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()
def hg19_transcript_mappings(db, hg19):
"""
Fixture for some selected transcript mappings in the GRCh37/hg19 genome
assembly.
"""
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chr11').one(),
'refseq',
'NM_003002',
'SDHD',
'forward',
111957571,
111966518,
[111957571, 111958581, 111959591, 111965529],
[111957683, 111958697, 111959735, 111966518],
'ncbi',
transcript=1,
cds=(111957632, 111965694),
select_transcript=False,
version=2))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chr11').one(),
'refseq',
'NM_012459',
'TIMM8B',
'reverse',
111955524,
111957522, [111955524, 111957364],
[111956186, 111957522],
'ncbi',
transcript=1,
cds=(111956019, 111957492),
select_transcript=False,
version=2))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chr11').one(),
'refseq',
'NR_028383',
'TIMM8B',
'reverse',
111955524,
111957522, [111955524, 111956702, 111957364],
[111956186, 111957034, 111957522],
'ncbi',
transcript=1,
cds=None,
select_transcript=False,
version=1))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chr6').one(),
'refseq',
'NM_000500',
'CYP21A2',
'forward',
32006082,
32009419, [
32006082, 32006499, 32006871, 32007133, 32007323,
32007526, 32007782, 32008183, 32008445, 32008646
], [
32006401, 32006588, 32007025, 32007234, 32007424,
32007612, 32007982, 32008361, 32008548, 32009419
],
'ncbi',
transcript=1,
cds=(32006200, 32008911),
select_transcript=False,
version=5))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chr22').one(),
'refseq',
'NM_001145134',
'CPT1B',
'reverse',
51007290,
51017096, [
51007290, 51007765, 51008005, 51008722, 51009320,
51009587, 51009804, 51010435, 51010632, 51011304,
51011949, 51012764, 51012922, 51014464, 51014627,
51015286, 51015753, 51016204, 51016978
], [
51007510, 51007850, 51008097, 51008835, 51009472,
51009721, 51009968, 51010551, 51010737, 51011489,
51012144, 51012848, 51013029, 51014541, 51014764,
51015463, 51015892, 51016363, 51017096
],
'ncbi',
transcript=1,
cds=(51007767, 51016344),
select_transcript=False,
version=1))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chr22').one(),
'refseq',
'NR_021492',
'LOC100144603',
'forward',
51021455,
51022356, [51021455, 51022027], [51021752, 51022356],
'ncbi',
transcript=1,
cds=None,
select_transcript=False,
version=1))
db.session.add(
TranscriptMapping(
hg19.chromosomes.filter_by(name='chr1').one(),
'refseq',
'NM_001007553',
'CSDE1',
'reverse',
115259538,
115300624, [
115259538, 115261234, 115262200, 115263160, 115266504,
115267842, 115268832, 115269604, 115272879, 115273129,
115275225, 115276353, 115276610, 115277063, 115279379,
115280092, 115280584, 115282313, 115292442, 115300546
], [
115260837, 115261366, 115262363, 115263338, 115266623,
115267954, 115269007, 115269711, 115273043, 115273269,
115275437, 115276478, 115276738, 115277144, 115279476,
115280184, 115280693, 115282511, 115292828, 115300624
],
'ncbi',
transcript=1,
cds=(115260790, 115282511),
select_transcript=False,
version=1))
db.session.add(
TranscriptMapping(
hg19.chromosomes.filter_by(name='chr1').one(),
'refseq',
'NM_001130523',
'CSDE1',
'reverse',
115259538,
115300671, [
115259538, 115261234, 115262200, 115263160, 115266504,
115267842, 115268832, 115269604, 115272879, 115273129,
115275225, 115276353, 115276610, 115277063, 115279379,
115280584, 115282313, 115284148, 115292442, 115300546
], [
115260837, 115261366, 115262363, 115263338, 115266623,
115267954, 115269007, 115269711, 115273043, 115273269,
115275437, 115276478, 115276738, 115277144, 115279476,
115280693, 115282511, 115284294, 115292828, 115300671
],
'ncbi',
transcript=1,
cds=(115260790, 115284285),
select_transcript=False,
version=1))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chr1').one(),
'refseq',
'NM_002241',
'KCNJ10',
'reverse',
160007257,
160040051, [160007257, 160039812],
