/
models.py
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/
models.py
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from django.db import models
from ensembl.core.models import HasSeqRegion, HasName, HasStableId
# class Allele(models.Model):
# allele_id = models.IntegerField(primary_key=True)
# variation_id = models.IntegerField()
# subsnp_id = models.IntegerField(null=True, blank=True)
# allele = models.CharField(max_length=765, blank=True)
# frequency = models.FloatField(null=True, blank=True)
# sample_id = models.IntegerField(null=True, blank=True)
# class Meta:
# db_table = u'allele'
#
# class AlleleGroup(models.Model):
# allele_group_id = models.IntegerField(primary_key=True)
# variation_group_id = models.IntegerField()
# sample_id = models.IntegerField(null=True, blank=True)
# name = models.CharField(unique=True, max_length=765, blank=True)
# source_id = models.IntegerField(null=True, blank=True)
# frequency = models.FloatField(null=True, blank=True)
# class Meta:
# db_table = u'allele_group'
#
# class AlleleGroupAllele(models.Model):
# allele_group_id = models.IntegerField()
# allele = models.CharField(max_length=765)
# variation_id = models.IntegerField()
# class Meta:
# db_table = u'allele_group_allele'
#
# class CompressedGenotypeSingleBp(models.Model):
# sample_id = models.IntegerField()
# seq_region_id = models.IntegerField()
# seq_region_start = models.IntegerField()
# seq_region_end = models.IntegerField()
# seq_region_strand = models.IntegerField()
# genotypes = models.TextField(blank=True)
# class Meta:
# db_table = u'compressed_genotype_single_bp'
#
# class FailedDescription(models.Model):
# failed_description_id = models.IntegerField(primary_key=True)
# description = models.TextField()
# class Meta:
# db_table = u'failed_description'
#
# class FailedVariation(models.Model):
# variation_id = models.IntegerField(primary_key=True)
# failed_description_id = models.IntegerField()
# class Meta:
# db_table = u'failed_variation'
#
# class FlankingSequence(models.Model):
# variation_id = models.IntegerField(primary_key=True)
# up_seq = models.TextField(blank=True)
# down_seq = models.TextField(blank=True)
# up_seq_region_start = models.IntegerField(null=True, blank=True)
# up_seq_region_end = models.IntegerField(null=True, blank=True)
# down_seq_region_start = models.IntegerField(null=True, blank=True)
# down_seq_region_end = models.IntegerField(null=True, blank=True)
# seq_region_id = models.IntegerField(null=True, blank=True)
# seq_region_strand = models.IntegerField(null=True, blank=True)
# class Meta:
# db_table = u'flanking_sequence'
#
# class Httag(models.Model):
# httag_id = models.IntegerField(primary_key=True)
# variation_group_id = models.IntegerField()
# name = models.CharField(max_length=765, blank=True)
# source_id = models.IntegerField()
# class Meta:
# db_table = u'httag'
#
# class Individual(models.Model):
# sample_id = models.IntegerField(primary_key=True)
# gender = models.CharField(max_length=21)
# father_individual_sample_id = models.IntegerField(null=True, blank=True)
# mother_individual_sample_id = models.IntegerField(null=True, blank=True)
# individual_type_id = models.IntegerField()
# class Meta:
# db_table = u'individual'
#
# class IndividualGenotypeMultipleBp(models.Model):
# variation_id = models.IntegerField()
# subsnp_id = models.IntegerField(null=True, blank=True)
# allele_1 = models.CharField(max_length=765, blank=True)
# allele_2 = models.CharField(max_length=765, blank=True)
# sample_id = models.IntegerField(null=True, blank=True)
# class Meta:
# db_table = u'individual_genotype_multiple_bp'
#
# class IndividualPopulation(models.Model):
# individual_sample_id = models.IntegerField()
# population_sample_id = models.IntegerField()
# class Meta:
# db_table = u'individual_population'
#
# class IndividualType(models.Model):
# individual_type_id = models.IntegerField(primary_key=True)
# name = models.CharField(max_length=765)
# description = models.TextField(blank=True)
# class Meta:
# db_table = u'individual_type'
#
# class Meta(models.Model):
# meta_id = models.IntegerField(primary_key=True)
# species_id = models.IntegerField(null=True, blank=True)
# meta_key = models.CharField(unique=True, max_length=120)
# meta_value = models.CharField(max_length=765)
# class Meta:
# db_table = u'meta'
#
# class MetaCoord(models.Model):
# table_name = models.CharField(unique=True, max_length=120)
# coord_system_id = models.IntegerField(unique=True)
# max_length = models.IntegerField(null=True, blank=True)
# class Meta:
# db_table = u'meta_coord'
#
# class Phenotype(models.Model):
# phenotype_id = models.IntegerField(primary_key=True)
# name = models.CharField(unique=True, max_length=150, blank=True)
# description = models.CharField(max_length=765, blank=True)
# class Meta:
# db_table = u'phenotype'
#
# class Population(models.Model):
# sample_id = models.IntegerField(primary_key=True)
# class Meta:
# db_table = u'population'
#
# class PopulationGenotype(models.Model):
# population_genotype_id = models.IntegerField(primary_key=True)
# variation_id = models.IntegerField()
# subsnp_id = models.IntegerField(null=True, blank=True)
# allele_1 = models.CharField(max_length=765, blank=True)
# allele_2 = models.CharField(max_length=765, blank=True)
# frequency = models.FloatField(null=True, blank=True)
# sample_id = models.IntegerField(null=True, blank=True)
# class Meta:
# db_table = u'population_genotype'
#
# class PopulationStructure(models.Model):
# super_population_sample_id = models.IntegerField()
# sub_population_sample_id = models.IntegerField()
