def build_mapping(record):
# Only use records on chromosomes we know.
try:
chromosome = next(c for c in chromosomes
if c.name == 'chr' + record['chromosome'])
except StopIteration:
raise ValueError()
accession, transcript = record['transcript'].split('t')
transcript = int(transcript)
orientation = 'reverse' if record['strand'] == '-1' else 'forward'
if record['cds_start']:
cds = record['cds_start'], record['cds_stop']
else:
cds = None
# TODO: Also take protein into account. For example, in LRG_321 (TP53)
# some transcripts occur twice (with different CDSs and different
# protein numbers).
# https://github.com/mutalyzer/mutalyzer/issues/372
return TranscriptMapping.create_or_update(
chromosome,
'lrg',
accession,
record['gene'],
orientation,
record['start'],
record['stop'], [start for start, _ in record['exons']],
[stop for _, stop in record['exons']],
'ebi',
transcript=transcript,
cds=cds,
select_transcript=True)
def build_mapping(record):
# Only use records on chromosomes we know.
try:
chromosome = next(c for c in chromosomes if
c.name == 'chr' + record['chromosome'])
except StopIteration:
raise ValueError()
accession, transcript = record['transcript'].split('t')
transcript = int(transcript)
orientation = 'reverse' if record['strand'] == '-1' else 'forward'
if record['cds_start']:
cds = record['cds_start'], record['cds_stop']
else:
cds = None
# TODO: Also take protein into account. For example, in LRG_321 (TP53)
# some transcripts occur twice (with different CDSs and different
# protein numbers).
# https://github.com/mutalyzer/mutalyzer/issues/372
return TranscriptMapping.create_or_update(
chromosome, 'lrg', accession, record['gene'], orientation,
record['start'], record['stop'],
[start for start, _ in record['exons']],
[stop for _, stop in record['exons']],
'ebi', transcript=transcript, cds=cds, select_transcript=True)
def build_mappings(records):
# We structure the records per transcript and per record type. This is
# generalized to a list of records for each type, but we expect only
# one GENE record (with `-` as transcript value).
# Note that there can be more than one RNA record per transcript if it
# is split over different reference contigs.
by_transcript = defaultdict(lambda: defaultdict(list))
for r in records:
by_transcript[r['transcript']][r['feature_type']].append(r)
gene = by_transcript['-']['GENE'][0]['feature_name']
for transcript, by_type in by_transcript.items():
if transcript == '-':
continue
accession, version = transcript.split('.')
version = int(version)
chromosome = by_type['RNA'][0]['chromosome']
orientation = 'reverse' if by_type['RNA'][0]['orientation'] == '-' else 'forward'
start = min(t['start'] for t in by_type['RNA'])
stop = max(t['stop'] for t in by_type['RNA'])
exon_starts = []
exon_stops = []
cds_positions = []
for exon in sorted(by_type['UTR'] + by_type['CDS'],
key=itemgetter('start')):
if exon_stops and exon_stops[-1] > exon['start'] - 1:
# This exon starts before the end of the previous exon. We
# have no idea what to do in this case, so we ignore it.
# The number of transcripts affected is very small (e.g.,
# NM_031860.1 and NM_001184961.1 in the GRCh37 assembly).
continue
if exon['feature_type'] == 'CDS':
cds_positions.extend([exon['start'], exon['stop']])
if exon_stops and exon_stops[-1] == exon['start'] - 1:
# This exon must be merged with the previous one because
# it is split over two entries (a CDS part and a UTR part
# or split over different reference contigs).
exon_stops[-1] = exon['stop']
else:
exon_starts.append(exon['start'])
exon_stops.append(exon['stop'])
if cds_positions:
cds = min(cds_positions), max(cds_positions)
else:
cds = None
# If no exons are annotated, we create one spanning the entire
# transcript.
if not exon_starts:
exon_starts = [start]
exon_stops = [stop]
yield TranscriptMapping.create_or_update(
chromosome, 'refseq', accession, gene, orientation, start,
stop, exon_starts, exon_stops, 'ncbi', cds=cds,
version=version)
def build_mappings(records):
# We structure the records per transcript and per record type. This is
# generalized to a list of records for each type, but we expect only
# one GENE record (with `-` as transcript value).
# Note that there can be more than one RNA record per transcript if it
# is split over different reference contigs.
by_transcript = defaultdict(lambda: defaultdict(list))
for r in records:
by_transcript[r['transcript']][r['feature_type']].append(r)
gene = by_transcript['-']['GENE'][0]['feature_name']
for transcript, by_type in by_transcript.items():
if transcript == '-':
continue
accession, version = transcript.split('.')
