Coverage for src/python/ensembl/core/models.py: 100%
787 statements
« prev ^ index » next coverage.py v7.6.1, created at 2024-09-17 13:09 +0000
1# See the NOTICE file distributed with this work for additional information
2# regarding copyright ownership.
3#
4# Licensed under the Apache License, Version 2.0 (the "License");
5# you may not use this file except in compliance with the License.
6# You may obtain a copy of the License at
7# http://www.apache.org/licenses/LICENSE-2.0
8#
9# Unless required by applicable law or agreed to in writing, software
10# distributed under the License is distributed on an "AS IS" BASIS,
11# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12# See the License for the specific language governing permissions and
13# limitations under the License.
14"""Ensembl Core database ORM."""
15# Ignore some pylint and mypy checks due to the nature of SQLAlchemy ORMs
16# pylint: disable=missing-class-docstring,too-many-lines,fixme
17# mypy: disable-error-code="misc, valid-type"
19# WIP: This module is not complete nor fully tested and will most likely change its public interface
20# TODO:
21# - Please help defining/fixing relationships.
22# There are several relationships that have not been mapped yet, please help
23# adding them to the models if you find they're missing
24# https://docs.sqlalchemy.org/en/14/orm/basic_relationships.html
25# - Please help with better names.
26# Class names and attributes were generated directly
27# from the SQL schema but might not be suitable for a ORM.
28# For instance, several class attributes are prepended with the class name.
29# That's redundant most of the times and will result in less readable code.
30# Some class names are somehow reserved (e.g. class Meta) and some attributes names
31# are actually reserved (e.g. type, map, id) please help changing them into
32# meaningful ones
34from typing import Any
36import sqlalchemy
37from sqlalchemy import (
38 Column,
39 DECIMAL,
40 DateTime,
41 Enum,
42 Float,
43 ForeignKey,
44 Index,
45 String,
46 Table,
47 Text,
48 UniqueConstraint,
49 text,
50)
51from sqlalchemy.dialects.mysql import (
52 BIGINT,
53 DOUBLE,
54 INTEGER,
55 LONGTEXT,
56 MEDIUMTEXT,
57 SET,
58 SMALLINT,
59 TINYINT,
60 TINYTEXT,
61 VARCHAR,
62)
63from sqlalchemy.ext.compiler import compiles
64from sqlalchemy.orm import declarative_base, relationship
66Base = declarative_base()
67metadata = Base.metadata
70class AltAlleleGroup(Base):
71 __tablename__ = "alt_allele_group"
73 alt_allele_group_id: Column = Column(INTEGER(10), primary_key=True)
76class Analysis(Base):
77 __tablename__ = "analysis"
79 analysis_id: Column = Column(SMALLINT(5), primary_key=True)
80 created: Column = Column(DateTime)
81 logic_name: Column = Column(String(128), nullable=False, unique=True)
82 db: Column = Column(String(120))
83 db_version: Column = Column(String(40))
84 db_file: Column = Column(String(120))
85 program: Column = Column(String(80))
86 program_version: Column = Column(String(40))
87 program_file: Column = Column(String(80))
88 parameters: Column = Column(Text)
89 module: Column = Column(String(80))
90 module_version: Column = Column(String(40))
91 gff_source: Column = Column(String(40))
92 gff_feature: Column = Column(String(40))
95class AssociatedGroup(Base):
96 __tablename__ = "associated_group"
98 associated_group_id: Column = Column(INTEGER(10), primary_key=True)
99 description: Column = Column(String(128))
102class AttribType(Base):
103 __tablename__ = "attrib_type"
105 attrib_type_id: Column = Column(SMALLINT(5), primary_key=True)
106 code: Column = Column(String(20), nullable=False, unique=True, server_default=text("''"))
107 name: Column = Column(String(255), nullable=False, server_default=text("''"))
108 description: Column = Column(Text)
110 seq_region_attrib = relationship("SeqRegionAttrib", back_populates="attrib_type")
113class Biotype(Base):
114 __tablename__ = "biotype"
115 __table_args__ = (Index("name_type_idx", "name", "object_type", unique=True),)
117 biotype_id: Column = Column(INTEGER(10), primary_key=True)
118 name: Column = Column(String(64), nullable=False)
119 object_type: Column = Column(Enum("gene", "transcript"), nullable=False, server_default=text("'gene'"))
120 db_type: Column = Column(
121 SET(
122 "cdna",
123 "core",
124 "coreexpressionatlas",
125 "coreexpressionest",
126 "coreexpressiongnf",
127 "funcgen",
128 "otherfeatures",
129 "rnaseq",
130 "variation",
131 "vega",
132 "presite",
133 "sangervega",
134 ),
135 nullable=False,
136 server_default=text("'core'"),
137 )
138 attrib_type_id: Column = Column(INTEGER(11))
139 description: Column = Column(Text)
140 biotype_group: Column = Column(
141 Enum(
142 "coding",
143 "pseudogene",
144 "snoncoding",
145 "lnoncoding",
146 "mnoncoding",
147 "LRG",
148 "undefined",
149 "no_group",
150 )
151 )
152 so_acc: Column = Column(String(64))
153 so_term: Column = Column(String(1023))
156class CoordSystem(Base):
157 __tablename__ = "coord_system"
158 __table_args__ = (
159 Index("name_idx", "name", "version", "species_id", unique=True),
160 Index("rank_idx", "rank", "species_id", unique=True),
161 )
163 coord_system_id: Column = Column(INTEGER(10), primary_key=True)
164 species_id: Column = Column(INTEGER(10), nullable=False, index=True, server_default=text("'1'"))
165 name: Column = Column(String(40), nullable=False)
166 version: Column = Column(String(255))
167 rank: Column = Column(INTEGER(11), nullable=False)
168 attrib: Column = Column(SET("default_version", "sequence_level"))
169 # Many to one relationship
170 seq_region = relationship("SeqRegion", back_populates="coord_system")
171 meta = relationship("Meta", back_populates="coord_system")
174class Ditag(Base):
175 __tablename__ = "ditag"
177 ditag_id: Column = Column(INTEGER(10), primary_key=True)
178 name: Column = Column(String(30), nullable=False)
179 tag_type: Column = Column("type", String(30), nullable=False)
180 tag_count: Column = Column(SMALLINT(6), nullable=False, server_default=text("'1'"))
181 sequence: Column = Column(TINYTEXT, nullable=False)
184class DNAAlignFeatureAttrib(Base):
185 __tablename__ = "dna_align_feature_attrib"
186 __table_args__ = (
187 Index(
188 "dna_align_feature_attribx",
189 "dna_align_feature_id",
190 "attrib_type_id",
191 "value",
192 unique=True,
193 mysql_length={"value": 10},
194 ),
195 Index("ditag_type_val_idx", "attrib_type_id", "value", mysql_length={"value": 10}),
196 Index("ditag_value_idx", "value", mysql_length=10),
197 )
199 dna_align_feature_id: Column = Column(
200 INTEGER(10),
201 ForeignKey("dna_align_feature.dna_align_feature_id"),
202 nullable=False,
203 index=True,
204 primary_key=True,
205 )
206 attrib_type_id: Column = Column(SMALLINT(5), nullable=False, primary_key=True)
207 value: Column = Column(String(500), nullable=False, primary_key=True)
210class ExternalDb(Base):
211 __tablename__ = "external_db"
212 __table_args__ = (Index("db_name_db_release_idx", "db_name", "db_release", unique=True),)
214 external_db_id: Column = Column(INTEGER(10), primary_key=True)
215 db_name: Column = Column(String(100), nullable=False)
216 db_release: Column = Column(String(255))
217 status: Column = Column(Enum("KNOWNXREF", "KNOWN", "XREF", "PRED", "ORTH", "PSEUDO"), nullable=False)
218 priority: Column = Column(INTEGER(11), nullable=False)
219 db_display_name: Column = Column(String(255))
220 db_type: Column = Column(
221 "type",
222 Enum(
223 "ARRAY",
224 "ALT_TRANS",
225 "ALT_GENE",
226 "MISC",
227 "LIT",
228 "PRIMARY_DB_SYNONYM",
229 "ENSEMBL",
230 ),
231 nullable=False,
232 )
233 secondary_db_name: Column = Column(String(255))
234 secondary_db_table: Column = Column(String(255))
235 description: Column = Column(Text)
236 seq_region_synonym = relationship("SeqRegionSynonym", back_populates="external_db")
239class Gene(Base):
240 __tablename__ = "gene"
241 __table_args__ = (
242 Index("gene_seq_region_idx", "seq_region_id", "seq_region_start"),
243 Index("gene_stable_id_idx", "stable_id", "version"),
244 )
246 gene_id: Column = Column(INTEGER(10), primary_key=True)
247 biotype: Column = Column(String(40), nullable=False)
248 analysis_id: Column = Column(
249 ForeignKey("analysis.analysis_id"),
250 nullable=False,
251 index=True,
252 )
253 seq_region_id: Column = Column(
254 ForeignKey("seq_region.seq_region_id"),
255 nullable=False,
256 )
257 seq_region_start: Column = Column(INTEGER(10), nullable=False)
258 seq_region_end: Column = Column(INTEGER(10), nullable=False)
259 seq_region_strand: Column = Column(TINYINT(2), nullable=False)
260 display_xref_id: Column = Column(ForeignKey("xref.xref_id"), index=True)
261 source: Column = Column(String(40), nullable=False)
262 description: Column = Column(Text)
