Blame - docs/dyn/genomics_v1.annotations.html - platform/external/python/google-api-python-client

"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of

186

# the reference genome may be transcribed as RNA. An alternative splicing

187

# pattern would be represented as a separate transcript object. This field

188

# is only set for annotations of type `TRANSCRIPT`.

189

# reference genome may be transcribed as RNA.

190

"codingSequence": { # The range of the coding sequence for this transcript, if any. To determine

191

# the exact ranges of coding sequence, intersect this range with those of the

192

# exons, if any. If there are any

193

# exons, the

194

# codingSequence must start

195

# and end within them.

196

#

197

# Note that in some cases, the reference genome will not exactly match the

198

# observed mRNA transcript e.g. due to variance in the source genome from

199

# reference. In these cases,

200

# exon.frame will not necessarily

201

# match the expected reference reading frame and coding exon reference bases

202

# cannot necessarily be concatenated to produce the original transcript mRNA.

203

"start": "A String", # The start of the coding sequence on this annotation's reference sequence,

204

# 0-based inclusive. Note that this position is relative to the reference

205

# start, and *not* the containing annotation start.

206

"end": "A String", # The end of the coding sequence on this annotation's reference sequence,

207

# 0-based exclusive. Note that this position is relative to the reference

208

# start, and *not* the containing annotation start.

209

},

210

"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.

211

"exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose

212

# this transcript. This field should be unset for genomes where transcript

213

# splicing does not occur, for example prokaryotes.

214

#

215

# Introns are regions of the transcript that are not included in the

216

# spliced RNA product. Though not explicitly modeled here, intron ranges can

217

# be deduced; all regions of this transcript that are not exons are introns.

218

#

219

# Exonic sequences do not necessarily code for a translational product

220

# (amino acids). Only the regions of exons bounded by the

221

# codingSequence correspond

222

# to coding DNA sequence.

223

#

224

# Exons are ordered by start position and may not overlap.

225

{

226

"start": "A String", # The start position of the exon on this annotation's reference sequence,

227

# 0-based inclusive. Note that this is relative to the reference start, and

228

# **not** the containing annotation start.

229

"frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates

230

# the offset of the first coding base of the exon within the reading frame

231

# of the coding DNA sequence, if any. This field is dependent on the

232

# strandedness of this annotation (see

233

# Annotation.reverse_strand).

234

# For forward stranded annotations, this offset is relative to the

235

# exon.start. For reverse

236

# strand annotations, this offset is relative to the

237

# exon.end `- 1`.

238

#

239

# Unset if this exon does not intersect the coding sequence. Upon creation

240

# of a transcript, the frame must be populated for all or none of the

241

# coding exons.

242

"end": "A String", # The end position of the exon on this annotation's reference sequence,

243

# 0-based exclusive. Note that this is relative to the reference start, and

244

# *not* the containing annotation start.

245

},

246

],

247

},

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

248

"id": "A String", # The server-generated annotation ID, unique across all annotations.

249

},

250

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

251

"requestId": "A String", # A unique request ID which enables the server to detect duplicated requests.

252

# If provided, duplicated requests will result in the same response; if not

253

# provided, duplicated requests may result in duplicated data. For a given

254

# annotation set, callers should not reuse `request_id`s when writing

255

# different batches of annotations - behavior in this case is undefined.

256

# A common approach is to use a UUID. For batch jobs where worker crashes are

257

# a possibility, consider using some unique variant of a worker or run ID.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

258

}

259

260

x__xgafv: string, V1 error format.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

261

Allowed values

262

1 - v1 error format

263

2 - v2 error format

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

264

265

Returns:

266

An object of the form:

267

268

{

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

269

"entries": [ # The resulting per-annotation entries, ordered consistently with the

270

# original request.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

271

{

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

272

"status": { # The `Status` type defines a logical error model that is suitable for different # The creation status.

