def main():
args = get_args()
#
n_processes = args.n_processes
eventalign_filepath = args.eventalign
summary_filepath = args.summary
chunk_size = args.chunk_size
out_dir = args.out_dir
ensembl_version = args.ensembl
ensembl_species = args.species
readcount_min = args.readcount_min
readcount_max = args.readcount_max
resume = args.resume
genome = args.genome
customised_genome = args.customised_genome
if customised_genome and (None in [
args.reference_name, args.annotation_name, args.gtf_path_or_url,
args.transcript_fasta_paths_or_urls
]):
print(
'If you have your own customised genome not in Ensembl, please provide the following'
)
print('- reference_name')
print('- annotation_name')
print('- gtf_path_or_url')
print('- transcript_fasta_paths_or_urls')
else:
reference_name = args.reference_name
annotation_name = args.annotation_name
gtf_path_or_url = args.gtf_path_or_url
transcript_fasta_paths_or_urls = args.transcript_fasta_paths_or_urls
misc.makedirs(out_dir) #todo: check every level.
# (1) For each read, combine multiple events aligned to the same positions, the results from nanopolish eventalign, into a single event per position.
if not args.skip_eventalign_indexing:
parallel_index(eventalign_filepath, summary_filepath, chunk_size,
out_dir, n_processes, resume)
# (2) Create a .json file, where the info of all reads are stored per position, for modelling.
if genome:
if customised_genome:
db = Genome(
reference_name=reference_name,
annotation_name=annotation_name,
gtf_path_or_url=gtf_path_or_url,
transcript_fasta_paths_or_urls=transcript_fasta_paths_or_urls)
# parse GTF and construct database of genomic features
db.index()
else:
db = EnsemblRelease(
ensembl_version, ensembl_species
) # Default: human reference genome GRCh38 release 91 used in the ont mapping.
parallel_preprocess_gene(eventalign_filepath, db, out_dir, n_processes,
readcount_min, readcount_max, resume)
else:
parallel_preprocess_tx(eventalign_filepath, out_dir, n_processes,
readcount_min, readcount_max, resume)
def setup_create_genome():
global mouse_genome
mouse_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,
protein_fasta_path_or_url=MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH)
mouse_genome.clear_cache()
mouse_genome.index()
def main():
bed = sys.argv[1]
gtf = "Homo_sapiens.GRCh38.90.gtf"
hg38 = Genome(reference_name='GRCh38',
annotation_name='my_genome_features',
gtf_path_or_url=gtf)
hg38.index()
with open(bed) as f:
for line in f:
chromosome, start, end, *left = line.strip().split()
r = Region(chromosome, start, end)
r.get_symbol(hg38)
print(line.strip(), r.gene)
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_mouse_ENSMUSG00000017167():
"""
GTF cropped from ftp://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/
Mus_musculus.GRCm38.81.gtf.gz via:
grep "ENSMUSG00000017167" Mus_musculus.GRCm38.81.gtf
Transcript FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/
fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz via:
grep "ENSMUSG00000017167" Mus_musculus.GRCm38.cdna.all.fa -A 50
Protein FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/fasta/
mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz via:
grep "ENSMUSG00000017167" Mus_musculus.GRCm38.pep.all.fa -A 50
Tested against:
http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000017167
"""
genome = Genome(
reference_name="GRCm38",
gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH,
transcript_fasta_path_or_url=MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH,
protein_fasta_path_or_url=MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH,
)
genome.install()
genes_cntnap1 = genome.genes_by_name("Cntnap1")
eq_(len(genes_cntnap1), 1)
gene_cntnap1 = genes_cntnap1[0]
transcripts_cntnap1 = gene_cntnap1.transcripts
eq_(len(transcripts_cntnap1), 2)
transcripts_coding_cntnap1 = [
transcript for transcript in transcripts_cntnap1 if transcript.biotype == "protein_coding"
]
eq_(len(transcripts_coding_cntnap1), 1)
transcript_cntnap1 = transcripts_coding_cntnap1[0]
eq_(
transcript_cntnap1.sequence[:120],
(
"GAGAGAAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA"
"GAGAGAGAGAGATTGGGGGTAGGAGAGAGGGAAGGGTGGATAAGGACGGAAAAAAGCTTT"
),
)
eq_(
transcript_cntnap1.protein_sequence[:120],
(
"MMSLRLFSILLATVVSGAWGWGYYGCNEELVGPLYARSLGASSYYGLFTTARFARLHGIS"
"GWSPRIGDPNPWLQIDLMKKHRIRAVATQGAFNSWDWVTRYMLLYGDRVDSWTPFYQKGH"
),
)
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 = 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_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 get_gene_ids_of_transcript_id(transcript_id: str,
ensembl: pyensembl.Genome,
raise_on_error: bool = False):
""" Extract all gene ids associated with the given transcript.