263 is_current: Column = Column(TINYINT(1), nullable=False, server_default=text("'1'"))
264 canonical_transcript_id: Column = Column(
265 ForeignKey("transcript.transcript_id"),
266 nullable=False,
267 index=True,
268 )
269 stable_id: Column = Column(String(128))
270 version: Column = Column(SMALLINT(5))
271 created_date: Column = Column(DateTime)
272 modified_date: Column = Column(DateTime)
274 analysis = relationship("Analysis", primaryjoin="Gene.analysis_id == Analysis.analysis_id")
275 canonical_transcript = relationship(
276 "Transcript",
277 primaryjoin="Gene.canonical_transcript_id == Transcript.transcript_id",
278 )
279 display_xref = relationship("Xref", primaryjoin="Gene.display_xref_id == Xref.xref_id")
280 seq_region = relationship("SeqRegion", primaryjoin="Gene.seq_region_id == SeqRegion.seq_region_id")
283class GenomeStatistics(Base):
284 __tablename__ = "genome_statistics"
285 __table_args__ = (Index("stats_uniq", "statistic", "attrib_type_id", "species_id", unique=True),)
287 genome_statistics_id: Column = Column(INTEGER(10), primary_key=True)
288 statistic: Column = Column(String(128), nullable=False)
289 value: Column = Column(BIGINT(11), nullable=False, server_default=text("'0'"))
290 species_id: Column = Column(INTEGER(10), server_default=text("'1'"))
291 attrib_type_id: Column = Column(INTEGER(10))
292 timestamp: Column = Column(DateTime)
295t_interpro = Table(
296 "interpro",
297 metadata,
298 Column("interpro_ac", String(40), nullable=False),
299 Column("id", VARCHAR(40), nullable=False, index=True),
300 Index("accession_idx", "interpro_ac", "id", unique=True),
301)
304class Map(Base):
305 __tablename__ = "map"
307 map_id: Column = Column(INTEGER(10), primary_key=True)
308 map_name: Column = Column(String(30), nullable=False)
311class MappingSession(Base):
312 __tablename__ = "mapping_session"
314 mapping_session_id: Column = Column(INTEGER(10), primary_key=True)
315 old_db_name: Column = Column(String(80), nullable=False, server_default=text("''"))
316 new_db_name: Column = Column(String(80), nullable=False, server_default=text("''"))
317 old_release: Column = Column(String(5), nullable=False, server_default=text("''"))
318 new_release: Column = Column(String(5), nullable=False, server_default=text("''"))
319 old_assembly: Column = Column(String(80), nullable=False, server_default=text("''"))
320 new_assembly: Column = Column(String(80), nullable=False, server_default=text("''"))
321 created: Column = Column(DateTime, nullable=False)
324class MappingSet(Base):
325 __tablename__ = "mapping_set"
326 __table_args__ = (Index("mapping_idx", "internal_schema_build", "external_schema_build", unique=True),)
328 mapping_set_id: Column = Column(INTEGER(10), primary_key=True)
329 internal_schema_build: Column = Column(String(20), nullable=False)
330 external_schema_build: Column = Column(String(20), nullable=False)
333class Marker(Base):
334 __tablename__ = "marker"
335 __table_args__ = (Index("marker_idx", "marker_id", "priority"),)
337 marker_id: Column = Column(INTEGER(10), primary_key=True)
338 display_marker_synonym_id: Column = Column(
339 ForeignKey("marker_synonym.marker_synonym_id"),
340 index=True,
341 )
342 left_primer: Column = Column(String(100), nullable=False)
343 right_primer: Column = Column(String(100), nullable=False)
344 min_primer_dist: Column = Column(INTEGER(10), nullable=False)
345 max_primer_dist: Column = Column(INTEGER(10), nullable=False)
346 priority: Column = Column(INTEGER(11))
347 marker_type: Column = Column("type", Enum("est", "microsatellite"))
349 display_marker_synonym = relationship(
350 "MarkerSynonym",
351 primaryjoin="Marker.display_marker_synonym_id == MarkerSynonym.marker_synonym_id",
352 )
355class MarkerSynonym(Base):
356 __tablename__ = "marker_synonym"
357 __table_args__ = (Index("marker_synonym_idx", "marker_synonym_id", "name"),)
359 marker_synonym_id: Column = Column(INTEGER(10), primary_key=True)
360 marker_id: Column = Column(
361 ForeignKey("marker.marker_id"),
362 nullable=False,
363 index=True,
364 )
365 source: Column = Column(String(20))
366 name: Column = Column(String(50))
368 marker = relationship("Marker", primaryjoin="MarkerSynonym.marker_id == Marker.marker_id")
371class PeptideArchive(Base):
372 __tablename__ = "peptide_archive"
374 peptide_archive_id: Column = Column(INTEGER(10), primary_key=True)
375 md5_checksum: Column = Column(String(32), index=True)
376 peptide_seq: Column = Column(MEDIUMTEXT, nullable=False)
379class RepeatConsensus(Base):
380 __tablename__ = "repeat_consensus"
381 __table_args__ = (Index("repeat_consensus_idx", "repeat_consensus", unique=True, mysql_length=10),)
383 repeat_consensus_id: Column = Column(INTEGER(10), primary_key=True)
384 repeat_name: Column = Column(String(255), nullable=False, index=True)
385 repeat_class: Column = Column(String(100), nullable=False, index=True)
386 repeat_type: Column = Column(String(40), nullable=False, index=True)
387 repeat_consensus: Column = Column(Text)
390class Rnaproduct(Base):
391 __tablename__ = "rnaproduct"
392 __table_args__ = (Index("rnaproduct_stable_id_idx", "stable_id", "version"),)
394 rnaproduct_id: Column = Column(INTEGER(10), primary_key=True)
395 rnaproduct_type_id: Column = Column(SMALLINT(5), nullable=False)
396 transcript_id: Column = Column(INTEGER(10), nullable=False, index=True)
397 seq_start: Column = Column(INTEGER(10), nullable=False)
398 start_exon_id: Column = Column(INTEGER(10))
399 seq_end: Column = Column(INTEGER(10), nullable=False)
400 end_exon_id: Column = Column(INTEGER(10))
401 stable_id: Column = Column(String(128))
402 version: Column = Column(SMALLINT(5))
403 created_date: Column = Column(DateTime)
404 modified_date: Column = Column(DateTime)
407class RNAproductAttrib(Base):
408 __tablename__ = "rnaproduct_attrib"
409 __table_args__ = (
410 Index(
411 "rnaproduct_attribx",
412 "rnaproduct_id",
413 "attrib_type_id",
414 "value",
415 unique=True,
416 mysql_length={"value": 10},
417 ),
418 Index("rnaproduct_type_val_idx", "attrib_type_id", "value", mysql_length={"value": 10}),
419 Index("rnaproduct_value_idx", "value", mysql_length=10),
420 )
421 rnaproduct_id: Column = Column(
422 ForeignKey("rnaproduct.rnaproduct_id"), nullable=False, index=True, primary_key=True
423 )
424 attrib_type_id: Column = Column(SMALLINT(5), nullable=False, primary_key=True)
425 value: Column = Column(String(500), nullable=False, primary_key=True)
428class RnaproductType(Base):
429 __tablename__ = "rnaproduct_type"
431 rnaproduct_type_id: Column = Column(SMALLINT(5), primary_key=True)
432 code: Column = Column(String(20), nullable=False, unique=True, server_default=text("''"))
433 name: Column = Column(String(255), nullable=False, server_default=text("''"))
434 description: Column = Column(Text)
437class Transcript(Base):
438 __tablename__ = "transcript"
439 __table_args__ = (
440 Index("transcript_seq_region_idx", "seq_region_id", "seq_region_start"),
441 Index("transcript_stable_id_idx", "stable_id", "version"),
442 )
444 transcript_id: Column = Column(INTEGER(10), primary_key=True)
445 gene_id: Column = Column(ForeignKey("gene.gene_id"), index=True)
446 analysis_id: Column = Column(
447 ForeignKey("analysis.analysis_id"),
448 nullable=False,
449 index=True,
450 )
451 seq_region_id: Column = Column(
452 ForeignKey("seq_region.seq_region_id"),
453 nullable=False,
454 )
455 seq_region_start: Column = Column(INTEGER(10), nullable=False)
456 seq_region_end: Column = Column(INTEGER(10), nullable=False)
457 seq_region_strand: Column = Column(TINYINT(2), nullable=False)
458 display_xref_id: Column = Column(ForeignKey("xref.xref_id"), index=True)
459 source: Column = Column(String(40), nullable=False, server_default=text("'ensembl'"))
460 biotype: Column = Column(String(40), nullable=False)
461 description: Column = Column(Text)
462 is_current: Column = Column(TINYINT(1), nullable=False, server_default=text("'1'"))
463 canonical_translation_id: Column = Column(
464 ForeignKey("translation.translation_id"),
465 unique=True,
466 )
467 stable_id: Column = Column(String(128))
468 version: Column = Column(SMALLINT(5))
469 created_date: Column = Column(DateTime)
470 modified_date: Column = Column(DateTime)
472 analysis = relationship("Analysis", primaryjoin="Transcript.analysis_id == Analysis.analysis_id")
473 canonical_translation = relationship(
474 "Translation",
475 primaryjoin="Transcript.canonical_translation_id == Translation.translation_id",
476 )
477 display_xref = relationship("Xref", primaryjoin="Transcript.display_xref_id == Xref.xref_id")
478 gene = relationship("Gene", primaryjoin="Transcript.gene_id == Gene.gene_id")