273

# programming environments, including REST APIs and RPC APIs. It is used by

274

# [gRPC](https://github.com/grpc). The error model is designed to be:

275

#

276

# - Simple to use and understand for most users

277

# - Flexible enough to meet unexpected needs

#

# # Overview

#

# The `Status` message contains three pieces of data: error code, error message,

282

# and error details. The error code should be an enum value of

283

# google.rpc.Code, but it may accept additional error codes if needed. The

284

# error message should be a developer-facing English message that helps

285

# developers *understand* and *resolve* the error. If a localized user-facing

286

# error message is needed, put the localized message in the error details or

287

# localize it in the client. The optional error details may contain arbitrary

288

# information about the error. There is a predefined set of error detail types

289

# in the package `google.rpc` which can be used for common error conditions.

#

# # Language mapping

#

# The `Status` message is the logical representation of the error model, but it

294

# is not necessarily the actual wire format. When the `Status` message is

295

# exposed in different client libraries and different wire protocols, it can be

296

# mapped differently. For example, it will likely be mapped to some exceptions

297

# in Java, but more likely mapped to some error codes in C.

#

# # Other uses

#

# The error model and the `Status` message can be used in a variety of

302

# environments, either with or without APIs, to provide a

303

# consistent developer experience across different environments.

304

#

305

# Example uses of this error model include:

306

#

307

# - Partial errors. If a service needs to return partial errors to the client,

308

# it may embed the `Status` in the normal response to indicate the partial

309

# errors.

310

#

311

# - Workflow errors. A typical workflow has multiple steps. Each step may

312

# have a `Status` message for error reporting purpose.

313

#

314

# - Batch operations. If a client uses batch request and batch response, the

315

# `Status` message should be used directly inside batch response, one for

316

# each error sub-response.

317

#

318

# - Asynchronous operations. If an API call embeds asynchronous operation

319

# results in its response, the status of those operations should be

320

# represented directly using the `Status` message.

321

#

322

# - Logging. If some API errors are stored in logs, the message `Status` could

323

# be used directly after any stripping needed for security/privacy reasons.

324

"message": "A String", # A developer-facing error message, which should be in English. Any

325

# user-facing error message should be localized and sent in the

326

# google.rpc.Status.details field, or localized by the client.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

327

"code": 42, # The status code, which should be an enum value of google.rpc.Code.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

328

"details": [ # A list of messages that carry the error details. There will be a

329

# common set of message types for APIs to use.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

330

{

Jon Wayne Parrott

7d5badb

2016-08-16 12:44:29 -0700

[diff] [blame]

331

"a_key": "", # Properties of the object. Contains field @type with type URL.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

332

},

333

],

334

},

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

335

"annotation": { # An annotation describes a region of reference genome. The value of an # The created annotation, if creation was successful.

336

# annotation may be one of several canonical types, supplemented by arbitrary

337

# info tags. An annotation is not inherently associated with a specific

338

# sample or individual (though a client could choose to use annotations in

339

# this way). Example canonical annotation types are `GENE` and

340

# `VARIANT`.

341

"info": { # A map of additional read alignment information. This must be of the form

342

# map<string, string[]> (string key mapping to a list of string values).

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

"a_key": [

"",

],

},

"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.

348

"end": "A String", # The end position of the range on the reference, 0-based exclusive.

349

"name": "A String", # The display name of this annotation.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

350

"type": "A String", # The data type for this annotation. Must match the containing annotation

351

# set's type.

352

"variant": { # A variant annotation, which describes the effect of a variant on the

353

# genome, the coding sequence, and/or higher level consequences at the

354

# organism level e.g. pathogenicity. This field is only set for annotations

355

# of type `VARIANT`.

356

"conditions": [ # The set of conditions associated with this variant.

357

# A condition describes the way a variant influences human health.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

358

{

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

359

"externalIds": [ # The set of external IDs for this condition.

360

{

361

"sourceName": "A String", # The name of the source of this data.

362

"id": "A String", # The id used by the source of this data.

363

},

364

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

365

"omimId": "A String", # The OMIM id for this condition.

366

# Search for these IDs at http://omim.org/

367

"conceptId": "A String", # The MedGen concept id associated with this gene.

368

# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

369

"names": [ # A set of names for the condition.

"A String",

],

},

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

374

"effect": "A String", # Effect of the variant on the coding sequence.

375

"transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These

376

# should be provided when the variant is created.

377

"A String",

378

],

379

"alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles

380

# exist at this location, create a separate variant for each one, as they

381

# may represent distinct conditions.

382

"clinicalSignificance": "A String", # Describes the clinical significance of a variant.

383

# It is adapted from the ClinVar controlled vocabulary for clinical

384

# significance described at:

385

# http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/

386

"type": "A String", # Type has been adapted from ClinVar's list of variant types.

387

"geneId": "A String", # Google annotation ID of the gene affected by this variant. This should

388

# be provided when the variant is created.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

389

},

390

"start": "A String", # The start position of the range on the reference, 0-based inclusive.

391

"annotationSetId": "A String", # The annotation set to which this annotation belongs.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

392

"referenceName": "A String", # The display name corresponding to the reference specified by

393

# `referenceId`, for example `chr1`, `1`, or `chrX`.

394

"reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward

395

# strand. Note that regardless of this field, the start/end position of the

396

# range always refer to the forward strand.

397

"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of

398

# the reference genome may be transcribed as RNA. An alternative splicing

399

# pattern would be represented as a separate transcript object. This field

400

# is only set for annotations of type `TRANSCRIPT`.

401

# reference genome may be transcribed as RNA.

402

"codingSequence": { # The range of the coding sequence for this transcript, if any. To determine

403

# the exact ranges of coding sequence, intersect this range with those of the

404

# exons, if any. If there are any

405

# exons, the

406

# codingSequence must start

407

# and end within them.

408

#

409

# Note that in some cases, the reference genome will not exactly match the

410

# observed mRNA transcript e.g. due to variance in the source genome from

411

# reference. In these cases,

412

# exon.frame will not necessarily

413

# match the expected reference reading frame and coding exon reference bases

414

# cannot necessarily be concatenated to produce the original transcript mRNA.

415

"start": "A String", # The start of the coding sequence on this annotation's reference sequence,

416

# 0-based inclusive. Note that this position is relative to the reference

417

# start, and *not* the containing annotation start.

418

"end": "A String", # The end of the coding sequence on this annotation's reference sequence,

419

# 0-based exclusive. Note that this position is relative to the reference

420

# start, and *not* the containing annotation start.

421

},

422

"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.