Parameters
----------
transcript_id: string
The transcript identifier
ensembl: pyensembl.Genome
The annotations
raise_on_error: bool
Whether to raise an exception if the transcript id is not found in the
annotations database
Returns
-------
transcript_gene_id_df: pd.DataFrame
A dataframe with columns to map between transcripts and genes. Its
columns are:
transcript_id
gene_id
"""
try:
gene_name = ensembl.gene_name_of_transcript_id(transcript_id)
gene_ids = ensembl.gene_ids_of_gene_name(gene_name)
except ValueError as ve:
msg = ("['pyensembl_utils.get_gene_ids_of_transcript_id]: could not "
"find transcript id in database: {}".format(transcript_id))
if raise_on_error:
raise ValueError(msg) from ve
else:
logger.warning(msg)
return None
ret = [{'transcript_id': transcript_id, 'gene_id': g} for g in gene_ids]
return ret
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_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_protein_fasta_only():
genome = Genome(reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
protein_fasta_paths_or_urls=[
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 annotate_xcnv():
with open(r'Z:\gatk\data\DATA.xcnv','r') as f1:
DATA_xcnv = list(csv.reader(f1, delimiter='\t'))
data = Genome(
reference_name='GRCh37',
annotation_name='GRCh37',
gtf_path_or_url=r'Z:\gatk\reference\Homo_sapiens.GRCh37.75.gtf')
data.index()
with open(r'./VPv1_exons_positive','r') as f2:
exons_positive = list(csv.reader(f2, delimiter='\t'))
with open(r'./VPv1_exons_negative_flipped','r') as f3:
exons_negative = list(csv.reader(f3, delimiter='\t'))
for index, row in enumerate(DATA_xcnv[1:]):
chr = str(row[4])
chr_start = int(re.split(':|-', row[2])[1])+1
CNV_start = data.gene_names_at_locus(contig=chr, position=int(chr_start))
try:
chr_end = int(re.split(':|-', row[2])[2])
except IndexError:
chr_end = chr_start
CNV_end = data.gene_names_at_locus(contig=chr, position=chr_end)
for row in exons_positive:
if chr == row[0][3:]:
if chr_start >= int(row[1]) and chr_start <= int(row[2]):
match = row[3].split('_')
CNV_start.append(match[0] + '_' + match[1] + ' ' + match[2] + ' ' + str(int(match[3])+1))
if chr_end >= int(row[1]) and chr_end <= int(row[2]):
match = row[3].split('_')
CNV_end.append(match[0] + '_' + match[1] + ' ' + match[2] + ' ' + str(int(match[3])+1))
for row in exons_negative:
if chr == row[0][3:]:
if chr_start >= int(row[1]) and chr_start <= int(row[2]):
match = row[3].split('_')
CNV_start.append(match[0] + '_' + match[1] + ' ' + match[2] + ' ' + match[3])
if chr_end >= int(row[1]) and chr_end <= int(row[2]):
match = row[3].split('_')
CNV_end.append(match[0] + '_' + match[1] + ' ' + match[2] + ' ' + match[3])
DATA_xcnv[index+1].append(CNV_start)
DATA_xcnv[index+1].append(CNV_end)
DATA_xcnv[0] += ['CNV_START', 'CNV_END']
with open(r'Z:\gatk\data\DATA_annotated.xcnv','w',newline='') as fo:
writer = csv.writer(fo, delimiter='\t')
for row in DATA_xcnv:
writer.writerow(row)
return
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_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")
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 get_gene_name_of_transcript_id(transcript_id: str,
ensembl: pyensembl.Genome,
raise_on_error: bool = False):
""" Extract the gene name (symbol) for this transcript id.
The difference between this function and gene_name_of_transcript_id is that
this function will (optionally) issue a warning rather than raise an
exception for transcript ids not in the database.
