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xref_update_db_model

python.ensembl.xrefs.xref_update_db_model

Xref Update database ORM.

Base = declarative_base() module-attribute

AltAllele

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class AltAllele(Base):
    __tablename__ = "alt_allele"

    alt_allele_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True)
    gene_id: Column = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
    is_reference: Column = Column(INTEGER(2, unsigned=True), server_default=text("0"))

alt_allele_id = Column(INTEGER(10, unsigned=True), primary_key=True) class-attribute instance-attribute

gene_id = Column(INTEGER(10, unsigned=True), index=True, primary_key=True) class-attribute instance-attribute

is_reference = Column(INTEGER(2, unsigned=True), server_default=(text('0'))) class-attribute instance-attribute

ChecksumXref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class ChecksumXref(Base):
    __tablename__ = "checksum_xref"
    __table_args__ = (Index("checksum_idx", "checksum", mysql_length=10),)

    checksum_xref_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
    source_id: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    accession: Column = Column(CHAR(14), nullable=False)
    checksum: Column = Column(CHAR(32), nullable=False)

accession = Column(CHAR(14), nullable=False) class-attribute instance-attribute

checksum = Column(CHAR(32), nullable=False) class-attribute instance-attribute

checksum_xref_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True) class-attribute instance-attribute

source_id = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

CoordinateXref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class CoordinateXref(Base):
    __tablename__ = "coordinate_xref"
    __table_args__ = (
        Index("start_pos_idx", "species_id", "chromosome", "strand", "txStart"),
        Index("end_pos_idx", "species_id", "chromosome", "strand", "txEnd"),
    )

    coord_xref_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
    source_id: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    species_id: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    accession: Column = Column(VARCHAR(255), nullable=False)
    chromosome: Column = Column(VARCHAR(255), nullable=False)
    strand: Column = Column(TINYINT(2), nullable=False)
    txStart: Column = Column(INTEGER(10), nullable=False)
    txEnd: Column = Column(INTEGER(10), nullable=False)
    cdsStart: Column = Column(INTEGER(10))
    cdsEnd: Column = Column(INTEGER(10))
    exonStarts: Column = Column(TEXT, nullable=False)
    exonEnds: Column = Column(TEXT, nullable=False)

accession = Column(VARCHAR(255), nullable=False) class-attribute instance-attribute

cdsEnd = Column(INTEGER(10)) class-attribute instance-attribute

cdsStart = Column(INTEGER(10)) class-attribute instance-attribute

chromosome = Column(VARCHAR(255), nullable=False) class-attribute instance-attribute

coord_xref_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True) class-attribute instance-attribute

exonEnds = Column(TEXT, nullable=False) class-attribute instance-attribute

exonStarts = Column(TEXT, nullable=False) class-attribute instance-attribute

source_id = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

species_id = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

strand = Column(TINYINT(2), nullable=False) class-attribute instance-attribute

txEnd = Column(INTEGER(10), nullable=False) class-attribute instance-attribute

txStart = Column(INTEGER(10), nullable=False) class-attribute instance-attribute

DependentXref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class DependentXref(Base):
    __tablename__ = "dependent_xref"

    object_xref_id: Column = Column(INTEGER(10, unsigned=True), index=True)
    master_xref_id: Column = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
    dependent_xref_id: Column = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
    linkage_annotation: Column = Column(VARCHAR(255))
    linkage_source_id: Column = Column(INTEGER(10, unsigned=True), nullable=False, primary_key=True)

dependent_xref_id = Column(INTEGER(10, unsigned=True), index=True, primary_key=True) class-attribute instance-attribute

linkage_annotation = Column(VARCHAR(255)) class-attribute instance-attribute

linkage_source_id = Column(INTEGER(10, unsigned=True), nullable=False, primary_key=True) class-attribute instance-attribute

master_xref_id = Column(INTEGER(10, unsigned=True), index=True, primary_key=True) class-attribute instance-attribute

object_xref_id = Column(INTEGER(10, unsigned=True), index=True) class-attribute instance-attribute