423

"exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose

424

# this transcript. This field should be unset for genomes where transcript

425

# splicing does not occur, for example prokaryotes.

426

#

427

# Introns are regions of the transcript that are not included in the

428

# spliced RNA product. Though not explicitly modeled here, intron ranges can

429

# be deduced; all regions of this transcript that are not exons are introns.

430

#

431

# Exonic sequences do not necessarily code for a translational product

432

# (amino acids). Only the regions of exons bounded by the

433

# codingSequence correspond

434

# to coding DNA sequence.

435

#

436

# Exons are ordered by start position and may not overlap.

437

{

438

"start": "A String", # The start position of the exon on this annotation's reference sequence,

439

# 0-based inclusive. Note that this is relative to the reference start, and

440

# **not** the containing annotation start.

441

"frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates

442

# the offset of the first coding base of the exon within the reading frame

443

# of the coding DNA sequence, if any. This field is dependent on the

444

# strandedness of this annotation (see

445

# Annotation.reverse_strand).

446

# For forward stranded annotations, this offset is relative to the

447

# exon.start. For reverse

448

# strand annotations, this offset is relative to the

449

# exon.end `- 1`.

450

#

451

# Unset if this exon does not intersect the coding sequence. Upon creation

452

# of a transcript, the frame must be populated for all or none of the

453

# coding exons.

454

"end": "A String", # The end position of the exon on this annotation's reference sequence,

455

# 0-based exclusive. Note that this is relative to the reference start, and

456

# *not* the containing annotation start.

457

},

458

],

459

},

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

460

"id": "A String", # The server-generated annotation ID, unique across all annotations.

},

},

],

}</pre>

</div>

<code class="details" id="create">create(body, x__xgafv=None)</code>

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

469

<pre>Creates a new annotation. Caller must have WRITE permission

470

for the associated annotation set.

471

472

The following fields are required:

* annotationSetId

* referenceName or

referenceId

### Transcripts

For annotations of type TRANSCRIPT, the following fields of

481

transcript must be provided:

* exons.start

* exons.end

All other fields may be optionally specified, unless documented as being

487

server-generated (for example, the `id` field). The annotated

488

range must be no longer than 100Mbp (mega base pairs). See the

489

Annotation resource

490

for additional restrictions on each field.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

491

492

Args:

493

body: object, The request body. (required)

494

The object takes the form of:

495

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

496

{ # An annotation describes a region of reference genome. The value of an

497

# annotation may be one of several canonical types, supplemented by arbitrary

498

# info tags. An annotation is not inherently associated with a specific

499

# sample or individual (though a client could choose to use annotations in

500

# this way). Example canonical annotation types are `GENE` and

501

# `VARIANT`.

502

"info": { # A map of additional read alignment information. This must be of the form

503

# map<string, string[]> (string key mapping to a list of string values).

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

"a_key": [

"",

],

},

"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.

509

"end": "A String", # The end position of the range on the reference, 0-based exclusive.

510

"name": "A String", # The display name of this annotation.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

511

"type": "A String", # The data type for this annotation. Must match the containing annotation

512

# set's type.

513

"variant": { # A variant annotation, which describes the effect of a variant on the

514

# genome, the coding sequence, and/or higher level consequences at the

515

# organism level e.g. pathogenicity. This field is only set for annotations

516

# of type `VARIANT`.

517

"conditions": [ # The set of conditions associated with this variant.

518

# A condition describes the way a variant influences human health.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

519

{

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

520

"externalIds": [ # The set of external IDs for this condition.

521

{

522

"sourceName": "A String", # The name of the source of this data.

523

"id": "A String", # The id used by the source of this data.

524

},

525

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

526

"omimId": "A String", # The OMIM id for this condition.

527

# Search for these IDs at http://omim.org/

528

"conceptId": "A String", # The MedGen concept id associated with this gene.

529

# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

530

"names": [ # A set of names for the condition.

"A String",

],

},

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

535

"effect": "A String", # Effect of the variant on the coding sequence.

536

"transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These

537

# should be provided when the variant is created.

538

"A String",

539

],

540

"alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles

541

# exist at this location, create a separate variant for each one, as they

542

# may represent distinct conditions.

543

"clinicalSignificance": "A String", # Describes the clinical significance of a variant.

544

# It is adapted from the ClinVar controlled vocabulary for clinical

545

# significance described at:

546

# http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/

547

"type": "A String", # Type has been adapted from ClinVar's list of variant types.

548

"geneId": "A String", # Google annotation ID of the gene affected by this variant. This should

549

# be provided when the variant is created.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

550

},

551

"start": "A String", # The start position of the range on the reference, 0-based inclusive.