479 seq_region = relationship("SeqRegion", primaryjoin="Transcript.seq_region_id == SeqRegion.seq_region_id")
482class TranscriptIntronSupportingEvidence(Base):
483 __tablename__ = "transcript_intron_supporting_evidence"
485 transcript_id: Column = Column(INTEGER(10), primary_key=True, nullable=False, index=True)
486 intron_supporting_evidence_id: Column = Column(INTEGER(10), primary_key=True, nullable=False)
487 previous_exon_id: Column = Column(INTEGER(10), nullable=False)
488 next_exon_id: Column = Column(INTEGER(10), nullable=False)
491class Translation(Base):
492 __tablename__ = "translation"
493 __table_args__ = (Index("translation_stable_id_idx", "stable_id", "version"),)
495 translation_id: Column = Column(INTEGER(10), primary_key=True)
496 transcript_id: Column = Column(
497 ForeignKey("transcript.transcript_id"),
498 nullable=False,
499 index=True,
500 )
501 seq_start: Column = Column(INTEGER(10), nullable=False)
502 start_exon_id: Column = Column(
503 ForeignKey("exon.exon_id"),
504 nullable=False,
505 index=True,
506 )
507 seq_end: Column = Column(INTEGER(10), nullable=False)
508 end_exon_id: Column = Column(
509 ForeignKey("exon.exon_id"),
510 nullable=False,
511 index=True,
512 )
513 stable_id: Column = Column(String(128))
514 version: Column = Column(SMALLINT(5))
515 created_date: Column = Column(DateTime)
516 modified_date: Column = Column(DateTime)
518 end_exon = relationship("Exon", primaryjoin="Translation.end_exon_id == Exon.exon_id")
519 start_exon = relationship("Exon", primaryjoin="Translation.start_exon_id == Exon.exon_id")
520 transcript = relationship(
521 "Transcript",
522 primaryjoin="Translation.transcript_id == Transcript.transcript_id",
523 )
526class UnmappedReason(Base):
527 __tablename__ = "unmapped_reason"
529 unmapped_reason_id: Column = Column(INTEGER(10), primary_key=True)
530 summary_description: Column = Column(String(255))
531 full_description: Column = Column(String(255))
534class AltAllele(Base):
535 __tablename__ = "alt_allele"
536 __table_args__ = (Index("alt_allele_gene_id_idx", "gene_id", "alt_allele_group_id"),)
538 alt_allele_id: Column = Column(INTEGER(10), primary_key=True)
539 alt_allele_group_id: Column = Column(
540 ForeignKey("alt_allele_group.alt_allele_group_id"),
541 nullable=False,
542 index=True,
543 )
544 gene_id: Column = Column(
545 ForeignKey("gene.gene_id"),
546 nullable=False,
547 unique=True,
548 )
550 alt_allele_group = relationship(
551 "AltAlleleGroup",
552 primaryjoin="AltAllele.alt_allele_group_id == AltAlleleGroup.alt_allele_group_id",
553 )
554 gene = relationship("Gene", primaryjoin="AltAllele.gene_id == Gene.gene_id")
557class AnalysisDescription(Base):
558 __tablename__ = "analysis_description"
560 analysis_id: Column = Column(
561 SMALLINT(5),
562 ForeignKey("analysis.analysis_id"),
563 primary_key=True,
564 nullable=False,
565 unique=True,
566 )
567 description: Column = Column(Text)
568 display_label: Column = Column(String(255), nullable=False)
569 displayable: Column = Column(TINYINT(1), nullable=False, server_default=text("'1'"))
570 web_data: Column = Column(Text)
573class DataFile(Base):
574 __tablename__ = "data_file"
575 __table_args__ = (
576 Index(
577 "df_unq_idx",
578 "coord_system_id",
579 "analysis_id",
580 "name",
581 "file_type",
582 unique=True,
583 ),
584 )
586 data_file_id: Column = Column(INTEGER(10), primary_key=True)
587 coord_system_id: Column = Column(
588 ForeignKey("coord_system.coord_system_id"),
589 nullable=False,
590 )
591 analysis_id: Column = Column(
592 ForeignKey("analysis.analysis_id"),
593 nullable=False,
594 index=True,
595 )
596 name: Column = Column(String(100), nullable=False, index=True)
597 version_lock: Column = Column(TINYINT(1), nullable=False, server_default=text("'0'"))
598 absolute: Column = Column(TINYINT(1), nullable=False, server_default=text("'0'"))
599 url: Column = Column(Text)
600 file_type: Column = Column(Enum("BAM", "BAMCOV", "BIGBED", "BIGWIG", "VCF"))
602 analysis = relationship("Analysis", primaryjoin="DataFile.analysis_id == Analysis.analysis_id")
603 coord_system = relationship(
604 "CoordSystem",
605 primaryjoin="DataFile.coord_system_id == CoordSystem.coord_system_id",
606 )
609class DensityType(Base):
610 __tablename__ = "density_type"
611 __table_args__ = (Index("analysis_idx", "analysis_id", "block_size", "region_features", unique=True),)
613 density_type_id: Column = Column(INTEGER(10), primary_key=True)
614 analysis_id: Column = Column(
615 ForeignKey("analysis.analysis_id"),
616 nullable=False,
617 )
618 block_size: Column = Column(INTEGER(11), nullable=False)
619 region_features: Column = Column(INTEGER(11), nullable=False)
620 value_type: Column = Column(Enum("sum", "ratio"), nullable=False)
622 analysis = relationship("Analysis", primaryjoin="DensityType.analysis_id == Analysis.analysis_id")
625t_gene_archive = Table(
626 "gene_archive",
627 metadata,
628 Column("gene_stable_id", String(128), nullable=False),
629 Column("gene_version", SMALLINT(6), nullable=False, server_default=text("'1'")),
630 Column("transcript_stable_id", String(128), nullable=False),
631 Column("transcript_version", SMALLINT(6), nullable=False, server_default=text("'1'")),
632 Column("translation_stable_id", String(128)),
633 Column("translation_version", SMALLINT(6), nullable=False, server_default=text("'1'")),
634 Column(
635 "peptide_archive_id",
636 ForeignKey("peptide_archive.peptide_archive_id"),
637 index=True,
638 ),
639 Column(
640 "mapping_session_id",
641 ForeignKey("mapping_session.mapping_session_id"),
642 nullable=False,
643 index=True,
644 ),
645 Index("transcript_idx", "transcript_stable_id", "transcript_version"),
646 Index("translation_idx", "translation_stable_id", "translation_version"),
647 Index("gene_idx", "gene_stable_id", "gene_version"),
648)
651class GeneAttrib(Base):
652 __tablename__ = "gene_attrib"
653 __table_args__ = (
654 Index("gene_attribx", "gene_id", "attrib_type_id", "value", unique=True, mysql_length={"value": 10}),
655 Index("gene_attrib_type_val_idx", "attrib_type_id", "value", mysql_length={"value": 10}),
656 Index("gene_attrib_value_idx", "value", mysql_length=10),
657 )
659 gene_id: Column = Column(
660 INTEGER(10),
661 ForeignKey("gene.gene_id"),
662 nullable=False,
663 index=True,
664 server_default=text("'0'"),
665 primary_key=True,
666 )
667 attrib_type_id: Column = Column(
668 SMALLINT(5),
669 ForeignKey("attrib_type.attrib_type_id"),
670 nullable=False,
671 server_default=text("'0'"),
672 primary_key=True,
673 )
674 value: Column = Column(String(500), nullable=False, primary_key=True)
677class MarkerMapLocation(Base):
678 __tablename__ = "marker_map_location"
679 __table_args__ = (Index("map_idx", "map_id", "chromosome_name", "position"),)
681 marker_id: Column = Column(
682 ForeignKey("marker.marker_id"),
683 primary_key=True,
684 nullable=False,
685 )
686 map_id: Column = Column(
687 ForeignKey("map.map_id"),
688 primary_key=True,
689 nullable=False,
690 )
691 chromosome_name: Column = Column(String(15), nullable=False)
692 marker_synonym_id: Column = Column(
693 ForeignKey("marker_synonym.marker_synonym_id"),
694 nullable=False,
695 index=True,
696 )
697 position: Column = Column(String(15), nullable=False)
698 lod_score: Column = Column(Float(asdecimal=True))
700 map_r = relationship("Map", primaryjoin="MarkerMapLocation.map_id == Map.map_id")
701 marker = relationship("Marker", primaryjoin="MarkerMapLocation.marker_id == Marker.marker_id")
702 marker_synonym = relationship(
703 "MarkerSynonym",
704 primaryjoin="MarkerMapLocation.marker_synonym_id == MarkerSynonym.marker_synonym_id",
705 )
708class Meta(Base):
709 __tablename__ = "meta"
710 __table_args__ = (
711 Index("species_value_idx", "species_id", "meta_value"),
712 Index("species_key_value_idx", "species_id", "meta_key", "meta_value", unique=True),
713 )
715 meta_id: Column = Column(INTEGER(11), primary_key=True)
716 species_id: Column = Column(
717 ForeignKey("coord_system.species_id"),
718 server_default=text("'1'"),
719 )
720 meta_key: Column = Column(String(40), nullable=False)
721 meta_value: Column = Column(String(255), nullable=False)
723 coord_system = relationship("CoordSystem", back_populates="meta")
726class MetaCoord(Base):
727 __tablename__ = "meta_coord"
728 __table_args__ = (Index("cs_table_name_idx", "coord_system_id", "table_name", unique=True),)
730 table_name: Column = Column(String(40), primary_key=True, nullable=False)
731 coord_system_id: Column = Column(
732 INTEGER(10),
733 ForeignKey("coord_system.coord_system_id"),
734 primary_key=True,
735 nullable=False,
736 )
737 max_length: Column = Column(INTEGER(11))
740class ProteinFeature(Base):
741 __tablename__ = "protein_feature"