version = int(version)
chromosome = by_type['RNA'][0]['chromosome']
orientation = 'reverse' if by_type['RNA'][0]['orientation'] == '-' else 'forward'
start = min(t['start'] for t in by_type['RNA'])
stop = max(t['stop'] for t in by_type['RNA'])
exon_starts = []
exon_stops = []
cds_positions = []
for exon in sorted(by_type['UTR'] + by_type['CDS'],
key=itemgetter('start')):
if exon_stops and exon_stops[-1] > exon['start'] - 1:
# This exon starts before the end of the previous exon. We
# have no idea what to do in this case, so we ignore it.
# The number of transcripts affected is very small (e.g.,
# NM_031860.1 and NM_001184961.1 in the GRCh37 assembly).
continue
if exon['feature_type'] == 'CDS':
cds_positions.extend([exon['start'], exon['stop']])
if exon_stops and exon_stops[-1] == exon['start'] - 1:
# This exon must be merged with the previous one because
# it is split over two entries (a CDS part and a UTR part
# or split over different reference contigs).
exon_stops[-1] = exon['stop']
else:
exon_starts.append(exon['start'])
exon_stops.append(exon['stop'])
if cds_positions:
cds = min(cds_positions), max(cds_positions)
else:
cds = None
# If no exons are annotated, we create one spanning the entire
# transcript.
if not exon_starts:
exon_starts = [start]
exon_stops = [stop]
yield TranscriptMapping.create_or_update(
chromosome, 'refseq', accession, gene, orientation, start,
stop, exon_starts, exon_stops, 'ncbi', cds=cds,
version=version)
def import_from_ucsc_by_gene(assembly, gene):
"""
Import transcript mappings for a gene from the UCSC.
"""
connection = MySQLdb.connect(user='******',
host='genome-mysql.cse.ucsc.edu',
db=assembly.alias,
charset='utf8',
use_unicode=True)
query = """
SELECT DISTINCT
acc, version, txStart, txEnd, cdsStart, cdsEnd, exonStarts,
exonEnds, name2 AS geneName, chrom, strand, protAcc
FROM gbStatus, refGene, refLink
WHERE type = "mRNA"
AND refGene.name = acc
AND acc = mrnaAcc
AND name2 = %s
"""
parameters = gene,
cursor = connection.cursor()
cursor.execute(query, parameters)
result = cursor.fetchall()
cursor.close()
# All ranges in the UCSC tables are zero-based and open-ended. We convert
# this to one-based, inclusive for our database.
for (acc, version, txStart, txEnd, cdsStart, cdsEnd, exonStarts, exonEnds,
geneName, chrom, strand, protAcc) in result:
chromosome = assembly.chromosomes.filter_by(name=chrom).one()
orientation = 'reverse' if strand == '-' else 'forward'
exon_starts = [int(i) + 1 for i in exonStarts.split(',') if i]
exon_stops = [int(i) for i in exonEnds.split(',') if i]
if cdsStart and cdsEnd:
cds = cdsStart + 1, cdsEnd
else:
cds = None
mapping = TranscriptMapping.create_or_update(chromosome,
'refseq',
acc,
geneName,
orientation,
txStart + 1,
txEnd,
exon_starts,
exon_stops,
'ucsc',
cds=cds,
version=int(version))
session.add(mapping)
session.commit()
def import_from_reference(assembly, reference):
"""
Import transcript mappings from a genomic reference.
.. todo: Also report how much was added/updated.
.. note: Currently no exon locations are supported, this has only been
tested on mtDNA.
