class Translation(models.Model):
MANY2ONE_RELATED = {
'SEQUENCE': 'sequence',
'SESSION': 'session',
'ASSEMBLY': 'assembly'
}
ONE2MANY_RELATED = {
'RELEASE_SET': 'translation_release_set',
'TRANSCRIPT': "transcripts"
}
translation_id = models.AutoField(primary_key=True)
stable_id = models.CharField(max_length=64)
stable_id_version = models.PositiveIntegerField()
assembly = models.ForeignKey(Assembly,
models.DO_NOTHING,
blank=True,
null=True)
loc_start = models.PositiveIntegerField(blank=True, null=True)
loc_end = models.PositiveIntegerField(blank=True, null=True)
loc_strand = models.IntegerField(blank=True, null=True)
loc_region = models.CharField(max_length=42, blank=True, null=True)
loc_checksum = ChecksumField(unique=True,
max_length=20,
blank=True,
null=True)
translation_checksum = ChecksumField(unique=True,
max_length=20,
blank=True,
null=True)
sequence = models.ForeignKey(Sequence,
models.DO_NOTHING,
db_column='seq_checksum',
blank=True,
null=True)
session = models.ForeignKey(Session,
models.DO_NOTHING,
blank=True,
null=True)
translation_release_set = models.ManyToManyField(
'release.ReleaseSet',
through='release.TranslationReleaseTag',
related_name='translation_release_set')
transcripts = models.ManyToManyField(
'transcript.Transcript', through='translation.TranslationTranscript')
class Meta:
managed = False
db_table = 'translation'
class ReleaseSet(models.Model):
MANY2ONE_RELATED = {'RELEASE_SOURCE': 'release_source'}
ONE2MANY_RELATED = {'RELEASE_SET': 'release_set'}
release_id = models.AutoField(primary_key=True)
shortname = models.CharField(max_length=24, blank=True, null=True)
description = models.CharField(max_length=256, blank=True, null=True)
assembly = models.ForeignKey(Assembly,
models.DO_NOTHING,
blank=True,
null=True)
release_date = models.DateField(blank=True, null=True)
session = models.ForeignKey(Session,
models.DO_NOTHING,
blank=True,
null=True)
release_checksum = ChecksumField(unique=True,
max_length=20,
blank=True,
null=True)
source = models.ForeignKey(ReleaseSource,
models.DO_NOTHING,
blank=True,
null=True)
class Meta:
managed = False
db_table = 'release_set'
unique_together = (('shortname', 'assembly', 'source'), )
class Gene(models.Model):
MANY2ONE_RELATED = {
'SESSION': 'session',
'ASSEMBLY': 'assembly',
'HGNC': 'name'
}
ONE2MANY_RELATED = {'RELEASE_SET': 'gene_release_set'}
gene_id = models.AutoField(primary_key=True)
stable_id = models.CharField(max_length=64)
stable_id_version = models.PositiveIntegerField()
assembly = models.ForeignKey(Assembly,
models.DO_NOTHING,
blank=True,
null=True)
loc_start = models.PositiveIntegerField(blank=True, null=True)
loc_end = models.PositiveIntegerField(blank=True, null=True)
loc_strand = models.IntegerField(blank=True, null=True)
loc_region = models.CharField(max_length=42, blank=True, null=True)
loc_checksum = ChecksumField(unique=True,
max_length=20,
blank=True,
null=True)
name = HGNCField(GeneNames,
models.DO_NOTHING,
to_field='external_id',
blank=True,
null=True)
gene_checksum = ChecksumField(unique=True,
max_length=20,
blank=True,
null=True)
session = models.ForeignKey(Session,
models.DO_NOTHING,
blank=True,
null=True)
gene_release_set = models.ManyToManyField('release.ReleaseSet',
through='release.GeneReleaseTag',
related_name='gene_release_set')
class Meta:
managed = False
db_table = 'gene'
class Sequence(models.Model):
seq_checksum = ChecksumField(max_length=20,
blank=False,
null=False,
primary_key=True)
sequence = models.TextField(blank=True, null=True)
session = models.ForeignKey(Session,
models.DO_NOTHING,
blank=True,
null=True)
class Meta:
managed = False
db_table = 'sequence'
class Transcript(models.Model):
MANY2ONE_RELATED = {
'SEQUENCE': 'sequence',
'SESSION': 'session',
'ASSEMBLY': 'assembly'
}
ONE2MANY_RELATED = {
'RELEASE_SET': 'transcript_release_set',
'GENE': 'genes',
'TRANSLATION': "translations",
"EXONTRANSCRIPT": "exons"