742 __table_args__ = (
743 Index(
744 "aln_idx",
745 "translation_id",
746 "hit_name",
747 "seq_start",
748 "seq_end",
749 "hit_start",
750 "hit_end",
751 "analysis_id",
752 unique=True,
753 ),
754 )
756 protein_feature_id: Column = Column(INTEGER(10), primary_key=True)
757 translation_id: Column = Column(
758 ForeignKey("translation.translation_id"),
759 nullable=False,
760 index=True,
761 )
762 seq_start: Column = Column(INTEGER(10), nullable=False)
763 seq_end: Column = Column(INTEGER(10), nullable=False)
764 hit_start: Column = Column(INTEGER(10), nullable=False)
765 hit_end: Column = Column(INTEGER(10), nullable=False)
766 hit_name: Column = Column(VARCHAR(40), nullable=False, index=True)
767 analysis_id: Column = Column(
768 ForeignKey("analysis.analysis_id"),
769 nullable=False,
770 index=True,
771 )
772 score: Column = Column(Float(asdecimal=True))
773 evalue: Column = Column(Float(asdecimal=True))
774 perc_ident: Column = Column(Float)
775 external_data: Column = Column(Text)
776 hit_description: Column = Column(Text)
777 cigar_line: Column = Column(Text)
778 align_type: Column = Column(Enum("ensembl", "cigar", "cigarplus", "vulgar", "mdtag"))
780 analysis = relationship("Analysis", primaryjoin="ProteinFeature.analysis_id == Analysis.analysis_id")
781 translation = relationship(
782 "Translation",
783 primaryjoin="ProteinFeature.translation_id == Translation.translation_id",
784 )
787class SeqRegion(Base):
788 __tablename__ = "seq_region"
789 __table_args__ = (Index("name_cs_idx", "name", "coord_system_id", unique=True),)
791 seq_region_id: Column = Column(INTEGER(10), primary_key=True)
792 name: Column = Column(String(255), nullable=False)
793 coord_system_id: Column = Column(
794 ForeignKey("coord_system.coord_system_id"),
795 nullable=False,
796 index=True,
797 )
798 length: Column = Column(INTEGER(10), nullable=False)
799 # Many to one relationship
800 coord_system = relationship("CoordSystem", back_populates="seq_region")
801 seq_region_attrib = relationship("SeqRegionAttrib", back_populates="seq_region")
802 seq_region_synonym = relationship("SeqRegionSynonym", back_populates="seq_region")
803 karyotype = relationship("Karyotype", back_populates="seq_region")
806class Dna(SeqRegion):
807 __tablename__ = "dna"
809 seq_region_id: Column = Column(
810 ForeignKey("seq_region.seq_region_id"),
811 primary_key=True,
812 )
813 sequence: Column = Column(LONGTEXT, nullable=False)
815 seq_region = relationship(
816 "SeqRegion",
817 uselist=False,
818 primaryjoin="Dna.seq_region_id == SeqRegion.seq_region_id",
819 )
822class StableIdEvent(Base):
823 __tablename__ = "stable_id_event"
824 __table_args__ = (
825 Index(
826 "uni_idx",
827 "mapping_session_id",
828 "old_stable_id",
829 "new_stable_id",
830 "type",
831 unique=True,
832 ),
833 )
835 old_stable_id: Column = Column(String(128), primary_key=True, index=True)
836 old_version: Column = Column(SMALLINT(6))
837 new_stable_id: Column = Column(String(128), primary_key=True, index=True)
838 new_version: Column = Column(SMALLINT(6))
839 mapping_session_id: Column = Column(
840 INTEGER(10),
841 ForeignKey("mapping_session.mapping_session_id"),
842 primary_key=True,
843 nullable=False,
844 server_default=text("'0'"),
845 )
846 id_type: Column = Column(
847 "type",
848 Enum("gene", "transcript", "translation", "rnaproduct"),
849 primary_key=True,
850 nullable=False,
851 )
852 score: Column = Column(Float, nullable=False, server_default=text("'0'"))
855class TranscriptAttrib(Base):
856 __tablename__ = "transcript_attrib"
857 __table_args__ = (
858 Index("transcript_attrib_type_val_idx", "attrib_type_id", "value", mysql_length={"value": 10}),
859 Index(
860 "transcript_attribx",
861 "transcript_id",
862 "attrib_type_id",
863 "value",
864 unique=True,
865 mysql_length={"value": 10},
866 ),
867 Index("transcript_attrib_value_idx", "value", mysql_length=10),
868 )
870 transcript_id: Column = Column(
871 INTEGER(10),
872 ForeignKey("transcript.transcript_id"),
873 nullable=False,
874 index=True,
875 server_default=text("'0'"),
876 primary_key=True,
877 )
878 attrib_type_id: Column = Column(
879 SMALLINT(5),
880 ForeignKey("attrib_type.attrib_type_id"),
881 nullable=False,
882 server_default=text("'0'"),
883 primary_key=True,
884 )
885 value: Column = Column(String(500), nullable=False, primary_key=True)
888class TranscriptSupportingFeature(Base):
889 __tablename__ = "transcript_supporting_feature"
890 __table_args__ = (
891 Index("transcript_supporting_feature_idx", "feature_type", "feature_id"),
892 Index(
893 "transcript_supporting_feature_all_idx",
894 "transcript_id",
895 "feature_type",
896 "feature_id",
897 unique=True,
898 ),
899 )
901 transcript_id: Column = Column(
902 INTEGER(10),
903 ForeignKey("transcript.transcript_id"),
904 primary_key=True,
905 nullable=False,
906 server_default=text("'0'"),
907 )
908 feature_type: Column = Column(Enum("dna_align_feature", "protein_align_feature"), primary_key=True)
909 feature_id: Column = Column(INTEGER(10), primary_key=True, nullable=False, server_default=text("'0'"))
912class TranslationAttrib(Base):
913 __tablename__ = "translation_attrib"
914 __table_args__ = (
915 Index("translation_attrib_type_val_idx", "attrib_type_id", "value", mysql_length={"value": 10}),
916 Index(
917 "translation_attribx",
918 "translation_id",
919 "attrib_type_id",
920 "value",
921 unique=True,
922 mysql_length={"value": 10},
923 ),
924 Index("translation_attrib_value_idx", "value", mysql_length=10),
925 )
927 translation_id: Column = Column(
928 ForeignKey("translation.translation_id"),
929 nullable=False,
930 index=True,
931 server_default=text("'0'"),
932 primary_key=True,
933 )
934 attrib_type_id: Column = Column(
935 ForeignKey("attrib_type.attrib_type_id"),
936 nullable=False,
937 server_default=text("'0'"),
938 primary_key=True,
939 )
940 value: Column = Column(String(500), nullable=False, primary_key=True)
943class UnmappedObject(Base):
944 __tablename__ = "unmapped_object"
945 __table_args__ = (
946 Index(
947 "unique_unmapped_obj_idx",
948 "ensembl_id",
949 "ensembl_object_type",
950 "identifier",
951 "unmapped_reason_id",
952 "parent",
953 "external_db_id",
954 unique=True,
955 ),
956 Index("anal_exdb_idx", "analysis_id", "external_db_id"),
957 Index("ext_db_identifier_idx", "external_db_id", "identifier"),
958 )
960 unmapped_object_id: Column = Column(INTEGER(10), primary_key=True)
961 unmapped_object_type: Column = Column("type", Enum("xref", "cDNA", "Marker"), nullable=False)
962 analysis_id: Column = Column(
963 ForeignKey("analysis.analysis_id"),
964 nullable=False,
965 )
966 external_db_id: Column = Column(
967 ForeignKey("external_db.external_db_id"),
968 )
969 identifier: Column = Column(String(255), nullable=False, index=True)
970 unmapped_reason_id: Column = Column(
971 ForeignKey("unmapped_reason.unmapped_reason_id"),
972 nullable=False,
973 index=True,
974 )
975 query_score: Column = Column(Float(asdecimal=True))
976 target_score: Column = Column(Float(asdecimal=True))
977 ensembl_id: Column = Column(INTEGER(10), server_default=text("'0'"))
978 ensembl_object_type: Column = Column(
979 Enum("RawContig", "Transcript", "Gene", "Translation"),
980 server_default=text("'RawContig'"),
981 )
982 parent: Column = Column(String(255))
984 analysis = relationship("Analysis", primaryjoin="UnmappedObject.analysis_id == Analysis.analysis_id")
985 external_db = relationship(
986 "ExternalDb",
987 primaryjoin="UnmappedObject.external_db_id == ExternalDb.external_db_id",
988 )
989 unmapped_reason = relationship(
990 "UnmappedReason",
991 primaryjoin="UnmappedObject.unmapped_reason_id == UnmappedReason.unmapped_reason_id",
992 )
995class Xref(Base):
996 __tablename__ = "xref"
997 __table_args__ = (
998 Index(
999 "id_index",
1000 "dbprimary_acc",
1001 "external_db_id",
1002 "info_type",
1003 "info_text",
1004 "version",
1005 unique=True,
1006 ),
1007 )
1009 xref_id: Column = Column(INTEGER(10), primary_key=True)
1010 external_db_id: Column = Column(
1011 ForeignKey("external_db.external_db_id"),
1012 nullable=False,
1013 index=True,
1014 )
1015 dbprimary_acc: Column = Column(String(512), nullable=False)
1016 display_label: Column = Column(String(512), nullable=False, index=True)
1017 version: Column = Column(String(10))
1018 description: Column = Column(Text)
1019 info_type: Column = Column(
1020 Enum(
1021 "NONE",
1022 "PROJECTION",
1023 "MISC",
1024 "DEPENDENT",
1025 "DIRECT",
1026 "SEQUENCE_MATCH",
1027 "INFERRED_PAIR",
1028 "PROBE",
1029 "UNMAPPED",
1030 "COORDINATE_OVERLAP",
1031 "CHECKSUM",
1032 ),
1033 nullable=False,
1034 index=True,
1035 server_default=text("'NONE'"),
1036 )
1037 info_text: Column = Column(String(255), nullable=False, server_default=text("''"))