"""
chromosome = assembly.chromosomes.filter_by(name='chrM').one()
output = Output(__file__)
retriever = Retriever.GenBankRetriever(output)
record = retriever.loadrecord(reference)
if record.molType != 'm':
raise ValueError('Only mitochondial references are supported')
select_transcript = len(record.geneList) > 1
for gene in record.geneList:
# We support exactly one transcript per gene.
try:
transcript = sorted(gene.transcriptList, key=attrgetter('name'))[0]
except IndexError:
continue
# We use gene.location for now, it is always present and the same
# for our purposes.
#start, stop = transcript.mRNA.location[0], transcript.mRNA.location[1]
start, stop = gene.location
orientation = 'reverse' if gene.orientation == -1 else 'forward'
try:
cds = transcript.CDS.location
except AttributeError:
cds = None
mapping = TranscriptMapping.create_or_update(
chromosome,
'refseq',
record.source_accession,
gene.name,
orientation,
start,
stop, [start], [stop],
'reference',
cds=cds,
select_transcript=select_transcript,
version=int(record.source_version))
session.add(mapping)
session.commit()
def import_from_reference(assembly, reference):
"""
Import transcript mappings from a genomic reference.
.. todo: Also report how much was added/updated.
.. note: Currently no exon locations are supported, this has only been
tested on mtDNA.
"""
chromosome = assembly.chromosomes.filter_by(name='chrM').one()
output = Output(__file__)
retriever = Retriever.GenBankRetriever(output)
record = retriever.loadrecord(reference)
if record.molType != 'm':
raise ValueError('Only mitochondial references are supported')
select_transcript = len(record.geneList) > 1
for gene in record.geneList:
# We support exactly one transcript per gene.
try:
transcript = sorted(gene.transcriptList, key=attrgetter('name'))[0]
except IndexError:
continue
# We use gene.location for now, it is always present and the same
# for our purposes.
#start, stop = transcript.mRNA.location[0], transcript.mRNA.location[1]
start, stop = gene.location
orientation = 'reverse' if gene.orientation == -1 else 'forward'
try:
cds = transcript.CDS.location
except AttributeError:
cds = None
mapping = TranscriptMapping.create_or_update(
chromosome, 'refseq', record.source_accession, gene.name,
orientation, start, stop, [start], [stop], 'reference', cds=cds,
select_transcript=select_transcript,
version=int(record.source_version))
session.add(mapping)
session.commit()
def import_from_ucsc_by_gene(assembly, gene):
"""
Import transcript mappings for a gene from the UCSC.
"""
connection = MySQLdb.connect(user='******',
host='genome-mysql.cse.ucsc.edu',
db=assembly.alias,
charset='utf8',
use_unicode=True)
query = """
SELECT DISTINCT
acc, version, txStart, txEnd, cdsStart, cdsEnd, exonStarts,
exonEnds, name2 AS geneName, chrom, strand, protAcc
FROM gbStatus, refGene, refLink
WHERE type = "mRNA"
AND refGene.name = acc
AND acc = mrnaAcc
AND name2 = %s
"""
parameters = gene,
cursor = connection.cursor()
cursor.execute(query, parameters)
result = cursor.fetchall()
cursor.close()
# All ranges in the UCSC tables are zero-based and open-ended. We convert
# this to one-based, inclusive for our database.
for (acc, version, txStart, txEnd, cdsStart, cdsEnd, exonStarts, exonEnds,
geneName, chrom, strand, protAcc) in result:
chromosome = assembly.chromosomes.filter_by(name=chrom).one()
orientation = 'reverse' if strand == '-' else 'forward'
exon_starts = [int(i) + 1 for i in exonStarts.split(',') if i]
exon_stops = [int(i) for i in exonEnds.split(',') if i]
if cdsStart and cdsEnd:
cds = cdsStart + 1, cdsEnd
else:
cds = None
mapping = TranscriptMapping.create_or_update(
chromosome, 'refseq', acc, geneName, orientation, txStart + 1,
txEnd, exon_starts, exon_stops, 'ucsc', cds=cds,
version=int(version))
session.add(mapping)
session.commit()