DisplayXrefPriority

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class DisplayXrefPriority(Base):
    __tablename__ = "display_xref_priority"

    ensembl_object_type: Column = Column(VARCHAR(100), primary_key=True)
    source_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True)
    priority: Column = Column(SMALLINT(unsigned=True), nullable=False)

ensembl_object_type = Column(VARCHAR(100), primary_key=True) class-attribute instance-attribute

priority = Column(SMALLINT(unsigned=True), nullable=False) class-attribute instance-attribute

source_id = Column(INTEGER(10, unsigned=True), primary_key=True) class-attribute instance-attribute

GeneDescPriority

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class GeneDescPriority(Base):
    __tablename__ = "gene_desc_priority"

    source_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True)
    priority: Column = Column(SMALLINT(unsigned=True), nullable=False)

priority = Column(SMALLINT(unsigned=True), nullable=False) class-attribute instance-attribute

source_id = Column(INTEGER(10, unsigned=True), primary_key=True) class-attribute instance-attribute

GeneDirectXref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class GeneDirectXref(Base):
    __tablename__ = "gene_direct_xref"

    general_xref_id: Column = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
    ensembl_stable_id: Column = Column(VARCHAR(255), index=True, primary_key=True)
    linkage_xref: Column = Column(VARCHAR(255))

ensembl_stable_id = Column(VARCHAR(255), index=True, primary_key=True) class-attribute instance-attribute

general_xref_id = Column(INTEGER(10, unsigned=True), index=True, primary_key=True) class-attribute instance-attribute

linkage_xref = Column(VARCHAR(255)) class-attribute instance-attribute

GeneStableId

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class GeneStableId(Base):
    __tablename__ = "gene_stable_id"

    internal_id: Column = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
    stable_id: Column = Column(VARCHAR(128), primary_key=True)
    display_xref_id: Column = Column(INTEGER(10, unsigned=True))
    desc_set: Column = Column(INTEGER(10, unsigned=True), server_default=text("0"))

desc_set = Column(INTEGER(10, unsigned=True), server_default=(text('0'))) class-attribute instance-attribute

display_xref_id = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

internal_id = Column(INTEGER(10, unsigned=True), nullable=False, index=True) class-attribute instance-attribute

stable_id = Column(VARCHAR(128), primary_key=True) class-attribute instance-attribute

GeneTranscriptTranslation

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class GeneTranscriptTranslation(Base):
    __tablename__ = "gene_transcript_translation"

    gene_id: Column = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
    transcript_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True)
    translation_id: Column = Column(INTEGER(10, unsigned=True), index=True)

gene_id = Column(INTEGER(10, unsigned=True), nullable=False, index=True) class-attribute instance-attribute

transcript_id = Column(INTEGER(10, unsigned=True), primary_key=True) class-attribute instance-attribute

translation_id = Column(INTEGER(10, unsigned=True), index=True) class-attribute instance-attribute

IdentityXref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class IdentityXref(Base):
    __tablename__ = "identity_xref"

    object_xref_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True)
    query_identity: Column = Column(INTEGER(5))
    target_identity: Column = Column(INTEGER(5))
    hit_start: Column = Column(INTEGER(10))
    hit_end: Column = Column(INTEGER(10))
    translation_start: Column = Column(INTEGER(10))
    translation_end: Column = Column(INTEGER(10))
    cigar_line: Column = Column(TEXT)
    score: Column = Column(DOUBLE)
    evalue: Column = Column(DOUBLE)

cigar_line = Column(TEXT) class-attribute instance-attribute

evalue = Column(DOUBLE) class-attribute instance-attribute

hit_end = Column(INTEGER(10)) class-attribute instance-attribute

hit_start = Column(INTEGER(10)) class-attribute instance-attribute

object_xref_id = Column(INTEGER(10, unsigned=True), primary_key=True) class-attribute instance-attribute

query_identity = Column(INTEGER(5)) class-attribute instance-attribute

score = Column(DOUBLE) class-attribute instance-attribute

target_identity = Column(INTEGER(5)) class-attribute instance-attribute

translation_end = Column(INTEGER(10)) class-attribute instance-attribute

translation_start = Column(INTEGER(10)) class-attribute instance-attribute

Mapping

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class Mapping(Base):
    __tablename__ = "mapping"

    job_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True)
    type: Column = Column(Enum("dna", "peptide", "UCSC"))
    command_line: Column = Column(TEXT)
    percent_query_cutoff: Column = Column(INTEGER(10, unsigned=True))
    percent_target_cutoff: Column = Column(INTEGER(10, unsigned=True))
    method: Column = Column(VARCHAR(255))
    array_size: Column = Column(INTEGER(10, unsigned=True))

