def random_variants(count,
ensembl_release=MAX_ENSEMBL_RELEASE,
deletions=True,
insertions=True,
random_seed=None):
"""
Generate a VariantCollection with random variants that overlap
at least one complete coding transcript.
"""
rng = random.Random(random_seed)
ensembl = EnsemblRelease(ensembl_release)
if ensembl_release in _transcript_ids_cache:
transcript_ids = _transcript_ids_cache[ensembl_release]
else:
transcript_ids = ensembl.transcript_ids()
_transcript_ids_cache[ensembl_release] = transcript_ids
variants = []
while len(variants) < count:
transcript_id = rng.choice(transcript_ids)
transcript = ensembl.transcript_by_id(transcript_id)
if not transcript.complete:
continue
exon = rng.choice(transcript.exons)
base1_genomic_position = rng.randint(exon.start, exon.end)
transcript_offset = transcript.spliced_offset(base1_genomic_position)
try:
seq = transcript.sequence
except ValueError as e:
logging.warn(e)
# can't get sequence for non-coding transcripts
continue
ref = str(seq[transcript_offset])
if transcript.on_backward_strand:
ref = reverse_complement(ref)
alt_nucleotides = [x for x in STANDARD_NUCLEOTIDES if x != ref]
if insertions:
nucleotide_pairs = [
x + y for x in STANDARD_NUCLEOTIDES
for y in STANDARD_NUCLEOTIDES
]
alt_nucleotides.extend(nucleotide_pairs)
if deletions:
alt_nucleotides.append("")
alt = rng.choice(alt_nucleotides)
variant = Variant(transcript.contig,
base1_genomic_position,
ref=ref,
alt=alt,
ensembl=ensembl)
variants.append(variant)
return VariantCollection(variants)
def random_variants(count,
ensembl_release=MAX_ENSEMBL_RELEASE,
deletions=True,
insertions=True,
random_seed=None):
"""
Generate a VariantCollection with random variants that overlap
at least one complete coding transcript.
"""
rng = random.Random(random_seed)
ensembl = EnsemblRelease(ensembl_release)
if ensembl_release in _transcript_ids_cache:
transcript_ids = _transcript_ids_cache[ensembl_release]
else:
transcript_ids = ensembl.transcript_ids()
_transcript_ids_cache[ensembl_release] = transcript_ids
variants = []
# we should finish way before this loop is over but just in case
# something is wrong with PyEnsembl we want to avoid an infinite loop
for _ in range(count * 100):
if len(variants) < count:
transcript_id = rng.choice(transcript_ids)
transcript = ensembl.transcript_by_id(transcript_id)
if not transcript.complete:
continue
exon = rng.choice(transcript.exons)
base1_genomic_position = rng.randint(exon.start, exon.end)
transcript_offset = transcript.spliced_offset(
base1_genomic_position)
seq = transcript.sequence
ref = str(seq[transcript_offset])
if transcript.on_backward_strand:
ref = reverse_complement(ref)
alt_nucleotides = [x for x in STANDARD_NUCLEOTIDES if x != ref]
if insertions:
nucleotide_pairs = [
x + y for x in STANDARD_NUCLEOTIDES
for y in STANDARD_NUCLEOTIDES
]
alt_nucleotides.extend(nucleotide_pairs)
if deletions:
alt_nucleotides.append("")
alt = rng.choice(alt_nucleotides)
variant = Variant(transcript.contig,
base1_genomic_position,
ref=ref,
alt=alt,
ensembl=ensembl)
variants.append(variant)
else:
return VariantCollection(variants)
raise ValueError(("Unable to generate %d random variants, "
"there may be a problem with PyEnsembl") % count)
def random_variants(
count,
ensembl_release=MAX_ENSEMBL_RELEASE,
deletions=True,
insertions=True,
random_seed=None):
"""
Generate a VariantCollection with random variants that overlap
at least one complete coding transcript.
"""
rng = random.Random(random_seed)
ensembl = EnsemblRelease(ensembl_release)
if ensembl_release in _transcript_ids_cache:
transcript_ids = _transcript_ids_cache[ensembl_release]
else:
transcript_ids = ensembl.transcript_ids()
_transcript_ids_cache[ensembl_release] = transcript_ids
variants = []
while len(variants) < count:
transcript_id = rng.choice(transcript_ids)
transcript = ensembl.transcript_by_id(transcript_id)
if not transcript.complete:
continue
exon = rng.choice(transcript.exons)
base1_genomic_position = rng.randint(exon.start, exon.end)
transcript_offset = transcript.spliced_offset(base1_genomic_position)
try:
seq = transcript.sequence
except ValueError as e:
logging.warn(e)
# can't get sequence for non-coding transcripts
continue
ref = str(seq[transcript_offset])
if transcript.on_backward_strand:
ref = reverse_complement(ref)
alt_nucleotides = [x for x in STANDARD_NUCLEOTIDES if x != ref]
if insertions:
nucleotide_pairs = [
x + y
for x in STANDARD_NUCLEOTIDES
for y in STANDARD_NUCLEOTIDES
]
alt_nucleotides.extend(nucleotide_pairs)
if deletions:
alt_nucleotides.append("")
alt = rng.choice(alt_nucleotides)
variant = Variant(
transcript.contig,
base1_genomic_position,
ref=ref,
alt=alt,
ensembl=ensembl)
variants.append(variant)
return VariantCollection(variants)
def random_variants(
count,
ensembl_release=MAX_ENSEMBL_RELEASE,
deletions=True,
insertions=True,
random_seed=None):
"""
Generate a VariantCollection with random variants that overlap
at least one complete coding transcript.
"""
rng = random.Random(random_seed)
ensembl = EnsemblRelease(ensembl_release)
if ensembl_release in _transcript_ids_cache:
transcript_ids = _transcript_ids_cache[ensembl_release]
else:
transcript_ids = ensembl.transcript_ids()
_transcript_ids_cache[ensembl_release] = transcript_ids
variants = []
# we should finish way before this loop is over but just in case
# something is wrong with PyEnsembl we want to avoid an infinite loop
for _ in range(count * 100):
if len(variants) < count:
transcript_id = rng.choice(transcript_ids)
transcript = ensembl.transcript_by_id(transcript_id)
if not transcript.complete:
continue
exon = rng.choice(transcript.exons)
base1_genomic_position = rng.randint(exon.start, exon.end)
transcript_offset = transcript.spliced_offset(base1_genomic_position)
seq = transcript.sequence
ref = str(seq[transcript_offset])
if transcript.on_backward_strand:
ref = reverse_complement(ref)
alt_nucleotides = [x for x in STANDARD_NUCLEOTIDES if x != ref]
if insertions:
nucleotide_pairs = [
x + y
for x in STANDARD_NUCLEOTIDES
for y in STANDARD_NUCLEOTIDES
]
alt_nucleotides.extend(nucleotide_pairs)
if deletions:
alt_nucleotides.append("")
alt = rng.choice(alt_nucleotides)
variant = Variant(
transcript.contig,
base1_genomic_position,
ref=ref,
alt=alt,
ensembl=ensembl)
variants.append(variant)
else:
return VariantCollection(variants)
raise ValueError(
("Unable to generate %d random variants, "
"there may be a problem with PyEnsembl") % count)