552

"annotationSetId": "A String", # The annotation set to which this annotation belongs.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

553

"referenceName": "A String", # The display name corresponding to the reference specified by

554

# `referenceId`, for example `chr1`, `1`, or `chrX`.

555

"reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward

556

# strand. Note that regardless of this field, the start/end position of the

557

# range always refer to the forward strand.

558

"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of

559

# the reference genome may be transcribed as RNA. An alternative splicing

560

# pattern would be represented as a separate transcript object. This field

561

# is only set for annotations of type `TRANSCRIPT`.

562

# reference genome may be transcribed as RNA.

563

"codingSequence": { # The range of the coding sequence for this transcript, if any. To determine

564

# the exact ranges of coding sequence, intersect this range with those of the

565

# exons, if any. If there are any

566

# exons, the

567

# codingSequence must start

568

# and end within them.

569

#

570

# Note that in some cases, the reference genome will not exactly match the

571

# observed mRNA transcript e.g. due to variance in the source genome from

572

# reference. In these cases,

573

# exon.frame will not necessarily

574

# match the expected reference reading frame and coding exon reference bases

575

# cannot necessarily be concatenated to produce the original transcript mRNA.

576

"start": "A String", # The start of the coding sequence on this annotation's reference sequence,

577

# 0-based inclusive. Note that this position is relative to the reference

578

# start, and *not* the containing annotation start.

579

"end": "A String", # The end of the coding sequence on this annotation's reference sequence,

580

# 0-based exclusive. Note that this position is relative to the reference

581

# start, and *not* the containing annotation start.

582

},

583

"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.

584

"exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose

585

# this transcript. This field should be unset for genomes where transcript

586

# splicing does not occur, for example prokaryotes.

587

#

588

# Introns are regions of the transcript that are not included in the

589

# spliced RNA product. Though not explicitly modeled here, intron ranges can

590

# be deduced; all regions of this transcript that are not exons are introns.

591

#

592

# Exonic sequences do not necessarily code for a translational product

593

# (amino acids). Only the regions of exons bounded by the

594

# codingSequence correspond

595

# to coding DNA sequence.

596

#

597

# Exons are ordered by start position and may not overlap.

598

{

599

"start": "A String", # The start position of the exon on this annotation's reference sequence,

600

# 0-based inclusive. Note that this is relative to the reference start, and

601

# **not** the containing annotation start.

602

"frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates

603

# the offset of the first coding base of the exon within the reading frame

604

# of the coding DNA sequence, if any. This field is dependent on the

605

# strandedness of this annotation (see

606

# Annotation.reverse_strand).

607

# For forward stranded annotations, this offset is relative to the

608

# exon.start. For reverse

609

# strand annotations, this offset is relative to the

610

# exon.end `- 1`.

611

#

612

# Unset if this exon does not intersect the coding sequence. Upon creation

613

# of a transcript, the frame must be populated for all or none of the

614

# coding exons.

615

"end": "A String", # The end position of the exon on this annotation's reference sequence,

616

# 0-based exclusive. Note that this is relative to the reference start, and

617

# *not* the containing annotation start.

618

},

619

],

620

},

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

621

"id": "A String", # The server-generated annotation ID, unique across all annotations.

622

}

623

624

x__xgafv: string, V1 error format.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

625

Allowed values

626

1 - v1 error format

627

2 - v2 error format

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

628

629

Returns:

630

An object of the form:

631

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

632

{ # An annotation describes a region of reference genome. The value of an

633

# annotation may be one of several canonical types, supplemented by arbitrary

634

# info tags. An annotation is not inherently associated with a specific

635

# sample or individual (though a client could choose to use annotations in

636

# this way). Example canonical annotation types are `GENE` and

637

# `VARIANT`.

638

"info": { # A map of additional read alignment information. This must be of the form

639

# map<string, string[]> (string key mapping to a list of string values).

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

"a_key": [

"",

],

},

"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.

645

"end": "A String", # The end position of the range on the reference, 0-based exclusive.

646

"name": "A String", # The display name of this annotation.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

647

"type": "A String", # The data type for this annotation. Must match the containing annotation

648

# set's type.

649

"variant": { # A variant annotation, which describes the effect of a variant on the

650

# genome, the coding sequence, and/or higher level consequences at the

651

# organism level e.g. pathogenicity. This field is only set for annotations

652

# of type `VARIANT`.

653

"conditions": [ # The set of conditions associated with this variant.

654

# A condition describes the way a variant influences human health.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

655

{

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

656

"externalIds": [ # The set of external IDs for this condition.

657

{

658

"sourceName": "A String", # The name of the source of this data.

659

"id": "A String", # The id used by the source of this data.

660

},

661

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

662

"omimId": "A String", # The OMIM id for this condition.

663

# Search for these IDs at http://omim.org/

664

"conceptId": "A String", # The MedGen concept id associated with this gene.

665

# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

666

"names": [ # A set of names for the condition.

"A String",

],

},

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

671

"effect": "A String", # Effect of the variant on the coding sequence.

672

"transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These

673

# should be provided when the variant is created.

674

"A String",

675

],

676

"alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles

677

# exist at this location, create a separate variant for each one, as they

678

# may represent distinct conditions.

679

"clinicalSignificance": "A String", # Describes the clinical significance of a variant.

680

# It is adapted from the ClinVar controlled vocabulary for clinical

681

# significance described at:

682

# http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/

683

"type": "A String", # Type has been adapted from ClinVar's list of variant types.

684

"geneId": "A String", # Google annotation ID of the gene affected by this variant. This should

685

# be provided when the variant is created.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

686

},

687

"start": "A String", # The start position of the range on the reference, 0-based inclusive.