array_size = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

command_line = Column(TEXT) class-attribute instance-attribute

job_id = Column(INTEGER(10, unsigned=True), primary_key=True) class-attribute instance-attribute

method = Column(VARCHAR(255)) class-attribute instance-attribute

percent_query_cutoff = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

percent_target_cutoff = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

type = Column(Enum('dna', 'peptide', 'UCSC')) class-attribute instance-attribute

MappingJobs

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class MappingJobs(Base):
    __tablename__ = "mapping_jobs"

    mapping_job_id: Column = Column(INTEGER(10), primary_key=True, autoincrement=True)
    root_dir: Column = Column(TEXT)
    map_file: Column = Column(VARCHAR(255))
    status: Column = Column(Enum("SUBMITTED", "FAILED", "SUCCESS"))
    out_file: Column = Column(VARCHAR(255))
    err_file: Column = Column(VARCHAR(255))
    array_number: Column = Column(INTEGER(10, unsigned=True))
    job_id: Column = Column(INTEGER(10, unsigned=True))
    failed_reason: Column = Column(VARCHAR(255))
    object_xref_start: Column = Column(INTEGER(10, unsigned=True))
    object_xref_end: Column = Column(INTEGER(10, unsigned=True))

array_number = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

err_file = Column(VARCHAR(255)) class-attribute instance-attribute

failed_reason = Column(VARCHAR(255)) class-attribute instance-attribute

job_id = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

map_file = Column(VARCHAR(255)) class-attribute instance-attribute

mapping_job_id = Column(INTEGER(10), primary_key=True, autoincrement=True) class-attribute instance-attribute

object_xref_end = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

object_xref_start = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

out_file = Column(VARCHAR(255)) class-attribute instance-attribute

root_dir = Column(TEXT) class-attribute instance-attribute

status = Column(Enum('SUBMITTED', 'FAILED', 'SUCCESS')) class-attribute instance-attribute

Meta

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class Meta(Base):
    __tablename__ = "meta"
    __table_args__ = (
        Index("species_key_value_idx", "meta_id", "species_id", "meta_key", "meta_value", unique=True),
        Index("species_value_idx", "species_id", "meta_value"),
    )

    meta_id: Column = Column(INTEGER(10), primary_key=True, autoincrement=True)
    species_id: Column = Column(INTEGER(10, unsigned=True), server_default=text("1"))
    meta_key: Column = Column(VARCHAR(40), nullable=False)
    meta_value: Column = Column(VARCHAR(255, binary=True), nullable=False)
    date: Column = Column(DateTime, nullable=False)

date = Column(DateTime, nullable=False) class-attribute instance-attribute

meta_id = Column(INTEGER(10), primary_key=True, autoincrement=True) class-attribute instance-attribute

meta_key = Column(VARCHAR(40), nullable=False) class-attribute instance-attribute

meta_value = Column(VARCHAR(255, binary=True), nullable=False) class-attribute instance-attribute

species_id = Column(INTEGER(10, unsigned=True), server_default=(text('1'))) class-attribute instance-attribute

ObjectXref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class ObjectXref(Base):
    __tablename__ = "object_xref"
    __table_args__ = (
        Index(
            "unique_idx",
            "ensembl_object_type",
            "ensembl_id",
            "xref_id",
            "ox_status",
            "master_xref_id",
            unique=True,
        ),
        Index("oxref_idx", "object_xref_id", "xref_id", "ensembl_object_type", "ensembl_id"),
        Index("xref_idx", "xref_id", "ensembl_object_type"),
    )

    object_xref_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
    ensembl_id: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    ensembl_object_type: Column = Column(
        Enum("RawContig", "Transcript", "Gene", "Translation"), nullable=False
    )
    xref_id: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    linkage_annotation: Column = Column(VARCHAR(255))
    linkage_type: Column = Column(
        Enum(
            "PROJECTION",
            "MISC",
            "DEPENDENT",
            "DIRECT",
            "SEQUENCE_MATCH",
            "INFERRED_PAIR",
            "PROBE",
            "UNMAPPED",
            "COORDINATE_OVERLAP",
            "CHECKSUM",
        )
    )
    ox_status: Column = Column(
        Enum("DUMP_OUT", "FAILED_PRIORITY", "FAILED_CUTOFF", "NO_DISPLAY", "MULTI_DELETE"),
        nullable=False,
        server_default=text("'DUMP_OUT'"),
    )
    unused_priority: Column = Column(INTEGER(10, unsigned=True))
    master_xref_id: Column = Column(INTEGER(10, unsigned=True))