[160012322, 160040051],
'ncbi',
transcript=1,
cds=(160011183, 160012322),
select_transcript=False,
version=4))
db.session.add(
TranscriptMapping(
hg19.chromosomes.filter_by(name='chr20').one(),
'refseq',
'NM_001162505',
'TMEM189',
'reverse',
48740274,
48770335,
[48740274, 48744512, 48746083, 48747402, 48760039, 48770054],
[48741716, 48744724, 48746227, 48747484, 48760158, 48770335],
'ncbi',
transcript=1,
cds=(48741595, 48770174),
select_transcript=False,
version=1))
db.session.add(
TranscriptMapping(
hg19.chromosomes.filter_by(name='chr8').one(),
'refseq',
'NM_017780',
'CHD7',
'forward',
61591339,
61779465, [
61591339, 61653818, 61693559, 61707545, 61712947, 61714087,
61720776, 61728946, 61732566, 61734349, 61734583, 61735062,
61736399, 61741222, 61742881, 61748632, 61749376, 61750227,
61750635, 61754203, 61754406, 61757423, 61757809, 61761074,
61761610, 61763052, 61763591, 61763821, 61764578, 61765057,
61765388, 61766922, 61768534, 61769004, 61773463, 61774755,
61775107, 61777575
], [
61591641, 61655656, 61693989, 61707686, 61713084, 61714152,
61720831, 61729060, 61732649, 61734486, 61734704, 61735305,
61736575, 61741365, 61743136, 61748842, 61749571, 61750394,
61750814, 61754313, 61754611, 61757622, 61757968, 61761163,
61761713, 61763181, 61763663, 61763878, 61764806, 61765265,
61766059, 61767082, 61768761, 61769447, 61773684, 61774895,
61775211, 61779465
],
'ncbi',
transcript=1,
cds=(61653992, 61778492),
select_transcript=False,
version=2))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chrM').one(),
'refseq',
'NC_012920',
'ND4',
'forward',
10760,
12137, [10760], [12137],
'reference',
transcript=1,
cds=(10760, 12137),
select_transcript=True,
version=1))
db.session.add(
TranscriptMapping(
hg19.chromosomes.filter_by(name='chr1').one(),
'refseq',
'NM_002001',
'FCER1A',
'forward',
159259504,
159278014,
[159259504, 159272096, 159272644, 159273718, 159275778, 159277538],
[159259543, 159272209, 159272664, 159273972, 159276035, 159278014],
'ncbi',
transcript=1,
cds=(159272155, 159277722),
select_transcript=False,
version=2))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chr7').one(),
'refseq',
'XM_001715131',
'LOC100132858',
'reverse',
19828,
36378, [19828, 20834, 31060, 32957, 35335, 36224],
[19895, 21029, 31437, 33107, 35541, 36378],
'ncbi',
transcript=1,
cds=(19828, 36378),
select_transcript=False,
version=2))
db.session.add(
TranscriptMapping(
hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_004011',
'DMD',
'reverse',
31137345,
32430371, [
31137345, 31144759, 31152219, 31164408, 31165392, 31187560,
31190465, 31191656, 31196049, 31196786, 31198487, 31200855,
31222078, 31224699, 31227615, 31241164, 31279072, 31341715,
31366673, 31462598, 31496223, 31497100, 31514905, 31525398,
31645790, 31676107, 31697492, 31747748, 31792077, 31838092,
31854835, 31893305, 31947713, 31950197, 31986456, 32235033,
32305646, 32328199, 32360217, 32361251, 32364060, 32366523,
32380905, 32382699, 32383137, 32398627, 32404427, 32407618,
32408188, 32429869, 32430279
], [
31140047, 31144790, 31152311, 31164531, 31165635, 31187718,
31190530, 31191721, 31196087, 31196922, 31198598, 31201021,
31222235, 31224784, 31227816, 31241238, 31279133, 31341775,
31366751, 31462744, 31496491, 31497220, 31515061, 31525570,
31645979, 31676261, 31697703, 31747865, 31792309, 31838200,
31854936, 31893490, 31947862, 31950344, 31986631, 32235180,
32305818, 32328393, 32360399, 32361403, 32364197, 32366645,
32381075, 32382827, 32383316, 32398797, 32404582, 32407791,
32408298, 32430030, 32430371
],
'ncbi',
transcript=1,
cds=(31140036, 32430326),
select_transcript=False,
version=3))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_004019',
'DMD',
'reverse',
31196312,
31285024, [
31196312, 31198487, 31200855, 31222078, 31224699,
31227615, 31241164, 31279072, 31284927
], [
31196922, 31198598, 31201021, 31222235, 31224784,