688

"annotationSetId": "A String", # The annotation set to which this annotation belongs.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

689

"referenceName": "A String", # The display name corresponding to the reference specified by

690

# `referenceId`, for example `chr1`, `1`, or `chrX`.

691

"reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward

692

# strand. Note that regardless of this field, the start/end position of the

693

# range always refer to the forward strand.

694

"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of

695

# the reference genome may be transcribed as RNA. An alternative splicing

696

# pattern would be represented as a separate transcript object. This field

697

# is only set for annotations of type `TRANSCRIPT`.

698

# reference genome may be transcribed as RNA.

699

"codingSequence": { # The range of the coding sequence for this transcript, if any. To determine

700

# the exact ranges of coding sequence, intersect this range with those of the

701

# exons, if any. If there are any

702

# exons, the

703

# codingSequence must start

704

# and end within them.

705

#

706

# Note that in some cases, the reference genome will not exactly match the

707

# observed mRNA transcript e.g. due to variance in the source genome from

708

# reference. In these cases,

709

# exon.frame will not necessarily

710

# match the expected reference reading frame and coding exon reference bases

711

# cannot necessarily be concatenated to produce the original transcript mRNA.

712

"start": "A String", # The start of the coding sequence on this annotation's reference sequence,

713

# 0-based inclusive. Note that this position is relative to the reference

714

# start, and *not* the containing annotation start.

715

"end": "A String", # The end of the coding sequence on this annotation's reference sequence,

716

# 0-based exclusive. Note that this position is relative to the reference

717

# start, and *not* the containing annotation start.

718

},

719

"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.

720

"exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose

721

# this transcript. This field should be unset for genomes where transcript

722

# splicing does not occur, for example prokaryotes.

723

#

724

# Introns are regions of the transcript that are not included in the

725

# spliced RNA product. Though not explicitly modeled here, intron ranges can

726

# be deduced; all regions of this transcript that are not exons are introns.

727

#

728

# Exonic sequences do not necessarily code for a translational product

729

# (amino acids). Only the regions of exons bounded by the

730

# codingSequence correspond

731

# to coding DNA sequence.

732

#

733

# Exons are ordered by start position and may not overlap.

734

{

735

"start": "A String", # The start position of the exon on this annotation's reference sequence,

736

# 0-based inclusive. Note that this is relative to the reference start, and

737

# **not** the containing annotation start.

738

"frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates

739

# the offset of the first coding base of the exon within the reading frame

740

# of the coding DNA sequence, if any. This field is dependent on the

741

# strandedness of this annotation (see

742

# Annotation.reverse_strand).

743

# For forward stranded annotations, this offset is relative to the

744

# exon.start. For reverse

745

# strand annotations, this offset is relative to the

746

# exon.end `- 1`.

747

#

748

# Unset if this exon does not intersect the coding sequence. Upon creation

749

# of a transcript, the frame must be populated for all or none of the

750

# coding exons.

751

"end": "A String", # The end position of the exon on this annotation's reference sequence,

752

# 0-based exclusive. Note that this is relative to the reference start, and

753

# *not* the containing annotation start.

754

},

755

],

756

},

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

757

"id": "A String", # The server-generated annotation ID, unique across all annotations.

}</pre>

</div>

<code class="details" id="delete">delete(annotationId, x__xgafv=None)</code>

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

763

<pre>Deletes an annotation. Caller must have WRITE permission for

764

the associated annotation set.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

765

766

Args:

767

annotationId: string, The ID of the annotation to be deleted. (required)

768

x__xgafv: string, V1 error format.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

769

Allowed values

770

1 - v1 error format

771

2 - v2 error format

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

772

773

Returns:

774

An object of the form:

775

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

776

{ # A generic empty message that you can re-use to avoid defining duplicated

777

# empty messages in your APIs. A typical example is to use it as the request

778

# or the response type of an API method. For instance:

779

#

780

# service Foo {

781

# rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);

782

# }

783

#

784

# The JSON representation for `Empty` is empty JSON object `{}`.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

}</pre>

</div>

<code class="details" id="get">get(annotationId, x__xgafv=None)</code>

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

790

<pre>Gets an annotation. Caller must have READ permission

791

for the associated annotation set.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

792

793

Args:

794

annotationId: string, The ID of the annotation to be retrieved. (required)

795

x__xgafv: string, V1 error format.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

796

Allowed values

797

1 - v1 error format

798

2 - v2 error format

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

799

800

Returns:

801

An object of the form:

802

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

803

{ # An annotation describes a region of reference genome. The value of an

804

# annotation may be one of several canonical types, supplemented by arbitrary

805

# info tags. An annotation is not inherently associated with a specific

806

# sample or individual (though a client could choose to use annotations in

807

# this way). Example canonical annotation types are `GENE` and

808

# `VARIANT`.

809

"info": { # A map of additional read alignment information. This must be of the form

810

# map<string, string[]> (string key mapping to a list of string values).

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

"a_key": [

"",

],

},

"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.

816

"end": "A String", # The end position of the range on the reference, 0-based exclusive.