1039 external_db = relationship("ExternalDb", primaryjoin="Xref.external_db_id == ExternalDb.external_db_id")
1042t_alt_allele_attrib = Table(
1043 "alt_allele_attrib",
1044 metadata,
1045 Column(
1046 "alt_allele_id",
1047 ForeignKey("alt_allele.alt_allele_id"),
1048 ),
1049 Column(
1050 "attrib",
1051 Enum(
1052 "IS_REPRESENTATIVE",
1053 "IS_MOST_COMMON_ALLELE",
1054 "IN_CORRECTED_ASSEMBLY",
1055 "HAS_CODING_POTENTIAL",
1056 "IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY",
1057 "IN_SYNTENIC_REGION",
1058 "HAS_SAME_UNDERLYING_DNA_SEQUENCE",
1059 "IN_BROKEN_ASSEMBLY_REGION",
1060 "IS_VALID_ALTERNATE",
1061 "SAME_AS_REPRESENTATIVE",
1062 "SAME_AS_ANOTHER_ALLELE",
1063 "MANUALLY_ASSIGNED",
1064 "AUTOMATICALLY_ASSIGNED",
1065 ),
1066 ),
1067 Index("aa_idx", "alt_allele_id", "attrib"),
1068)
1071class Assembly(Base):
1072 __tablename__ = "assembly"
1073 __table_args__ = (
1074 Index("asm_seq_region_idx", "asm_seq_region_id", "asm_start"),
1075 Index(
1076 "asm_all_idx",
1077 "asm_seq_region_id",
1078 "cmp_seq_region_id",
1079 "asm_start",
1080 "asm_end",
1081 "cmp_start",
1082 "cmp_end",
1083 "ori",
1084 unique=True,
1085 ),
1086 )
1088 asm_seq_region_id: Column = Column(
1089 INTEGER(10),
1090 ForeignKey("seq_region.seq_region_id"),
1091 primary_key=True,
1092 nullable=False,
1093 )
1094 cmp_seq_region_id: Column = Column(
1095 INTEGER(10),
1096 ForeignKey("seq_region.seq_region_id"),
1097 primary_key=True,
1098 nullable=False,
1099 )
1100 asm_start: Column = Column(INTEGER(10), primary_key=True, nullable=False)
1101 asm_end: Column = Column(INTEGER(10), primary_key=True, nullable=False)
1102 cmp_start: Column = Column(INTEGER(10), primary_key=True, nullable=False)
1103 cmp_end: Column = Column(INTEGER(10), primary_key=True, nullable=False)
1104 ori: Column = Column(TINYINT(4), primary_key=True, nullable=False)
1107class AssemblyException(Base):
1108 __tablename__ = "assembly_exception"
1109 __table_args__ = (
1110 Index("ex_idx", "exc_seq_region_id", "exc_seq_region_start"),
1111 Index("sr_idx", "seq_region_id", "seq_region_start"),
1112 )
1114 assembly_exception_id: Column = Column(INTEGER(10), primary_key=True)
1115 seq_region_id: Column = Column(
1116 ForeignKey("seq_region.seq_region_id"),
1117 nullable=False,
1118 )
1119 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1120 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1121 exc_type: Column = Column(Enum("HAP", "PAR", "PATCH_FIX", "PATCH_NOVEL"), nullable=False)
1122 exc_seq_region_id: Column = Column(
1123 ForeignKey("seq_region.seq_region_id"),
1124 nullable=False,
1125 )
1126 exc_seq_region_start: Column = Column(INTEGER(10), nullable=False)
1127 exc_seq_region_end: Column = Column(INTEGER(10), nullable=False)
1128 ori: Column = Column(INTEGER(11), nullable=False)
1130 exc_seq_region = relationship(
1131 "SeqRegion",
1132 primaryjoin="AssemblyException.exc_seq_region_id == SeqRegion.seq_region_id",
1133 )
1134 seq_region = relationship(
1135 "SeqRegion",
1136 primaryjoin="AssemblyException.seq_region_id == SeqRegion.seq_region_id",
1137 )
1140class DensityFeature(Base):
1141 __tablename__ = "density_feature"
1142 __table_args__ = (
1143 Index("density_seq_region_idx", "density_type_id", "seq_region_id", "seq_region_start"),
1144 )
1146 density_feature_id: Column = Column(INTEGER(10), primary_key=True)
1147 density_type_id: Column = Column(
1148 ForeignKey("density_type.density_type_id"),
1149 nullable=False,
1150 )
1151 seq_region_id: Column = Column(
1152 ForeignKey("seq_region.seq_region_id"),
1153 nullable=False,
1154 index=True,
1155 )
1156 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1157 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1158 density_value: Column = Column(Float, nullable=False)
1160 density_type = relationship(
1161 "DensityType",
1162 primaryjoin="DensityFeature.density_type_id == DensityType.density_type_id",
1163 )
1164 seq_region = relationship(
1165 "SeqRegion",
1166 primaryjoin="DensityFeature.seq_region_id == SeqRegion.seq_region_id",
1167 )
1170class DitagFeature(Base):
1171 __tablename__ = "ditag_feature"
1172 __table_args__ = (Index("ditag_seq_region_idx", "seq_region_id", "seq_region_start", "seq_region_end"),)
1174 ditag_feature_id: Column = Column(INTEGER(10), primary_key=True)
1175 ditag_id: Column = Column(
1176 ForeignKey("ditag.ditag_id"),
1177 nullable=False,
1178 index=True,
1179 server_default=text("'0'"),
1180 )
1181 ditag_pair_id: Column = Column(INTEGER(10), nullable=False, index=True, server_default=text("'0'"))
1182 seq_region_id: Column = Column(
1183 ForeignKey("seq_region.seq_region_id"),
1184 nullable=False,
1185 server_default=text("'0'"),
1186 )
1187 seq_region_start: Column = Column(INTEGER(10), nullable=False, server_default=text("'0'"))
1188 seq_region_end: Column = Column(INTEGER(10), nullable=False, server_default=text("'0'"))
1189 seq_region_strand: Column = Column(TINYINT(1), nullable=False, server_default=text("'0'"))
1190 analysis_id: Column = Column(
1191 ForeignKey("analysis.analysis_id"),
1192 nullable=False,
1193 index=True,
1194 server_default=text("'0'"),
1195 )
1196 hit_start: Column = Column(INTEGER(10), nullable=False, server_default=text("'0'"))
1197 hit_end: Column = Column(INTEGER(10), nullable=False, server_default=text("'0'"))
1198 hit_strand: Column = Column(TINYINT(1), nullable=False, server_default=text("'0'"))
1199 cigar_line: Column = Column(TINYTEXT, nullable=False)
1200 ditag_side: Column = Column(Enum("F", "L", "R"), nullable=False)
1202 analysis = relationship("Analysis", primaryjoin="DitagFeature.analysis_id == Analysis.analysis_id")
1203 ditag = relationship("Ditag", primaryjoin="DitagFeature.ditag_id == Ditag.ditag_id")
1204 seq_region = relationship(
1205 "SeqRegion", primaryjoin="DitagFeature.seq_region_id == SeqRegion.seq_region_id"
1206 )
1209class DnaAlignFeature(Base):
1210 __tablename__ = "dna_align_feature"
1211 __table_args__ = (
1212 Index("dna_align_seq_region_idx_2", "seq_region_id", "seq_region_start"),
1213 Index(
1214 "dna_align_seq_region_idx",
1215 "seq_region_id",
1216 "analysis_id",
1217 "seq_region_start",
1218 "score",
1219 ),
1220 )
1222 dna_align_feature_id: Column = Column(INTEGER(10), primary_key=True)
1223 seq_region_id: Column = Column(
1224 ForeignKey("seq_region.seq_region_id"),
1225 nullable=False,
1226 )
1227 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1228 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1229 seq_region_strand: Column = Column(TINYINT(1), nullable=False)
1230 hit_start: Column = Column(INTEGER(11), nullable=False)
1231 hit_end: Column = Column(INTEGER(11), nullable=False)
1232 hit_strand: Column = Column(TINYINT(1), nullable=False)
1233 hit_name: Column = Column(String(40), nullable=False, index=True)
1234 analysis_id: Column = Column(
1235 ForeignKey("analysis.analysis_id"),
1236 nullable=False,
1237 index=True,
1238 )
1239 score: Column = Column(Float(asdecimal=True))
1240 evalue: Column = Column(Float(asdecimal=True))
1241 perc_ident: Column = Column(Float)
1242 cigar_line: Column = Column(Text)
1243 external_db_id: Column = Column(
1244 ForeignKey("external_db.external_db_id"),
1245 index=True,
1246 )
1247 hcoverage: Column = Column(Float(asdecimal=True))
1248 align_type: Column = Column(Enum("ensembl", "cigar", "vulgar", "mdtag"), server_default=text("'ensembl'"))
1250 analysis = relationship("Analysis", primaryjoin="DnaAlignFeature.analysis_id == Analysis.analysis_id")
1251 external_db = relationship(
1252 "ExternalDb",
1253 primaryjoin="DnaAlignFeature.external_db_id == ExternalDb.external_db_id",
1254 )
1255 seq_region = relationship(
1256 "SeqRegion",
1257 primaryjoin="DnaAlignFeature.seq_region_id == SeqRegion.seq_region_id",
1258 )
1261class Exon(Base):
1262 __tablename__ = "exon"
1263 __table_args__ = (
1264 Index("exon_seq_region_idx", "seq_region_id", "seq_region_start"),
1265 Index("exon_stable_id_idx", "stable_id", "version"),
1266 )
1268 exon_id: Column = Column(INTEGER(10), primary_key=True)
1269 seq_region_id: Column = Column(
1270 ForeignKey("seq_region.seq_region_id"),
1271 nullable=False,
1272 )
1273 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1274 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1275 seq_region_strand: Column = Column(TINYINT(2), nullable=False)
1276 phase: Column = Column(TINYINT(2), nullable=False)
1277 end_phase: Column = Column(TINYINT(2), nullable=False)
1278 is_current: Column = Column(TINYINT(1), nullable=False, server_default=text("'1'"))
1279 is_constitutive: Column = Column(TINYINT(1), nullable=False, server_default=text("'0'"))
1280 stable_id: Column = Column(String(128))