ensembl_id = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

ensembl_object_type = Column(Enum('RawContig', 'Transcript', 'Gene', 'Translation'), nullable=False) class-attribute instance-attribute

linkage_annotation = Column(VARCHAR(255)) class-attribute instance-attribute

linkage_type = Column(Enum('PROJECTION', 'MISC', 'DEPENDENT', 'DIRECT', 'SEQUENCE_MATCH', 'INFERRED_PAIR', 'PROBE', 'UNMAPPED', 'COORDINATE_OVERLAP', 'CHECKSUM')) class-attribute instance-attribute

master_xref_id = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

object_xref_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True) class-attribute instance-attribute

ox_status = Column(Enum('DUMP_OUT', 'FAILED_PRIORITY', 'FAILED_CUTOFF', 'NO_DISPLAY', 'MULTI_DELETE'), nullable=False, server_default=(text("'DUMP_OUT'"))) class-attribute instance-attribute

unused_priority = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

xref_id = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

Pairs

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class Pairs(Base):
    __tablename__ = "pairs"

    pair_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
    source_id: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    accession1: Column = Column(VARCHAR(255), nullable=False, index=True)
    accession2: Column = Column(VARCHAR(255), nullable=False, index=True)

accession1 = Column(VARCHAR(255), nullable=False, index=True) class-attribute instance-attribute

accession2 = Column(VARCHAR(255), nullable=False, index=True) class-attribute instance-attribute

pair_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True) class-attribute instance-attribute

source_id = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

PrimaryXref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class PrimaryXref(Base):
    __tablename__ = "primary_xref"

    xref_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True)
    sequence: Column = Column(MEDIUMTEXT)
    sequence_type: Column = Column(Enum("dna", "peptide"))
    status: Column = Column(Enum("experimental", "predicted"))

sequence = Column(MEDIUMTEXT) class-attribute instance-attribute

sequence_type = Column(Enum('dna', 'peptide')) class-attribute instance-attribute

status = Column(Enum('experimental', 'predicted')) class-attribute instance-attribute

xref_id = Column(INTEGER(10, unsigned=True), primary_key=True) class-attribute instance-attribute

ProcessStatus

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class ProcessStatus(Base):
    __tablename__ = "process_status"

    id: Column = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
    status: Column = Column(
        Enum(
            "xref_created",
            "parsing_started",
            "parsing_finished",
            "alt_alleles_added",
            "xref_fasta_dumped",
            "core_fasta_dumped",
            "core_data_loaded",
            "mapping_submitted",
            "mapping_finished",
            "mapping_processed",
            "direct_xrefs_parsed",
            "prioritys_flagged",
            "processed_pairs",
            "biomart_test_finished",
            "source_level_move_finished",
            "alt_alleles_processed",
            "official_naming_done",
            "checksum_xrefs_started",
            "checksum_xrefs_finished",
            "coordinate_xrefs_started",
            "coordinate_xref_finished",
            "tests_started",
            "tests_failed",
            "tests_finished",
            "core_loaded",
            "display_xref_done",
            "gene_description_done",
        )
    )
    date: Column = Column(DateTime, nullable=False)

date = Column(DateTime, nullable=False) class-attribute instance-attribute

id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True) class-attribute instance-attribute

status = Column(Enum('xref_created', 'parsing_started', 'parsing_finished', 'alt_alleles_added', 'xref_fasta_dumped', 'core_fasta_dumped', 'core_data_loaded', 'mapping_submitted', 'mapping_finished', 'mapping_processed', 'direct_xrefs_parsed', 'prioritys_flagged', 'processed_pairs', 'biomart_test_finished', 'source_level_move_finished', 'alt_alleles_processed', 'official_naming_done', 'checksum_xrefs_started', 'checksum_xrefs_finished', 'coordinate_xrefs_started', 'coordinate_xref_finished', 'tests_started', 'tests_failed', 'tests_finished', 'core_loaded', 'display_xref_done', 'gene_description_done')) class-attribute instance-attribute