817

"name": "A String", # The display name of this annotation.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

818

"type": "A String", # The data type for this annotation. Must match the containing annotation

819

# set's type.

820

"variant": { # A variant annotation, which describes the effect of a variant on the

821

# genome, the coding sequence, and/or higher level consequences at the

822

# organism level e.g. pathogenicity. This field is only set for annotations

823

# of type `VARIANT`.

824

"conditions": [ # The set of conditions associated with this variant.

825

# A condition describes the way a variant influences human health.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

826

{

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

827

"externalIds": [ # The set of external IDs for this condition.

828

{

829

"sourceName": "A String", # The name of the source of this data.

830

"id": "A String", # The id used by the source of this data.

831

},

832

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

833

"omimId": "A String", # The OMIM id for this condition.

834

# Search for these IDs at http://omim.org/

835

"conceptId": "A String", # The MedGen concept id associated with this gene.

836

# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

837

"names": [ # A set of names for the condition.

"A String",

],

},

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

842

"effect": "A String", # Effect of the variant on the coding sequence.

843

"transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These

844

# should be provided when the variant is created.

845

"A String",

846

],

847

"alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles

848

# exist at this location, create a separate variant for each one, as they

849

# may represent distinct conditions.

850

"clinicalSignificance": "A String", # Describes the clinical significance of a variant.

851

# It is adapted from the ClinVar controlled vocabulary for clinical

852

# significance described at:

853

# http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/

854

"type": "A String", # Type has been adapted from ClinVar's list of variant types.

855

"geneId": "A String", # Google annotation ID of the gene affected by this variant. This should

856

# be provided when the variant is created.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

857

},

858

"start": "A String", # The start position of the range on the reference, 0-based inclusive.

859

"annotationSetId": "A String", # The annotation set to which this annotation belongs.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

860

"referenceName": "A String", # The display name corresponding to the reference specified by

861

# `referenceId`, for example `chr1`, `1`, or `chrX`.

862

"reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward

863

# strand. Note that regardless of this field, the start/end position of the

864

# range always refer to the forward strand.

865

"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of

866

# the reference genome may be transcribed as RNA. An alternative splicing

867

# pattern would be represented as a separate transcript object. This field

868

# is only set for annotations of type `TRANSCRIPT`.

869

# reference genome may be transcribed as RNA.

870

"codingSequence": { # The range of the coding sequence for this transcript, if any. To determine

871

# the exact ranges of coding sequence, intersect this range with those of the

872

# exons, if any. If there are any

873

# exons, the

874

# codingSequence must start

875

# and end within them.

876

#

877

# Note that in some cases, the reference genome will not exactly match the

878

# observed mRNA transcript e.g. due to variance in the source genome from

879

# reference. In these cases,

880

# exon.frame will not necessarily

881

# match the expected reference reading frame and coding exon reference bases

882

# cannot necessarily be concatenated to produce the original transcript mRNA.

883

"start": "A String", # The start of the coding sequence on this annotation's reference sequence,

884

# 0-based inclusive. Note that this position is relative to the reference

885

# start, and *not* the containing annotation start.

886

"end": "A String", # The end of the coding sequence on this annotation's reference sequence,

887

# 0-based exclusive. Note that this position is relative to the reference

888

# start, and *not* the containing annotation start.

889

},

890

"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.

891

"exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose

892

# this transcript. This field should be unset for genomes where transcript

893

# splicing does not occur, for example prokaryotes.

894

#

895

# Introns are regions of the transcript that are not included in the

896

# spliced RNA product. Though not explicitly modeled here, intron ranges can

897

# be deduced; all regions of this transcript that are not exons are introns.

898

#

899

# Exonic sequences do not necessarily code for a translational product

900

# (amino acids). Only the regions of exons bounded by the

901

# codingSequence correspond

902

# to coding DNA sequence.

903

#

904

# Exons are ordered by start position and may not overlap.

905

{

906

"start": "A String", # The start position of the exon on this annotation's reference sequence,

907

# 0-based inclusive. Note that this is relative to the reference start, and

908

# **not** the containing annotation start.

909

"frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates

910

# the offset of the first coding base of the exon within the reading frame

911

# of the coding DNA sequence, if any. This field is dependent on the

912

# strandedness of this annotation (see

913

# Annotation.reverse_strand).

914

# For forward stranded annotations, this offset is relative to the

915

# exon.start. For reverse

916

# strand annotations, this offset is relative to the

917

# exon.end `- 1`.

918

#

919

# Unset if this exon does not intersect the coding sequence. Upon creation

920

# of a transcript, the frame must be populated for all or none of the

921

# coding exons.

922

"end": "A String", # The end position of the exon on this annotation's reference sequence,

923

# 0-based exclusive. Note that this is relative to the reference start, and

924

# *not* the containing annotation start.

925

},

926

],

927

},

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

928

"id": "A String", # The server-generated annotation ID, unique across all annotations.

}</pre>

</div>

<code class="details" id="search">search(body, x__xgafv=None)</code>

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

934

<pre>Searches for annotations that match the given criteria. Results are

935

ordered by genomic coordinate (by reference sequence, then position).

