def peptide_from_protein_transcript_variant(transcript_id, pos, ref, alt):
"""
Given an ensembl transcript ID, mutate amino acid `ref` to `alt` at
position `pos`.
"""
transcript = _ensembl.get_protein(transcript_id)
if transcript:
try:
return str(mutate(transcript, pos, ref, alt))
except:
logging.warning("Failed to mutate transcript %s (%s)",
transcript_id,
gene_mutation_description(pos, ref, alt))
return None
return None
def peptide_from_protein_transcript_variant(transcript_id, pos, ref, alt):
"""
Given an ensembl transcript ID, mutate amino acid `ref` to `alt` at
position `pos`.
"""
transcript = _ensembl.get_protein(transcript_id)
if transcript:
try:
return str(mutate(transcript, pos, ref, alt))
except:
logging.warning(
"Failed to mutate transcript %s (%s)",
transcript_id,
gene_mutation_description(pos, ref, alt)
)
return None
return None
def peptide_from_transcript_variant(transcript_id,
pos,
ref,
alt,
padding=None,
max_length=None):
# sometimes empty strings get represented with a '.'
if ref == ".":
ref = ""
if alt == ".":
alt = ""
forward = annotation.is_forward_strand(transcript_id)
ref = ref if forward else annotation.reverse_complement(ref)
alt = alt if forward else annotation.reverse_complement(alt)
transcript = _ensembl.get_cds(transcript_id)
def error_result(msg, *args):
logging.warning(msg, *args)
return None, -1, -1, msg % args
if not transcript:
return error_result("Couldn't find transcript for ID %s",
transcript_id)
idx = annotation.get_transcript_index_from_pos(
pos, transcript_id, skip_untranslated_region=True)
if idx is None:
return error_result(
"Couldn't translate gene position %s into transcript index for %s",
pos, transcript_id)
elif idx >= len(transcript):
return error_result(
"Index %d longer than sequence (len %d) for transcript %s (%s)",
idx, len(transcript), transcript_id,
gene_mutation_description(pos, ref, alt))
idx = idx if forward else idx - len(ref) + 1
# 'ref' represents what the VCF file thought were the reference bases
# at this position, now we actually check to make sure the transcript
# agrees
transcript_ref = str(transcript[idx:idx + len(ref)])
if transcript_ref != ref:
mutation_description = gene_mutation_description(pos, ref, alt)
return error_result(
"VCF/MAF expected %s at idx %d of transcript %s, found %s (%s)" % \
(ref, idx, transcript_id, transcript_ref, mutation_description)
)
region = mutate_protein_from_transcript(transcript,
idx,
ref,
alt,
padding=padding)
start = region.mutation_start
stop = start + region.n_inserted
if max_length and len(region.seq) > max_length:
seq = region.seq[:max_length]
stop = min(stop, max_length)
else:
seq = region.seq
return seq, start, stop, region.annot
def peptide_from_transcript_variant(
transcript_id, pos, ref, alt,
padding = None,
max_length = None):
# sometimes empty strings get represented with a '.'
if ref == ".":
ref = ""
if alt == ".":
alt = ""
forward = annotation.is_forward_strand(transcript_id)
ref = ref if forward else annotation.reverse_complement(ref)
alt = alt if forward else annotation.reverse_complement(alt)
transcript = _ensembl.get_cds(transcript_id)
def error_result(msg, *args):
logging.warning(msg, *args)
return None, -1, -1, msg % args
if not transcript:
return error_result("Couldn't find transcript for ID %s", transcript_id)
idx = annotation.get_transcript_index_from_pos(
pos,
transcript_id,
skip_untranslated_region = True)
if idx is None:
return error_result(
"Couldn't translate gene position %s into transcript index for %s",
pos,
transcript_id)
elif idx >= len(transcript):
return error_result(
"Index %d longer than sequence (len %d) for transcript %s (%s)",
idx,
len(transcript),
transcript_id,
gene_mutation_description(pos, ref, alt))
idx = idx if forward else idx - len(ref) + 1
# 'ref' represents what the VCF file thought were the reference bases
# at this position, now we actually check to make sure the transcript
# agrees
transcript_ref = str(transcript[idx:idx+len(ref)])
if transcript_ref != ref:
mutation_description = gene_mutation_description(pos, ref, alt)
return error_result(
"VCF/MAF expected %s at idx %d of transcript %s, found %s (%s)" % \
(ref, idx, transcript_id, transcript_ref, mutation_description)
)
region = mutate_protein_from_transcript(
transcript,
idx,
ref,
alt,
padding = padding)
start = region.mutation_start
stop = start + region.n_inserted
if max_length and len(region.seq) > max_length:
seq = region.seq[:max_length]
stop = min(stop, max_length)
else:
seq = region.seq
return seq, start, stop, region.annot