Source

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class Source(Base):
    __tablename__ = "source"

    source_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
    name: Column = Column(VARCHAR(255), nullable=False, index=True)
    status: Column = Column(
        Enum("KNOWN", "XREF", "PRED", "ORTH", "PSEUDO", "LOWEVIDENCE", "NOIDEA"),
        nullable=False,
        server_default=text("'NOIDEA'"),
    )
    source_release: Column = Column(VARCHAR(255))
    ordered: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    priority: Column = Column(INTEGER(5, unsigned=True), server_default=text("1"))
    priority_description: Column = Column(VARCHAR(40), server_default=text("''"))

name = Column(VARCHAR(255), nullable=False, index=True) class-attribute instance-attribute

ordered = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

priority = Column(INTEGER(5, unsigned=True), server_default=(text('1'))) class-attribute instance-attribute

priority_description = Column(VARCHAR(40), server_default=(text("''"))) class-attribute instance-attribute

source_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True) class-attribute instance-attribute

source_release = Column(VARCHAR(255)) class-attribute instance-attribute

status = Column(Enum('KNOWN', 'XREF', 'PRED', 'ORTH', 'PSEUDO', 'LOWEVIDENCE', 'NOIDEA'), nullable=False, server_default=(text("'NOIDEA'"))) class-attribute instance-attribute

SourceURL

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class SourceURL(Base):
    __tablename__ = "source_url"

    source_url_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
    source_id: Column = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
    species_id: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    parser: Column = Column(VARCHAR(255))

parser = Column(VARCHAR(255)) class-attribute instance-attribute

source_id = Column(INTEGER(10, unsigned=True), nullable=False, index=True) class-attribute instance-attribute

source_url_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True) class-attribute instance-attribute

species_id = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

Species

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class Species(Base):
    __tablename__ = "species"

    species_id: Column = Column(INTEGER(10, unsigned=True), nullable=False, index=True, primary_key=True)
    taxonomy_id: Column = Column(INTEGER(10, unsigned=True), nullable=False, index=True, primary_key=True)
    name: Column = Column(VARCHAR(255), nullable=False, index=True)
    aliases: Column = Column(VARCHAR(255))

aliases = Column(VARCHAR(255)) class-attribute instance-attribute

name = Column(VARCHAR(255), nullable=False, index=True) class-attribute instance-attribute

species_id = Column(INTEGER(10, unsigned=True), nullable=False, index=True, primary_key=True) class-attribute instance-attribute

taxonomy_id = Column(INTEGER(10, unsigned=True), nullable=False, index=True, primary_key=True) class-attribute instance-attribute

Synonym

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class Synonym(Base):
    __tablename__ = "synonym"

    xref_id: Column = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
    synonym: Column = Column(VARCHAR(255), index=True, primary_key=True)

synonym = Column(VARCHAR(255), index=True, primary_key=True) class-attribute instance-attribute

xref_id = Column(INTEGER(10, unsigned=True), index=True, primary_key=True) class-attribute instance-attribute

TranscriptDirectXref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class TranscriptDirectXref(Base):
    __tablename__ = "transcript_direct_xref"

    general_xref_id: Column = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
    ensembl_stable_id: Column = Column(VARCHAR(255), index=True, primary_key=True)
    linkage_xref: Column = Column(VARCHAR(255))

ensembl_stable_id = Column(VARCHAR(255), index=True, primary_key=True) class-attribute instance-attribute

general_xref_id = Column(INTEGER(10, unsigned=True), index=True, primary_key=True) class-attribute instance-attribute

linkage_xref = Column(VARCHAR(255)) class-attribute instance-attribute

TranscriptStableId

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class TranscriptStableId(Base):
    __tablename__ = "transcript_stable_id"

    internal_id: Column = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
    stable_id: Column = Column(VARCHAR(128), primary_key=True)
    display_xref_id: Column = Column(INTEGER(10, unsigned=True))
    biotype: Column = Column(VARCHAR(40), nullable=False)

biotype = Column(VARCHAR(40), nullable=False) class-attribute instance-attribute

display_xref_id = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

internal_id = Column(INTEGER(10, unsigned=True), nullable=False, index=True) class-attribute instance-attribute

stable_id = Column(VARCHAR(128), primary_key=True) class-attribute instance-attribute