936

Annotations with equivalent genomic coordinates are returned in an

937

unspecified order. This order is consistent, such that two queries for the

938

same content (regardless of page size) yield annotations in the same order

939

across their respective streams of paginated responses. Caller must have

940

READ permission for the queried annotation sets.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

941

942

Args:

943

body: object, The request body. (required)

944

The object takes the form of:

945

946

{

947

"referenceId": "A String", # The ID of the reference to query.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

948

"end": "A String", # The end position of the range on the reference, 0-based exclusive. If

949

# referenceId or

950

# referenceName

951

# must be specified, Defaults to the length of the reference.

952

"pageSize": 42, # The maximum number of results to return in a single page. If unspecified,

953

# defaults to 256. The maximum value is 2048.

954

"start": "A String", # The start position of the range on the reference, 0-based inclusive. If

# specified,

# referenceId or

# referenceName

# must be specified. Defaults to 0.

959

"annotationSetIds": [ # Required. The annotation sets to search within. The caller must have

960

# `READ` access to these annotation sets.

961

# All queried annotation sets must have the same type.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

962

"A String",

963

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

964

"pageToken": "A String", # The continuation token, which is used to page through large result sets.

965

# To get the next page of results, set this parameter to the value of

966

# `nextPageToken` from the previous response.

967

"referenceName": "A String", # The name of the reference to query, within the reference set associated

968

# with this query.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

969

}

970

971

x__xgafv: string, V1 error format.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

972

Allowed values

973

1 - v1 error format

974

2 - v2 error format

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

975

976

Returns:

977

An object of the form:

978

979

{

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

980

"nextPageToken": "A String", # The continuation token, which is used to page through large result sets.

981

# Provide this value in a subsequent request to return the next page of

982

# results. This field will be empty if there aren't any additional results.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

983

"annotations": [ # The matching annotations.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

984

{ # An annotation describes a region of reference genome. The value of an

985

# annotation may be one of several canonical types, supplemented by arbitrary

986

# info tags. An annotation is not inherently associated with a specific

987

# sample or individual (though a client could choose to use annotations in

988

# this way). Example canonical annotation types are `GENE` and

989

# `VARIANT`.

990

"info": { # A map of additional read alignment information. This must be of the form

991

# map<string, string[]> (string key mapping to a list of string values).

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

"a_key": [

"",

],

},

"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.

997

"end": "A String", # The end position of the range on the reference, 0-based exclusive.

998

"name": "A String", # The display name of this annotation.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

999

"type": "A String", # The data type for this annotation. Must match the containing annotation

1000

# set's type.

1001

"variant": { # A variant annotation, which describes the effect of a variant on the

1002

# genome, the coding sequence, and/or higher level consequences at the

1003

# organism level e.g. pathogenicity. This field is only set for annotations

1004

# of type `VARIANT`.

1005

"conditions": [ # The set of conditions associated with this variant.

1006

# A condition describes the way a variant influences human health.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1007

{

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1008

"externalIds": [ # The set of external IDs for this condition.

1009

{

1010

"sourceName": "A String", # The name of the source of this data.

1011

"id": "A String", # The id used by the source of this data.

1012

},

1013

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1014

"omimId": "A String", # The OMIM id for this condition.

1015

# Search for these IDs at http://omim.org/

1016

"conceptId": "A String", # The MedGen concept id associated with this gene.

1017

# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1018

"names": [ # A set of names for the condition.

"A String",

],

},

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1023

"effect": "A String", # Effect of the variant on the coding sequence.

1024

"transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These

1025

# should be provided when the variant is created.

1026

"A String",

1027

],

1028

"alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles

1029

# exist at this location, create a separate variant for each one, as they

1030

# may represent distinct conditions.

1031

"clinicalSignificance": "A String", # Describes the clinical significance of a variant.

1032

# It is adapted from the ClinVar controlled vocabulary for clinical

1033

# significance described at:

1034

# http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/

1035

"type": "A String", # Type has been adapted from ClinVar's list of variant types.

1036

"geneId": "A String", # Google annotation ID of the gene affected by this variant. This should

1037

# be provided when the variant is created.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1038

},

1039

"start": "A String", # The start position of the range on the reference, 0-based inclusive.

1040

"annotationSetId": "A String", # The annotation set to which this annotation belongs.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1041

"referenceName": "A String", # The display name corresponding to the reference specified by

1042

# `referenceId`, for example `chr1`, `1`, or `chrX`.

1043

"reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward

1044

# strand. Note that regardless of this field, the start/end position of the

1045

# range always refer to the forward strand.

1046

"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of

1047

# the reference genome may be transcribed as RNA. An alternative splicing

1048

# pattern would be represented as a separate transcript object. This field

1049

# is only set for annotations of type `TRANSCRIPT`.

1050

# reference genome may be transcribed as RNA.

1051

"codingSequence": { # The range of the coding sequence for this transcript, if any. To determine

1052

# the exact ranges of coding sequence, intersect this range with those of the

1053

# exons, if any. If there are any

1054

# exons, the

1055

# codingSequence must start

1056

# and end within them.

1057

#

1058

# Note that in some cases, the reference genome will not exactly match the

1059

# observed mRNA transcript e.g. due to variance in the source genome from

1060

# reference. In these cases,

1061

# exon.frame will not necessarily

1062

# match the expected reference reading frame and coding exon reference bases

1063

# cannot necessarily be concatenated to produce the original transcript mRNA.

1064

"start": "A String", # The start of the coding sequence on this annotation's reference sequence,

1065

# 0-based inclusive. Note that this position is relative to the reference

1066

# start, and *not* the containing annotation start.

1067

"end": "A String", # The end of the coding sequence on this annotation's reference sequence,

1068

# 0-based exclusive. Note that this position is relative to the reference

1069

# start, and *not* the containing annotation start.

1070

},

1071

"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.