1281 version: Column = Column(SMALLINT(5))
1282 created_date: Column = Column(DateTime)
1283 modified_date: Column = Column(DateTime)
1285 seq_region = relationship("SeqRegion", primaryjoin="Exon.seq_region_id == SeqRegion.seq_region_id")
1288class ExternalSynonym(Base):
1289 __tablename__ = "external_synonym"
1291 xref_id: Column = Column(
1292 ForeignKey("xref.xref_id"),
1293 primary_key=True,
1294 nullable=False,
1295 )
1296 synonym: Column = Column(String(100), primary_key=True, nullable=False, index=True)
1298 xref = relationship("Xref", primaryjoin="ExternalSynonym.xref_id == Xref.xref_id")
1301class IntronSupportingEvidence(Base):
1302 __tablename__ = "intron_supporting_evidence"
1303 __table_args__ = (
1304 Index(
1305 "analysis_id",
1306 "analysis_id",
1307 "seq_region_id",
1308 "seq_region_start",
1309 "seq_region_end",
1310 "seq_region_strand",
1311 "hit_name",
1312 unique=True,
1313 ),
1314 Index("intron_evidence_seq_region_idx", "seq_region_id", "seq_region_start"),
1315 )
1317 intron_supporting_evidence_id: Column = Column(INTEGER(10), primary_key=True)
1318 analysis_id: Column = Column(
1319 ForeignKey("analysis.analysis_id"),
1320 nullable=False,
1321 )
1322 seq_region_id: Column = Column(
1323 ForeignKey("seq_region.seq_region_id"),
1324 nullable=False,
1325 )
1326 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1327 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1328 seq_region_strand: Column = Column(TINYINT(2), nullable=False)
1329 hit_name: Column = Column(String(100), nullable=False)
1330 score: Column = Column(DECIMAL(10, 3))
1331 score_type: Column = Column(Enum("NONE", "DEPTH"), server_default=text("'NONE'"))
1332 is_splice_canonical: Column = Column(TINYINT(1), nullable=False, server_default=text("'0'"))
1334 analysis = relationship(
1335 "Analysis",
1336 primaryjoin="IntronSupportingEvidence.analysis_id == Analysis.analysis_id",
1337 )
1338 seq_region = relationship(
1339 "SeqRegion",
1340 primaryjoin="IntronSupportingEvidence.seq_region_id == SeqRegion.seq_region_id",
1341 )
1344class Karyotype(Base):
1345 __tablename__ = "karyotype"
1346 __table_args__ = (Index("region_band_idx", "seq_region_id", "band"),)
1348 karyotype_id: Column = Column(INTEGER(10), primary_key=True)
1349 seq_region_id: Column = Column(
1350 ForeignKey("seq_region.seq_region_id"),
1351 nullable=False,
1352 )
1353 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1354 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1355 band: Column = Column(String(40))
1356 stain: Column = Column(String(40))
1358 seq_region = relationship("SeqRegion", primaryjoin="Karyotype.seq_region_id == SeqRegion.seq_region_id")
1361class MarkerFeature(Base):
1362 __tablename__ = "marker_feature"
1363 __table_args__ = (Index("marker_seq_region_idx", "seq_region_id", "seq_region_start"),)
1365 marker_feature_id: Column = Column(INTEGER(10), primary_key=True)
1366 marker_id: Column = Column(
1367 ForeignKey("marker.marker_id"),
1368 nullable=False,
1369 index=True,
1370 )
1371 seq_region_id: Column = Column(
1372 ForeignKey("seq_region.seq_region_id"),
1373 nullable=False,
1374 )
1375 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1376 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1377 analysis_id: Column = Column(
1378 ForeignKey("analysis.analysis_id"),
1379 nullable=False,
1380 index=True,
1381 )
1382 map_weight: Column = Column(INTEGER(10))
1384 analysis = relationship("Analysis", primaryjoin="MarkerFeature.analysis_id == Analysis.analysis_id")
1385 marker = relationship("Marker", primaryjoin="MarkerFeature.marker_id == Marker.marker_id")
1386 seq_region = relationship(
1387 "SeqRegion",
1388 primaryjoin="MarkerFeature.seq_region_id == SeqRegion.seq_region_id",
1389 )
1392t_misc_feature_misc_set = Table(
1393 "misc_feature_misc_set",
1394 metadata,
1395 Column(
1396 "misc_feature_id",
1397 ForeignKey("misc_feature.misc_feature_id"),
1398 primary_key=True,
1399 nullable=False,
1400 server_default=text("'0'"),
1401 ),
1402 Column(
1403 "misc_set_id",
1404 ForeignKey("misc_set.misc_set_id"),
1405 primary_key=True,
1406 nullable=False,
1407 server_default=text("'0'"),
1408 ),
1409 Index("reverse_idx", "misc_set_id", "misc_feature_id"),
1410)
1413class MiscSet(Base):
1414 __tablename__ = "misc_set"
1416 misc_set_id: Column = Column(SMALLINT(5), primary_key=True)
1417 code: Column = Column(String(25), nullable=False, unique=True, server_default=text("''"))
1418 name: Column = Column(String(255), nullable=False, server_default=text("''"))
1419 description: Column = Column(Text, nullable=False)
1420 max_length: Column = Column(INTEGER(10), nullable=False)
1422 # misc_features = relationship("MiscFeature", secondary=t_misc_feature_misc_set)
1425class MiscFeature(Base):
1426 __tablename__ = "misc_feature"
1427 __table_args__ = (Index("misc_seq_region_idx", "seq_region_id", "seq_region_start"),)
1429 misc_feature_id: Column = Column(INTEGER(10), primary_key=True)
1430 seq_region_id: Column = Column(
1431 ForeignKey("seq_region.seq_region_id"),
1432 nullable=False,
1433 server_default=text("'0'"),
1434 )
1435 seq_region_start: Column = Column(INTEGER(10), nullable=False, server_default=text("'0'"))
1436 seq_region_end: Column = Column(INTEGER(10), nullable=False, server_default=text("'0'"))
1437 seq_region_strand: Column = Column(TINYINT(4), nullable=False, server_default=text("'0'"))
1439 seq_region = relationship("SeqRegion", primaryjoin="MiscFeature.seq_region_id == SeqRegion.seq_region_id")
1440 # misc_sets = relationship("MiscSet", secondary=t_misc_feature_misc_set)
1443class ObjectXref(Base):
1444 __tablename__ = "object_xref"
1445 __table_args__ = (
1446 Index("ensembl_idx", "ensembl_object_type", "ensembl_id"),
1447 Index(
1448 "xref_idx",
1449 "xref_id",
1450 "ensembl_object_type",
1451 "ensembl_id",
1452 "analysis_id",
1453 unique=True,
1454 ),
1455 )
1457 object_xref_id: Column = Column(INTEGER(10), primary_key=True)
1458 ensembl_id: Column = Column(INTEGER(10), nullable=False)
1459 ensembl_object_type: Column = Column(
1460 Enum(
1461 "RawContig",
1462 "Transcript",
1463 "Gene",
1464 "Translation",
1465 "Operon",
1466 "OperonTranscript",
1467 "Marker",
1468 "RNAProduct",
1469 ),
1470 nullable=False,
1471 )
1472 xref_id: Column = Column(ForeignKey("xref.xref_id"), nullable=False)
1473 linkage_annotation: Column = Column(String(255))
1474 analysis_id: Column = Column(
1475 ForeignKey("analysis.analysis_id"),
1476 index=True,
1477 )
1479 analysis = relationship("Analysis", primaryjoin="ObjectXref.analysis_id == Analysis.analysis_id")
1480 xref = relationship("Xref", primaryjoin="ObjectXref.xref_id == Xref.xref_id")
1483class DependentXref(ObjectXref):
1484 __tablename__ = "dependent_xref"
1486 object_xref_id: Column = Column(
1487 ForeignKey("object_xref.object_xref_id"),
1488 primary_key=True,
1489 )
1490 master_xref_id: Column = Column(
1491 ForeignKey("xref.xref_id"),
1492 nullable=False,
1493 index=True,
1494 )
1495 dependent_xref_id: Column = Column(
1496 ForeignKey("xref.xref_id"),
1497 nullable=False,
1498 index=True,
1499 )
1502class IdentityXref(ObjectXref):
1503 __tablename__ = "identity_xref"
1505 object_xref_id: Column = Column(
1506 ForeignKey("object_xref.object_xref_id"),
1507 primary_key=True,
1508 )
1509 xref_identity: Column = Column(INTEGER(5))
1510 ensembl_identity: Column = Column(INTEGER(5))
1511 xref_start: Column = Column(INTEGER(11))
1512 xref_end: Column = Column(INTEGER(11))
1513 ensembl_start: Column = Column(INTEGER(11))
1514 ensembl_end: Column = Column(INTEGER(11))
1515 cigar_line: Column = Column(Text)
1516 score: Column = Column(Float(asdecimal=True))
1517 evalue: Column = Column(Float(asdecimal=True))
1519 object_xref = relationship(
1520 "ObjectXref",
1521 uselist=False,
1522 primaryjoin="IdentityXref.object_xref_id == ObjectXref.object_xref_id",
1523 )
1526class Operon(Base):
1527 __tablename__ = "operon"
1528 __table_args__ = (
1529 Index("operon_seq_region_idx", "seq_region_id", "seq_region_start"),
1530 Index("operon_stable_id_idx", "stable_id", "version"),
1531 )
1533 operon_id: Column = Column(INTEGER(10), primary_key=True)
1534 seq_region_id: Column = Column(
1535 ForeignKey("seq_region.seq_region_id"),
1536 nullable=False,
1537 )
1538 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1539 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1540 seq_region_strand: Column = Column(TINYINT(2), nullable=False)
1541 display_label: Column = Column(String(255), index=True)
1542 analysis_id: Column = Column(
1543 ForeignKey("analysis.analysis_id"),
1544 nullable=False,
1545 index=True,
1546 )
1547 stable_id: Column = Column(String(128))
1548 version: Column = Column(SMALLINT(5))