Parameters
----------
transcript_id: string
The transcript identifier (e.g., "ENSMUST00000035194")
ensembl: pyensembl.Genome
The annotation database
raise_on_error: bool
Whether to issue a warning (False) or raise a ValueError (True) if the
transcript identifier is not in the annotation database
Returns
-------
gene_name: string
The gene name (also called gene symbol, e.g., "Mapkapk3")
--- OR ---
None, if the transcript id is not in the database of annotations
"""
gene_name = None
try:
gene_name = ensembl.gene_name_of_transcript_id(transcript_id)
except ValueError as ve:
msg = ("[pyensembl_utils.get_gene_name_of_transcript_id]: could not "
"find match for transcript id: {}".format(transcript_id))
if raise_on_error:
raise ValueError(msg) from ve
else:
logger.warning(msg)
return gene_name
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_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)
SERVER = "ftp://ftp.ensembl.org"
MOUSE_GTF_PATH = \
SERVER + "/pub/release-%d/gtf/mus_musculus/Mus_musculus.GRCm38.%d.gtf.gz" % (
MOUSE_ENSEMBL_RELEASE, MOUSE_ENSEMBL_RELEASE)
MOUSE_TRANSCRIPT_FASTA_PATH = \
SERVER + "/pub/release-%d/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz"
MOUSE_PROTEIN_FASTA_PATH = \
SERVER + "/pub/release-%d/fasta/mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz" % (
MOUSE_ENSEMBL_RELEASE)
MOUSE_VCF = data_path("mouse_vcf_dbsnp_chr1_partial.vcf")
explicit_url_genome = Genome(
reference_name="GRCm38",
annotation_name="ensembl",
annotation_version=MOUSE_ENSEMBL_RELEASE,
gtf_path_or_url=MOUSE_GTF_PATH,
transcript_fasta_paths_or_urls=[MOUSE_TRANSCRIPT_FASTA_PATH],
protein_fasta_paths_or_urls=[MOUSE_PROTEIN_FASTA_PATH])
ensembl_mouse_genome = EnsemblRelease(MOUSE_ENSEMBL_RELEASE, species="mouse")
def test_load_vcf_mouse_with_explicit_urls():
variants = load_vcf(MOUSE_VCF, genome=explicit_url_genome)
eq_(len(variants), 217)
def test_load_vcf_mouse_with_ensembl_release():
variants = load_vcf(MOUSE_VCF, genome=ensembl_mouse_genome)
eq_(len(variants), 217)
# Protein FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/fasta/
# mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz via:
# grep "ENSMUSG00000017167" Mus_musculus.GRCm38.pep.all.fa -A 50
# Tested against:
# http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000017167
MOUSE_ENSMUSG00000017167_PATH = data_path(
"mouse.ensembl.81.partial.ENSMUSG00000017167.gtf")
MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH = data_path(
"mouse.ensembl.81.partial.ENSMUSG00000017167.fa")
MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH = data_path(
"mouse.ensembl.81.partial.ENSMUSG00000017167.pep")
custom_mouse_genome_grcm38_subset = 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,
protein_fasta_path_or_url=MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH)
def setup_init_custom_mouse_genome():
"""
If a unit test needs to start from a cleared cache, add this to the test
setup.
"""
custom_mouse_genome_grcm38_subset.clear_cache()
custom_mouse_genome_grcm38_subset.index()
def test_custom_genome_to_dict():
reconstructed = Genome.from_dict(
custom_mouse_genome_grcm38_subset.to_dict())
eq_(custom_mouse_genome_grcm38_subset, reconstructed)
def load_genome(file):
global data
data = Genome(reference_name='GRCh38',
annotation_name='ENSEMBL',
gtf_path_or_url=file)
data.index()
def test_custom_genome_to_dict():
reconstructed = Genome.from_dict(custom_mouse_genome_grcm38_subset.to_dict())
eq_(custom_mouse_genome_grcm38_subset, reconstructed)
def test_custom_genome_to_json():
json = custom_mouse_genome_grcm38_subset.to_json()
reconstructed = Genome.from_json(json)
eq_(custom_mouse_genome_grcm38_subset, reconstructed)
def test_custom_genome_to_json():
json = custom_mouse_genome_grcm38_subset.to_json()
reconstructed = Genome.from_json(json)
eq_(custom_mouse_genome_grcm38_subset, reconstructed)
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_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)
