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 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 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_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 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 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 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_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_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_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_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 load_genome(file):
global data
data = Genome(reference_name='GRCh38',
annotation_name='ENSEMBL',
gtf_path_or_url=file)
data.index()