1549 created_date: Column = Column(DateTime)
1550 modified_date: Column = Column(DateTime)
1552 analysis = relationship("Analysis", primaryjoin="Operon.analysis_id == Analysis.analysis_id")
1553 seq_region = relationship("SeqRegion", primaryjoin="Operon.seq_region_id == SeqRegion.seq_region_id")
1556class PredictionTranscript(Base):
1557 __tablename__ = "prediction_transcript"
1558 __table_args__ = (Index("prediction_transcript_seq_region_idx", "seq_region_id", "seq_region_start"),)
1560 prediction_transcript_id: Column = Column(INTEGER(10), primary_key=True)
1561 seq_region_id: Column = Column(
1562 ForeignKey("seq_region.seq_region_id"),
1563 nullable=False,
1564 )
1565 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1566 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1567 seq_region_strand: Column = Column(TINYINT(4), nullable=False)
1568 analysis_id: Column = Column(
1569 ForeignKey("analysis.analysis_id"),
1570 nullable=False,
1571 index=True,
1572 )
1573 display_label: Column = Column(String(255))
1575 analysis = relationship(
1576 "Analysis",
1577 primaryjoin="PredictionTranscript.analysis_id == Analysis.analysis_id",
1578 )
1579 seq_region = relationship(
1580 "SeqRegion",
1581 primaryjoin="PredictionTranscript.seq_region_id == SeqRegion.seq_region_id",
1582 )
1585class ProteinAlignFeature(Base):
1586 __tablename__ = "protein_align_feature"
1587 __table_args__ = (
1588 Index("protein_align_seq_region_idx_2", "seq_region_id", "seq_region_start"),
1589 Index(
1590 "seq_region_idx",
1591 "seq_region_id",
1592 "analysis_id",
1593 "seq_region_start",
1594 "score",
1595 ),
1596 )
1598 protein_align_feature_id: Column = Column(INTEGER(10), primary_key=True)
1599 seq_region_id: Column = Column(
1600 ForeignKey("seq_region.seq_region_id"),
1601 nullable=False,
1602 )
1603 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1604 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1605 seq_region_strand: Column = Column(TINYINT(1), nullable=False, server_default=text("'1'"))
1606 hit_start: Column = Column(INTEGER(10), nullable=False)
1607 hit_end: Column = Column(INTEGER(10), nullable=False)
1608 hit_name: Column = Column(String(40), nullable=False, index=True)
1609 analysis_id: Column = Column(
1610 ForeignKey("analysis.analysis_id"),
1611 nullable=False,
1612 index=True,
1613 )
1614 score: Column = Column(Float(asdecimal=True))
1615 evalue: Column = Column(Float(asdecimal=True))
1616 perc_ident: Column = Column(Float)
1617 cigar_line: Column = Column(Text)
1618 external_db_id: Column = Column(
1619 ForeignKey("external_db.external_db_id"),
1620 index=True,
1621 )
1622 hcoverage: Column = Column(Float(asdecimal=True))
1623 align_type: Column = Column(Enum("ensembl", "cigar", "vulgar", "mdtag"), server_default=text("'ensembl'"))
1625 analysis = relationship(
1626 "Analysis",
1627 primaryjoin="ProteinAlignFeature.analysis_id == Analysis.analysis_id",
1628 )
1629 external_db = relationship(
1630 "ExternalDb",
1631 primaryjoin="ProteinAlignFeature.external_db_id == ExternalDb.external_db_id",
1632 )
1633 seq_region = relationship(
1634 "SeqRegion",
1635 primaryjoin="ProteinAlignFeature.seq_region_id == SeqRegion.seq_region_id",
1636 )
1639class RepeatFeature(Base):
1640 __tablename__ = "repeat_feature"
1641 __table_args__ = (Index("repeat_feature_seq_region_idx", "seq_region_id", "seq_region_start"),)
1643 repeat_feature_id: Column = Column(INTEGER(10), primary_key=True)
1644 seq_region_id: Column = Column(
1645 ForeignKey("seq_region.seq_region_id"),
1646 nullable=False,
1647 )
1648 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1649 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1650 seq_region_strand: Column = Column(TINYINT(1), nullable=False, server_default=text("'1'"))
1651 repeat_start: Column = Column(INTEGER(10), nullable=False)
1652 repeat_end: Column = Column(INTEGER(10), nullable=False)
1653 repeat_consensus_id: Column = Column(
1654 ForeignKey("repeat_consensus.repeat_consensus_id"),
1655 nullable=False,
1656 index=True,
1657 )
1658 analysis_id: Column = Column(
1659 ForeignKey("analysis.analysis_id"),
1660 nullable=False,
1661 index=True,
1662 )
1663 score: Column = Column(Float(asdecimal=True))
1665 analysis = relationship("Analysis", primaryjoin="RepeatFeature.analysis_id == Analysis.analysis_id")
1666 repeat_consensus = relationship(
1667 "RepeatConsensus",
1668 primaryjoin="RepeatFeature.repeat_consensus_id == RepeatConsensus.repeat_consensus_id",
1669 )
1670 seq_region = relationship(
1671 "SeqRegion",
1672 primaryjoin="RepeatFeature.seq_region_id == SeqRegion.seq_region_id",
1673 )
1676class SeqRegionAttrib(Base):
1677 __tablename__ = "seq_region_attrib"
1678 __table_args__ = (
1679 Index(
1680 "region_attribx",
1681 "seq_region_id",
1682 "attrib_type_id",
1683 "value",
1684 unique=True,
1685 mysql_length={"value": 10},
1686 ),
1687 Index("region_attrib_type_val_idx", "attrib_type_id", "value", mysql_length={"value": 10}),
1688 Index("region_attrib_value_idx", "value", mysql_length=10),
1689 )
1691 seq_region_id: Column = Column(
1692 ForeignKey("seq_region.seq_region_id"),
1693 nullable=False,
1694 index=True,
1695 server_default=text("'0'"),
1696 primary_key=True,
1697 )
1698 attrib_type_id: Column = Column(
1699 ForeignKey("attrib_type.attrib_type_id"),
1700 nullable=False,
1701 server_default=text("'0'"),
1702 primary_key=True,
1703 )
1704 value: Column = Column(String(500), nullable=False, primary_key=True)
1706 UniqueConstraint("seq_region_id", "attrib_type_id", "value", name="region_attribx")
1707 seq_region = relationship("SeqRegion", back_populates="seq_region_attrib")
1708 attrib_type = relationship("AttribType", back_populates="seq_region_attrib")
1711# Not in first normal form, can't be mapped (i.e. it has fully duplicated rows for homo_sapiens_core)
1712t_seq_region_mapping = Table(
1713 "seq_region_mapping",
1714 metadata,
1715 Column("external_seq_region_id", INTEGER(10), nullable=False),
1716 Column(
1717 "internal_seq_region_id",
1718 ForeignKey("seq_region.seq_region_id"),
1719 nullable=False,
1720 index=True,
1721 ),
1722 Column(
1723 "mapping_set_id",
1724 ForeignKey("mapping_set.mapping_set_id"),
1725 nullable=False,
1726 index=True,
1727 ),
1728)
1731class SeqRegionSynonym(Base):
1732 __tablename__ = "seq_region_synonym"
1733 __table_args__ = (Index("syn_idx", "synonym", "seq_region_id", unique=True),)
1735 seq_region_synonym_id: Column = Column(INTEGER(10), primary_key=True)
1736 seq_region_id: Column = Column(
1737 ForeignKey("seq_region.seq_region_id"),
1738 nullable=False,
1739 index=True,
1740 )
1741 synonym: Column = Column(String(250), nullable=False)
1742 external_db_id: Column = Column(ForeignKey("external_db.external_db_id"))
1744 seq_region = relationship("SeqRegion", back_populates="seq_region_synonym")
1745 external_db = relationship("ExternalDb", back_populates="seq_region_synonym")
1748class SimpleFeature(Base):
1749 __tablename__ = "simple_feature"
1750 __table_args__ = (Index("simple_feature_seq_region_idx", "seq_region_id", "seq_region_start"),)
1752 simple_feature_id: Column = Column(INTEGER(10), primary_key=True)
1753 seq_region_id: Column = Column(
1754 ForeignKey("seq_region.seq_region_id"),
1755 nullable=False,
1756 )
1757 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1758 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1759 seq_region_strand: Column = Column(TINYINT(1), nullable=False)
1760 display_label: Column = Column(String(255), nullable=False, index=True)
1761 analysis_id: Column = Column(
1762 ForeignKey("analysis.analysis_id"),
1763 nullable=False,
1764 index=True,
1765 )
1766 score: Column = Column(Float(asdecimal=True))
1768 analysis = relationship("Analysis", primaryjoin="SimpleFeature.analysis_id == Analysis.analysis_id")
1769 seq_region = relationship(
1770 "SeqRegion",
1771 primaryjoin="SimpleFeature.seq_region_id == SeqRegion.seq_region_id",
1772 )
1775class AssociatedXref(Base):
1776 __tablename__ = "associated_xref"
1777 __table_args__ = (
1778 Index(
1779 "object_associated_source_type_idx",
1780 "object_xref_id",
1781 "xref_id",
1782 "source_xref_id",
1783 "condition_type",
1784 "associated_group_id",
1785 unique=True,
1786 ),
1787 )
1789 associated_xref_id: Column = Column(INTEGER(10), primary_key=True)
1790 object_xref_id: Column = Column(
1791 ForeignKey("object_xref.object_xref_id"),
1792 nullable=False,
1793 index=True,
1794 server_default=text("'0'"),
1795 )
1796 xref_id: Column = Column(
1797 ForeignKey("xref.xref_id"),
1798 nullable=False,
1799 index=True,
1800 server_default=text("'0'"),
1801 )
1802 source_xref_id: Column = Column(INTEGER(10), index=True)
1803 condition_type: Column = Column(String(128))