31227816, 31241238, 31279133, 31285024
],
'ncbi',
transcript=1,
cds=(31196782, 31284946),
select_transcript=False,
version=2))
db.session.add(
TranscriptMapping(
hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_004007',
'DMD',
'reverse',
31137345,
33038317, [
31137345, 31144759, 31152219, 31164408, 31165392, 31187560,
31190465, 31191656, 31196049, 31196786, 31198487, 31200855,
31222078, 31224699, 31227615, 31241164, 31279072, 31341715,
31366673, 31462598, 31496223, 31497100, 31514905, 31525398,
31645790, 31676107, 31697492, 31747748, 31792077, 31838092,
31854835, 31893305, 31947713, 31950197, 31986456, 32235033,
32305646, 32328199, 32360217, 32361251, 32364060, 32366523,
32380905, 32382699, 32383137, 32398627, 32404427, 32407618,
32408188, 32429869, 32456358, 32459297, 32466573, 32472779,
32481556, 32482703, 32486615, 32490281, 32503036, 32509394,
32519872, 32536125, 32563276, 32583819, 32591647, 32591862,
32613874, 32632420, 32662249, 32663081, 32715987, 32717229,
32827610, 32834585, 32841412, 32862900, 32867845, 33038256
], [
31140047, 31144790, 31152311, 31164531, 31165635, 31187718,
31190530, 31191721, 31196087, 31196922, 31198598, 31201021,
31222235, 31224784, 31227816, 31241238, 31279133, 31341775,
31366751, 31462744, 31496491, 31497220, 31515061, 31525570,
31645979, 31676261, 31697703, 31747865, 31792309, 31838200,
31854936, 31893490, 31947862, 31950344, 31986631, 32235180,
32305818, 32328393, 32360399, 32361403, 32364197, 32366645,
32381075, 32382827, 32383316, 32398797, 32404582, 32407791,
32408298, 32430030, 32456507, 32459431, 32466755, 32472949,
32481711, 32482816, 32486827, 32490426, 32503216, 32509635,
32519959, 32536248, 32563451, 32583998, 32591754, 32591963,
32613993, 32632570, 32662430, 32663269, 32716115, 32717410,
32827728, 32834757, 32841504, 32862977, 32867937, 33038317
],
'ncbi',
transcript=1,
cds=(31140036, 32834745),
select_transcript=False,
version=2))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_203473',
'PORCN',
'forward',
48367371,
48379202, [
48367371, 48368172, 48369683, 48370280, 48370714,
48370977, 48371223, 48372628, 48372913, 48374105,
48374278, 48374449, 48375571, 48378763
], [
48367491, 48368344, 48369875, 48370323, 48370895,
48371107, 48371240, 48372753, 48373013, 48374181,
48374341, 48374534, 48375681, 48379202
],
'ncbi',
transcript=1,
cds=(48368209, 48378864),
select_transcript=False,
version=1))
db.session.add(
TranscriptMapping(
hg19.chromosomes.filter_by(name='chrX').one(),
'refseq',
'NM_000132',
'F8',
'reverse',
154064063,
154250998, [
154064063, 154088707, 154089993, 154091358, 154124352,
154128141, 154129646, 154130326, 154132181, 154132571,
154133086, 154134695, 154156846, 154175973, 154182167,
154185232, 154189350, 154194245, 154194701, 154197606,
154212962, 154215512, 154221211, 154225248, 154227754,
154250685
], [
154066027, 154088883, 154090141, 154091502, 154124507,
154128226, 154129717, 154130442, 154132363, 154132799,
154133298, 154134848, 154159951, 154176182, 154182317,
154185446, 154189443, 154194416, 154194962, 154197827,
154213078, 154215580, 154221423, 154225370, 154227875,
154250998
],
'ncbi',
transcript=1,
cds=(154065872, 154250827),
select_transcript=False,
version=3))
db.session.add(
TranscriptMapping(hg19.chromosomes.filter_by(name='chr3').one(),
'refseq',
'NM_000249',
'MLH1',
'forward',
37034841,
37092337, [
37034841, 37038110, 37042446, 37045892, 37048482,
37050305, 37053311, 37053502, 37055923, 37058997,
37061801, 37067128, 37070275, 37081677, 37083759,
37089010, 37090008, 37090395, 37091977
], [
37035154, 37038200, 37042544, 37045965, 37048554,
37050396, 37053353, 37053590, 37056035, 37059090,
37061954, 37067498, 37070423, 37081785, 37083822,
37089174, 37090100, 37090508, 37092337
],
'ncbi',
transcript=1,
cds=(37035039, 37092144),
select_transcript=False,
version=3))
db.session.commit()