TranslationDirectXref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class TranslationDirectXref(Base):
    __tablename__ = "translation_direct_xref"

    general_xref_id: Column = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
    ensembl_stable_id: Column = Column(VARCHAR(255), index=True, primary_key=True)
    linkage_xref: Column = Column(VARCHAR(255))

ensembl_stable_id = Column(VARCHAR(255), index=True, primary_key=True) class-attribute instance-attribute

general_xref_id = Column(INTEGER(10, unsigned=True), index=True, primary_key=True) class-attribute instance-attribute

linkage_xref = Column(VARCHAR(255)) class-attribute instance-attribute

TranslationStableId

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class TranslationStableId(Base):
    __tablename__ = "translation_stable_id"

    internal_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True)
    stable_id: Column = Column(VARCHAR(128), nullable=False, index=True)

internal_id = Column(INTEGER(10, unsigned=True), primary_key=True) class-attribute instance-attribute

stable_id = Column(VARCHAR(128), nullable=False, index=True) class-attribute instance-attribute

Xref

Bases: Base

Source code in src/python/ensembl/xrefs/xref_update_db_model.py 
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class Xref(Base):
    __tablename__ = "xref"
    __table_args__ = (
        Index(
            "acession_idx",
            "accession",
            "source_id",
            "species_id",
            "label",
            unique=True,
            mysql_length={"accession": 100, "label": 100},
        ),
        Index("species_source_idx", "species_id", "source_id"),
    )

    xref_id: Column = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
    accession: Column = Column(VARCHAR(255), nullable=False)
    version: Column = Column(INTEGER(10, unsigned=True))
    label: Column = Column(VARCHAR(255))
    description: Column = Column(TEXT)
    source_id: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    species_id: Column = Column(INTEGER(10, unsigned=True), nullable=False)
    info_type: Column = Column(
        Enum(
            "NONE",
            "PROJECTION",
            "MISC",
            "DEPENDENT",
            "DIRECT",
            "SEQUENCE_MATCH",
            "INFERRED_PAIR",
            "PROBE",
            "UNMAPPED",
            "COORDINATE_OVERLAP",
            "CHECKSUM",
        ),
        nullable=False,
        server_default=text("'NONE'"),
    )
    info_text: Column = Column(VARCHAR(255), nullable=False, server_default=text("''"))
    dumped: Column = Column(
        Enum(
            "MAPPED",
            "NO_DUMP_ANOTHER_PRIORITY",
            "UNMAPPED_NO_MAPPING",
            "UNMAPPED_NO_MASTER",
            "UNMAPPED_MASTER_FAILED",
            "UNMAPPED_NO_STABLE_ID",
            "UNMAPPED_INTERPRO",
        )
    )

accession = Column(VARCHAR(255), nullable=False) class-attribute instance-attribute

description = Column(TEXT) class-attribute instance-attribute

dumped = Column(Enum('MAPPED', 'NO_DUMP_ANOTHER_PRIORITY', 'UNMAPPED_NO_MAPPING', 'UNMAPPED_NO_MASTER', 'UNMAPPED_MASTER_FAILED', 'UNMAPPED_NO_STABLE_ID', 'UNMAPPED_INTERPRO')) class-attribute instance-attribute

info_text = Column(VARCHAR(255), nullable=False, server_default=(text("''"))) class-attribute instance-attribute

info_type = Column(Enum('NONE', 'PROJECTION', 'MISC', 'DEPENDENT', 'DIRECT', 'SEQUENCE_MATCH', 'INFERRED_PAIR', 'PROBE', 'UNMAPPED', 'COORDINATE_OVERLAP', 'CHECKSUM'), nullable=False, server_default=(text("'NONE'"))) class-attribute instance-attribute

label = Column(VARCHAR(255)) class-attribute instance-attribute

source_id = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

species_id = Column(INTEGER(10, unsigned=True), nullable=False) class-attribute instance-attribute

version = Column(INTEGER(10, unsigned=True)) class-attribute instance-attribute

xref_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True) class-attribute instance-attribute