1804 associated_group_id: Column = Column(
1805 ForeignKey("associated_group.associated_group_id"),
1806 index=True,
1807 )
1808 rank: Column = Column(INTEGER(10), server_default=text("'0'"))
1810 associated_group = relationship(
1811 "AssociatedGroup",
1812 primaryjoin="AssociatedXref.associated_group_id == AssociatedGroup.associated_group_id",
1813 )
1814 object_xref = relationship(
1815 "ObjectXref",
1816 primaryjoin="AssociatedXref.object_xref_id == ObjectXref.object_xref_id",
1817 )
1818 xref = relationship("Xref", primaryjoin="AssociatedXref.xref_id == Xref.xref_id")
1821class ExonTranscript(Base):
1822 __tablename__ = "exon_transcript"
1824 exon_id: Column = Column(
1825 ForeignKey("exon.exon_id"),
1826 primary_key=True,
1827 nullable=False,
1828 index=True,
1829 )
1830 transcript_id: Column = Column(
1831 ForeignKey("transcript.transcript_id"),
1832 primary_key=True,
1833 nullable=False,
1834 index=True,
1835 )
1836 rank: Column = Column(INTEGER(10), primary_key=True, nullable=False)
1838 exon = relationship("Exon", primaryjoin="ExonTranscript.exon_id == Exon.exon_id")
1839 transcript = relationship(
1840 "Transcript",
1841 primaryjoin="ExonTranscript.transcript_id == Transcript.transcript_id",
1842 )
1845class MiscAttrib(Base):
1846 __tablename__ = "misc_attrib"
1847 __table_args__ = (
1848 Index("misc_attrib_type_val_idx", "attrib_type_id", "value", mysql_length={"value": 10}),
1849 Index(
1850 "misc_attribx",
1851 "misc_feature_id",
1852 "attrib_type_id",
1853 "value",
1854 unique=True,
1855 mysql_length={"value": 10},
1856 ),
1857 Index("misc_attrib_value_idx", "value", mysql_length=10),
1858 )
1860 misc_feature_id: Column = Column(
1861 INTEGER(10),
1862 ForeignKey("misc_feature.misc_feature_id"),
1863 nullable=False,
1864 index=True,
1865 server_default=text("'0'"),
1866 primary_key=True,
1867 )
1868 attrib_type_id: Column = Column(
1869 SMALLINT(5),
1870 ForeignKey("attrib_type.attrib_type_id"),
1871 nullable=False,
1872 server_default=text("'0'"),
1873 primary_key=True,
1874 )
1875 value: Column = Column(String(500), nullable=False, primary_key=True)
1878class OntologyXref(Base):
1879 __tablename__ = "ontology_xref"
1880 __table_args__ = (
1881 Index(
1882 "object_source_type_idx",
1883 "object_xref_id",
1884 "source_xref_id",
1885 "linkage_type",
1886 unique=True,
1887 ),
1888 )
1890 object_xref_id: Column = Column(
1891 INTEGER(10),
1892 ForeignKey("object_xref.object_xref_id"),
1893 primary_key=True,
1894 nullable=False,
1895 index=True,
1896 server_default=text("'0'"),
1897 )
1898 source_xref_id: Column = Column(
1899 INTEGER(10),
1900 ForeignKey("xref.xref_id"),
1901 primary_key=True,
1902 index=True,
1903 )
1904 linkage_type: Column = Column(String(3), primary_key=True)
1907class OperonTranscript(Base):
1908 __tablename__ = "operon_transcript"
1909 __table_args__ = (
1910 Index("operon_transcript_stable_id_idx", "stable_id", "version"),
1911 Index("operon_transcript_seq_region_idx", "seq_region_id", "seq_region_start"),
1912 )
1914 operon_transcript_id: Column = Column(INTEGER(10), primary_key=True)
1915 seq_region_id: Column = Column(
1916 ForeignKey("seq_region.seq_region_id"),
1917 nullable=False,
1918 )
1919 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1920 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1921 seq_region_strand: Column = Column(TINYINT(2), nullable=False)
1922 operon_id: Column = Column(
1923 ForeignKey("operon.operon_id"),
1924 nullable=False,
1925 index=True,
1926 )
1927 display_label: Column = Column(String(255))
1928 analysis_id: Column = Column(
1929 ForeignKey("analysis.analysis_id"),
1930 nullable=False,
1931 index=True,
1932 )
1933 stable_id: Column = Column(String(128))
1934 version: Column = Column(SMALLINT(5))
1935 created_date: Column = Column(DateTime)
1936 modified_date: Column = Column(DateTime)
1938 analysis = relationship("Analysis", primaryjoin="OperonTranscript.analysis_id == Analysis.analysis_id")
1939 operon = relationship("Operon", primaryjoin="OperonTranscript.operon_id == Operon.operon_id")
1940 seq_region = relationship(
1941 "SeqRegion",
1942 primaryjoin="OperonTranscript.seq_region_id == SeqRegion.seq_region_id",
1943 )
1946class PredictionExon(Base):
1947 __tablename__ = "prediction_exon"
1948 __table_args__ = (Index("prediction_exon_seq_region_idx", "seq_region_id", "seq_region_start"),)
1950 prediction_exon_id: Column = Column(INTEGER(10), primary_key=True)
1951 prediction_transcript_id: Column = Column(
1952 ForeignKey("prediction_transcript.prediction_transcript_id"),
1953 nullable=False,
1954 index=True,
1955 )
1956 exon_rank: Column = Column(SMALLINT(5), nullable=False)
1957 seq_region_id: Column = Column(
1958 ForeignKey("seq_region.seq_region_id"),
1959 nullable=False,
1960 )
1961 seq_region_start: Column = Column(INTEGER(10), nullable=False)
1962 seq_region_end: Column = Column(INTEGER(10), nullable=False)
1963 seq_region_strand: Column = Column(TINYINT(4), nullable=False)
1964 start_phase: Column = Column(TINYINT(4), nullable=False)
1965 score: Column = Column(Float(asdecimal=True))
1966 p_value: Column = Column(Float(asdecimal=True))
1968 prediction_transcript = relationship(
1969 "PredictionTranscript",
1970 primaryjoin=(
1971 "PredictionExon.prediction_transcript_id ==" "PredictionTranscript.prediction_transcript_id"
1972 ),
1973 )
1974 seq_region = relationship(
1975 "SeqRegion",
1976 primaryjoin="PredictionExon.seq_region_id == SeqRegion.seq_region_id",
1977 )
1980class SupportingFeature(Base):
1981 __tablename__ = "supporting_feature"
1982 __table_args__ = (
1983 Index("supporting_feature_all_idx", "exon_id", "feature_type", "feature_id", unique=True),
1984 Index("supporting_feature_idx", "feature_type", "feature_id"),
1985 )
1987 exon_id: Column = Column(
1988 INTEGER(10),
1989 ForeignKey("exon.exon_id"),
1990 primary_key=True,
1991 nullable=False,
1992 server_default=text("'0'"),
1993 )
1994 feature_type: Column = Column(Enum("dna_align_feature", "protein_align_feature"), primary_key=True)
1995 feature_id: Column = Column(INTEGER(10), primary_key=True, nullable=False, server_default=text("'0'"))
1998t_operon_transcript_gene = Table(
1999 "operon_transcript_gene",
2000 metadata,
2001 Column(
2002 "operon_transcript_id",
2003 ForeignKey("operon_transcript.operon_transcript_id"),
2004 ),
2005 Column("gene_id", ForeignKey("gene.gene_id"), index=True),
2006 Index("operon_transcript_gene_idx", "operon_transcript_id", "gene_id"),
2007)
2010@compiles(SET, "sqlite")
2011def compile_set_sqlite(
2012 type_: sqlalchemy.sql.expression.ColumnClause, # pylint: disable=unused-argument
2013 compiler: sqlalchemy.engine.interfaces.Compiled, # pylint: disable=unused-argument
2014 **kw: Any, # pylint: disable=unused-argument
2015) -> str:
2016 """Cast MySQL SET to SQLite TEXT."""
2017 return "TEXT"
2020@compiles(TINYTEXT, "sqlite")
2021def compile_tinytext_sqlite(
2022 type_: sqlalchemy.sql.expression.ColumnClause, # pylint: disable=unused-argument
2023 compiler: sqlalchemy.engine.interfaces.Compiled, # pylint: disable=unused-argument
2024 **kw: Any, # pylint: disable=unused-argument
2025) -> str:
2026 """Cast MySQL TINYTEXT to SQLite TEXT."""
2027 return "TEXT"
2030@compiles(MEDIUMTEXT, "sqlite")
2031def compile_mediumtext_sqlite(
2032 type_: sqlalchemy.sql.expression.ColumnClause, # pylint: disable=unused-argument
2033 compiler: sqlalchemy.engine.interfaces.Compiled, # pylint: disable=unused-argument
2034 **kw: Any, # pylint: disable=unused-argument
2035) -> str:
2036 """Cast MySQL MEDIUMTEXT to SQLite TEXT."""
2037 return "TEXT"
2040@compiles(LONGTEXT, "sqlite")
2041def compile_longtext_sqlite(
2042 type_: sqlalchemy.sql.expression.ColumnClause, # pylint: disable=unused-argument
2043 compiler: sqlalchemy.engine.interfaces.Compiled, # pylint: disable=unused-argument
2044 **kw: Any, # pylint: disable=unused-argument
2045) -> str:
2046 """Cast MySQL LONGTEXT to SQLite TEXT."""
2047 return "TEXT"
2050@compiles(TINYINT, "sqlite")
2051def compile_tinyint_sqlite(
2052 type_: sqlalchemy.sql.expression.ColumnClause, # pylint: disable=unused-argument
2053 compiler: sqlalchemy.engine.interfaces.Compiled, # pylint: disable=unused-argument
2054 **kw: Any, # pylint: disable=unused-argument
2055) -> str:
2056 """Cast MySQL TINYINT to SQLite INT."""
2057 return "INT"
2060@compiles(DOUBLE, "sqlite")
2061def compile_double_sqlite(
2062 type_: sqlalchemy.sql.expression.ColumnClause, # pylint: disable=unused-argument
2063 compiler: sqlalchemy.engine.interfaces.Compiled, # pylint: disable=unused-argument
2064 **kw: Any, # pylint: disable=unused-argument
2065) -> str:
2066 """Cast MySQL DOUBLE to SQLite NUMBER."""
2067 return "NUMBER"