ids)
def test_protein_fasta_only():
genome_only_proteins = Genome(
reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
protein_fasta_paths_or_urls=[MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH])
genome_only_proteins.index()
eq_(4, len(genome_only_proteins.protein_sequences.fasta_dictionary))
with assert_raises(ValueError) as cm:
genome_only_proteins.genes()
no_gtf_(cm)
with assert_raises(ValueError) as cm:
genome_only_proteins.transcript_sequence("DOES_NOT_EXIST")
no_transcript_(cm)
def test_ucsc_refseq_genome():
"""
Test Genome object with a small RefSeq GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
with TemporaryDirectory() as tmpdir:
genome = Genome(
reference_name="GRCh38",
annotation_name="ucsc_test",
gtf_path_or_url=UCSC_REFSEQ_PATH,
cache_directory_path=tmpdir)
genome.index()
genes = genome.genes()
for gene in genes:
assert gene.id, \
"Gene with missing ID in %s" % (genome.gtf.dataframe(),)
assert len(genes) == 2, \
"Expected 2 genes, got %d: %s" % (
len(genes), genes)
transcripts = genome.transcripts()
for transcript in transcripts:
assert transcript.id, \
"Transcript with missing ID in %s" % (genome.gtf.dataframe(),)
assert len(transcripts) == 2, \
"Expected 2 transcripts, got %d: %s" % (
len(transcripts), transcripts)
genes_at_locus = genome.genes_at_locus(1, 67092176)
assert len(genes_at_locus) == 2, \
"Expected 2 genes at locus chr1:67092176, got %d: %s" % (
len(genes_at_locus), genes_at_locus)
ids = set([gene.id for gene in genes_at_locus])
eq_(set(["NM_001276352", "NR_075077"]), ids)
def test_ucsc_gencode_genome():
"""
Testing with a small GENCODE GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
with TemporaryDirectory() as tmpdir:
genome = Genome(
reference_name="GRCh38",
annotation_name="ucsc_test",
gtf_path_or_url=UCSC_GENCODE_PATH,
cache_directory_path=tmpdir,
)
genome.index()
genes = genome.genes()
for gene in genes:
assert gene.id, "Gene with missing ID in %s" % (genome.gtf.dataframe(),)
assert len(genes) == 7, "Expected 7 genes, got %d: %s" % (len(genes), genes)
transcripts = genome.transcripts()
for transcript in transcripts:
assert transcript.id, "Transcript with missing ID in %s" % (genome.gtf.dataframe(),)
assert len(transcripts) == 7, "Expected 7 transcripts, got %d: %s" % (len(transcripts), transcripts)
gene_uc001aak4 = genome.gene_by_id("uc001aak.4")
eq_(gene_uc001aak4.id, "uc001aak.4")
eq_(gene_uc001aak4.name, None)
eq_(gene_uc001aak4.biotype, None)
gene_1_17369 = genome.genes_at_locus(1, 17369)
eq_(gene_1_17369[0].id, "uc031tla.1")
transcript_1_30564 = genome.transcripts_at_locus(1, 30564)
eq_(transcript_1_30564[0].id, "uc057aty.1")
def test_ucsc_refseq():
"""
Testing with a small RefSeq GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
genome = Genome("GRCh38", gtf_path_or_url=UCSC_REFSEQ_PATH)
genome.install()
eq_(len(genome.genes()), 2)
eq_(len(genome.transcripts()), 2)
genes_at_locus = genome.genes_at_locus(1, 67092176)
eq_(len(genes_at_locus), 2)
ids = set([gene.id for gene in genes_at_locus])
eq_(set(["NM_001276352", "NR_075077"]), ids)
def test_gtf_only():
genome = Genome(
reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH)
genome.index()
eq_(1, len(genome.genes()))
with assert_raises(ValueError) as cm:
genome.transcript_sequence("test")
no_transcript_(cm)
with assert_raises(ValueError) as cm:
genome.protein_sequence("test")
no_protein_(cm)
def test_gtf_transcript_only():
genome = Genome(
reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH,
transcript_fasta_path_or_url=MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH)
genome.index()
eq_(1, len(genome.genes()))
transcript = genome.transcripts()[0]
ok_(transcript.sequence)
with assert_raises(ValueError) as cm:
transcript.protein_sequence
no_protein_(cm)
def test_gtf_transcript_only():
genome = Genome(reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH,
transcript_fasta_path_or_url=
MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH)
genome.index()
eq_(1, len(genome.genes()))
transcript = genome.transcripts()[0]
ok_(transcript.sequence)
with assert_raises(ValueError) as cm:
transcript.protein_sequence
no_protein_(cm)
def test_gtf_only():
genome_only_gtf = Genome(reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH)
genome_only_gtf.index()
eq_(1, len(genome_only_gtf.genes()))
with assert_raises(ValueError) as cm:
genome_only_gtf.transcript_sequence("DOES_NOT_EXIST")
no_transcript_(cm)
with assert_raises(ValueError) as cm:
genome_only_gtf.protein_sequence("genome_only_gtf")
no_protein_(cm)
def test_ucsc_gencode():
"""
Testing with a small GENCODE GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
genome = Genome("GRCh38", gtf_path_or_url=UCSC_GENCODE_PATH)
genome.install()
eq_(len(genome.genes()), 7)
eq_(len(genome.transcripts()), 7)
gene_uc001aak4 = genome.gene_by_id("uc001aak.4")
eq_(gene_uc001aak4.id, "uc001aak.4")
eq_(gene_uc001aak4.name, None)
eq_(gene_uc001aak4.biotype, None)
gene_1_17369 = genome.genes_at_locus(1, 17369)
eq_(gene_1_17369[0].id, "uc031tla.1")
transcript_1_30564 = genome.transcripts_at_locus(1, 30564)
eq_(transcript_1_30564[0].id, "uc057aty.1")
def test_ucsc_gencode_genome():
"""
Testing with a small GENCODE GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
with TemporaryDirectory() as tmpdir:
genome = Genome(
reference_name="GRCh38",
annotation_name="ucsc_test",
gtf_path_or_url=UCSC_GENCODE_PATH,
cache_directory_path=tmpdir)
genome.index()
genes = genome.genes()
for gene in genes:
assert gene.id, \
"Gene with missing ID in %s" % (genome.gtf.dataframe(),)
assert len(genes) == 7, \
"Expected 7 genes, got %d: %s" % (
len(genes), genes)
transcripts = genome.transcripts()
for transcript in transcripts:
assert transcript.id, \
"Transcript with missing ID in %s" % (genome.gtf.dataframe(),)
assert len(transcripts) == 7, \
"Expected 7 transcripts, got %d: %s" % (
len(transcripts), transcripts)
gene_uc001aak4 = genome.gene_by_id("uc001aak.4")
eq_(gene_uc001aak4.id, "uc001aak.4")
eq_(gene_uc001aak4.name, None)
eq_(gene_uc001aak4.biotype, None)
gene_1_17369 = genome.genes_at_locus("chr1", 17369)
eq_(gene_1_17369[0].id, "uc031tla.1")
transcript_1_30564 = genome.transcripts_at_locus("chr1", 30564)
eq_(transcript_1_30564[0].id, "uc057aty.1")