}
# You'll normally want to ensure that you've set an appropriate related_name argument on the relationship,
# that you can use as the field name.
transcript_id = models.AutoField(primary_key=True)
stable_id = models.CharField(max_length=64)
stable_id_version = models.PositiveIntegerField()
assembly = models.ForeignKey(Assembly,
models.DO_NOTHING,
blank=True,
null=True)
loc_start = models.PositiveIntegerField(blank=True, null=True)
loc_end = models.PositiveIntegerField(blank=True, null=True)
loc_strand = models.IntegerField(blank=True, null=True)
loc_region = models.CharField(max_length=42, blank=True, null=True)
loc_checksum = ChecksumField(unique=True,
max_length=20,
blank=True,
null=True)
exon_set_checksum = ChecksumField(unique=True,
max_length=20,
blank=True,
null=True)
transcript_checksum = ChecksumField(unique=True,
max_length=20,
blank=True,
null=True)
sequence = models.ForeignKey(Sequence,
models.DO_NOTHING,
db_column='seq_checksum',
blank=True,
null=True)
session = models.ForeignKey(Session,
models.DO_NOTHING,
blank=True,
null=True)
transcript_release_set = models.ManyToManyField(
'release.ReleaseSet',
through='release.TranscriptReleaseTag',
related_name='transcript_release_set')
biotype = models.CharField(max_length=40, blank=True, null=True)
genes = models.ManyToManyField('gene.Gene',
through='transcript.TranscriptGene')
exons = models.ManyToManyField('exon.Exon', through='exon.ExonTranscript')
translations = models.ManyToManyField(
'translation.Translation', through='translation.TranslationTranscript')
class Meta:
managed = False
db_table = 'transcript'
@classmethod
def fetch_mane_transcript_and_type(cls, transcript_id=None):
transcript = None
source = "Ensembl"
if transcript_id is not None:
transcript = Transcript.objects.get(pk=transcript_id)
if transcript is not None:
try:
source = transcript.transcript_release_set.all()[:1].get(
).source.shortname
except Exception as e:
logger.error("Exception from get_mane_transcript " + str(e))
if "Ensembl" in source:
raw_sql = "SELECT DISTINCT\
t1.transcript_id, t1.stable_id as ens_stable_id, t1.stable_id_version as ens_stable_id_version,\
relationship_type.shortname as mane_type,\
t2.stable_id as refseq_stable_id, t2.stable_id_version as refseq_stable_id_version \
FROM \
transcript t1 \
JOIN transcript_release_tag trt1 ON t1.transcript_id=trt1.feature_id \
JOIN transcript_release_tag_relationship ON \
trt1.transcript_release_id=transcript_release_tag_relationship.transcript_release_object_id \
JOIN transcript_release_tag trt2 ON \
transcript_release_tag_relationship.transcript_release_subject_id=trt2.transcript_release_id \
JOIN transcript t2 ON trt2.feature_id=t2.transcript_id \
JOIN relationship_type ON \
transcript_release_tag_relationship.relationship_type_id=relationship_type.relationship_type_id"
else:
raw_sql = "SELECT DISTINCT\
t1.transcript_id, t1.stable_id as ens_stable_id, t1.stable_id_version as ens_stable_id_version,\
relationship_type.shortname as mane_type,\
t2.stable_id as refseq_stable_id, t2.stable_id_version as refseq_stable_id_version \
FROM \
transcript t1 \
JOIN transcript_release_tag trt1 ON t1.transcript_id=trt1.feature_id \
JOIN transcript_release_tag_relationship ON \
trt1.transcript_release_id=transcript_release_tag_relationship.transcript_release_subject_id \
JOIN transcript_release_tag trt2 ON \
transcript_release_tag_relationship.transcript_release_object_id=trt2.transcript_release_id \
JOIN transcript t2 ON trt2.feature_id=t2.transcript_id \
JOIN relationship_type ON \
transcript_release_tag_relationship.relationship_type_id=relationship_type.relationship_type_id"
if transcript_id is not None:
raw_sql = raw_sql + " WHERE t1.transcript_id=%s limit 1"
mane_transcripts = Transcript.objects.raw(raw_sql, [transcript_id])
mane_transcript_dict = {}
if mane_transcripts is not None and len(
list(mane_transcripts)) > 0:
mane_transcript = mane_transcripts[0]
mane_transcript_dict = {
"mane_transcript_stableid":
"{}.{}".format(mane_transcript.refseq_stable_id,
mane_transcript.refseq_stable_id_version),
"mane_transcript_type":
mane_transcript.mane_type
}
return mane_transcript_dict
else:
raw_sql = "SELECT DISTINCT\
t1.transcript_id, t1.stable_id as ens_stable_id, t1.stable_id_version as ens_stable_id_version,\
relationship_type.shortname as mane_type,\
t2.stable_id as refseq_stable_id, t2.stable_id_version as refseq_stable_id_version,\
gn1.name as ens_gene_name \
FROM \
transcript t1 \
JOIN transcript_release_tag trt1 ON t1.transcript_id=trt1.feature_id \
JOIN transcript_release_tag_relationship ON \
trt1.transcript_release_id=transcript_release_tag_relationship.transcript_release_object_id \
JOIN transcript_release_tag trt2 ON \
transcript_release_tag_relationship.transcript_release_subject_id=trt2.transcript_release_id \
JOIN transcript t2 ON trt2.feature_id=t2.transcript_id \
JOIN relationship_type ON \
transcript_release_tag_relationship.relationship_type_id=relationship_type.relationship_type_id\
JOIN transcript_gene tg1 ON \
t1.transcript_id=tg1.transcript_id \
JOIN gene gene1 ON \
tg1.gene_id=gene1.gene_id \
JOIN gene_names gn1 ON \
gene1.name_id=gn1.external_id \
where gn1.primary_id=1"
mane_transcripts = Transcript.objects.raw(raw_sql)
return mane_transcripts