# class Meta:
# db_table = u'population_structure'
#
# class ReadCoverage(models.Model):
# seq_region_id = models.IntegerField()
# seq_region_start = models.IntegerField()
# seq_region_end = models.IntegerField()
# level = models.IntegerField()
# sample_id = models.IntegerField()
# class Meta:
# db_table = u'read_coverage'
#
# class Sample(models.Model):
# sample_id = models.IntegerField(primary_key=True)
# name = models.CharField(max_length=765)
# size = models.IntegerField(null=True, blank=True)
# description = models.TextField(blank=True)
# display = models.CharField(max_length=39, blank=True)
# class Meta:
# db_table = u'sample'
#
# class SampleSynonym(models.Model):
# sample_synonym_id = models.IntegerField(primary_key=True)
# sample_id = models.IntegerField()
# source_id = models.IntegerField()
# name = models.CharField(max_length=765, blank=True)
# class Meta:
# db_table = u'sample_synonym'
#
# class SeqRegion(models.Model):
# seq_region_id = models.IntegerField(primary_key=True)
# name = models.CharField(unique=True, max_length=120)
# class Meta:
# db_table = u'seq_region'
class Source(models.Model):
source_id = models.IntegerField(primary_key=True)
name = models.CharField(max_length=765, blank=True)
version = models.IntegerField(null=True, blank=True)
description = models.CharField(max_length=765, blank=True)
class Meta:
db_table = u'source'
# class SubsnpHandle(models.Model):
# subsnp_id = models.IntegerField(primary_key=True)
# handle = models.CharField(max_length=60, blank=True)
# class Meta:
# db_table = u'subsnp_handle'
#
# class TaggedVariationFeature(models.Model):
# variation_feature_id = models.IntegerField(primary_key=True)
# sample_id = models.IntegerField(primary_key=True)
# class Meta:
# db_table = u'tagged_variation_feature'
#
# class TranscriptVariation(models.Model):
# transcript_variation_id = models.IntegerField(primary_key=True)
# transcript_id = models.IntegerField()
# variation_feature_id = models.IntegerField()
# cdna_start = models.IntegerField(null=True, blank=True)
# cdna_end = models.IntegerField(null=True, blank=True)
# translation_start = models.IntegerField(null=True, blank=True)
# translation_end = models.IntegerField(null=True, blank=True)
# peptide_allele_string = models.CharField(max_length=765, blank=True)
# consequence_type = models.CharField(max_length=717)
# class Meta:
# db_table = u'transcript_variation'
class Variation(models.Model, HasName):
variation_id = models.IntegerField(primary_key=True)
source = models.ForeignKey('Source')
name = models.CharField(unique=True, max_length=765, blank=True)
validation_status = models.CharField(max_length=138, blank=True)
ancestral_allele = models.TextField(blank=True)
class Meta:
db_table = u'variation'
# class VariationAnnotation(models.Model):
# variation_annotation_id = models.IntegerField(primary_key=True)
# variation_id = models.IntegerField()
# phenotype_id = models.IntegerField()
# source_id = models.IntegerField()
# study = models.CharField(max_length=90, blank=True)
# study_type = models.CharField(max_length=12, blank=True)
# local_stable_id = models.CharField(max_length=765, blank=True)
# associated_gene = models.CharField(max_length=765, blank=True)
# associated_variant_risk_allele = models.CharField(max_length=765, blank=True)
# variation_names = models.CharField(max_length=765, blank=True)
# risk_allele_freq_in_controls = models.CharField(max_length=90, blank=True)
# p_value = models.CharField(max_length=60, blank=True)
# class Meta:
# db_table = u'variation_annotation'
class VariationFeature(HasSeqRegion):
variation_feature_id = models.IntegerField(primary_key=True)
# seq_region_id = models.IntegerField()
# seq_region_start = models.IntegerField()
# seq_region_end = models.IntegerField()
# seq_region_strand = models.IntegerField()
variation = models.ForeignKey('Variation')
allele_string = models.TextField(blank=True)
variation_name = models.CharField(max_length=765, blank=True)
map_weight = models.IntegerField()
flags = models.CharField(max_length=27, blank=True)
source_id = models.IntegerField()
validation_status = models.CharField(max_length=117, blank=True)
consequence_type = models.CharField(max_length=795)
class Meta:
db_table = u'variation_feature'
# class VariationGroup(models.Model):
# variation_group_id = models.IntegerField(primary_key=True)
# name = models.CharField(unique=True, max_length=765, blank=True)
# source_id = models.IntegerField()
# type = models.CharField(max_length=27, blank=True)
# class Meta:
# db_table = u'variation_group'
#
# class VariationGroupFeature(models.Model):
# variation_group_feature_id = models.IntegerField(primary_key=True)
# seq_region_id = models.IntegerField()
# seq_region_start = models.IntegerField()
# seq_region_end = models.IntegerField()
# seq_region_strand = models.IntegerField()
# variation_group_id = models.IntegerField()
# variation_group_name = models.CharField(max_length=765, blank=True)
# class Meta:
# db_table = u'variation_group_feature'
#
# class VariationGroupVariation(models.Model):
# variation_id = models.IntegerField()
# variation_group_id = models.IntegerField()
# class Meta:
# db_table = u'variation_group_variation'
#
# class VariationSynonym(models.Model):
# variation_synonym_id = models.IntegerField(primary_key=True)
# variation_id = models.IntegerField()
# subsnp_id = models.IntegerField(null=True, blank=True)
# source_id = models.IntegerField()
# name = models.CharField(unique=True, max_length=765, blank=True)
# moltype = models.CharField(max_length=150, blank=True)
# class Meta:
# db_table = u'variation_synonym'
#