1072

"exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose

1073

# this transcript. This field should be unset for genomes where transcript

1074

# splicing does not occur, for example prokaryotes.

1075

#

1076

# Introns are regions of the transcript that are not included in the

1077

# spliced RNA product. Though not explicitly modeled here, intron ranges can

1078

# be deduced; all regions of this transcript that are not exons are introns.

1079

#

1080

# Exonic sequences do not necessarily code for a translational product

1081

# (amino acids). Only the regions of exons bounded by the

1082

# codingSequence correspond

1083

# to coding DNA sequence.

1084

#

1085

# Exons are ordered by start position and may not overlap.

1086

{

1087

"start": "A String", # The start position of the exon on this annotation's reference sequence,

1088

# 0-based inclusive. Note that this is relative to the reference start, and

1089

# **not** the containing annotation start.

1090

"frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates

1091

# the offset of the first coding base of the exon within the reading frame

1092

# of the coding DNA sequence, if any. This field is dependent on the

1093

# strandedness of this annotation (see

1094

# Annotation.reverse_strand).

1095

# For forward stranded annotations, this offset is relative to the

1096

# exon.start. For reverse

1097

# strand annotations, this offset is relative to the

1098

# exon.end `- 1`.

1099

#

1100

# Unset if this exon does not intersect the coding sequence. Upon creation

1101

# of a transcript, the frame must be populated for all or none of the

1102

# coding exons.

1103

"end": "A String", # The end position of the exon on this annotation's reference sequence,

1104

# 0-based exclusive. Note that this is relative to the reference start, and

1105

# *not* the containing annotation start.

1106

},

1107

],

1108

},

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1109

"id": "A String", # The server-generated annotation ID, unique across all annotations.

},

],

}</pre>

</div>

Sai Cheemalapati

2017-03-13 12:12:03 -0400

[diff] [blame^]

1116

<code class="details" id="search_next">search_next(previous_request, previous_response)</code>

1117

<pre>Retrieves the next page of results.

1118

1119

Args:

1120

previous_request: The request for the previous page. (required)

1121

previous_response: The response from the request for the previous page. (required)

1122

1123

Returns:

1124

A request object that you can call 'execute()' on to request the next

1125

page. Returns None if there are no more items in the collection.

</pre>

</div>

Jon Wayne Parrott

2016-05-19 10:54:38 -0700

[diff] [blame]

1130

<code class="details" id="update">update(annotationId, body, updateMask=None, x__xgafv=None)</code>

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1131

<pre>Updates an annotation. Caller must have

1132

WRITE permission for the associated dataset.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1133

1134

Args:

1135

annotationId: string, The ID of the annotation to be updated. (required)

1136

body: object, The request body. (required)

1137

The object takes the form of:

1138

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1139

{ # An annotation describes a region of reference genome. The value of an

1140

# annotation may be one of several canonical types, supplemented by arbitrary

1141

# info tags. An annotation is not inherently associated with a specific

1142

# sample or individual (though a client could choose to use annotations in

1143

# this way). Example canonical annotation types are `GENE` and

1144

# `VARIANT`.

1145

"info": { # A map of additional read alignment information. This must be of the form

1146

# map<string, string[]> (string key mapping to a list of string values).

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

"a_key": [

"",

],

},

"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.

1152

"end": "A String", # The end position of the range on the reference, 0-based exclusive.

1153

"name": "A String", # The display name of this annotation.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1154

"type": "A String", # The data type for this annotation. Must match the containing annotation

1155

# set's type.

1156

"variant": { # A variant annotation, which describes the effect of a variant on the

1157

# genome, the coding sequence, and/or higher level consequences at the

1158

# organism level e.g. pathogenicity. This field is only set for annotations

1159

# of type `VARIANT`.

1160

"conditions": [ # The set of conditions associated with this variant.

1161

# A condition describes the way a variant influences human health.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1162

{

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1163

"externalIds": [ # The set of external IDs for this condition.

1164

{

1165

"sourceName": "A String", # The name of the source of this data.

1166

"id": "A String", # The id used by the source of this data.

1167

},

1168

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1169

"omimId": "A String", # The OMIM id for this condition.

1170

# Search for these IDs at http://omim.org/

1171

"conceptId": "A String", # The MedGen concept id associated with this gene.

1172

# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1173

"names": [ # A set of names for the condition.

"A String",

],

},

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1178

"effect": "A String", # Effect of the variant on the coding sequence.

1179

"transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These

1180

# should be provided when the variant is created.

1181

"A String",

1182

],

1183

"alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles

1184

# exist at this location, create a separate variant for each one, as they

1185

# may represent distinct conditions.

1186

"clinicalSignificance": "A String", # Describes the clinical significance of a variant.

1187

# It is adapted from the ClinVar controlled vocabulary for clinical

1188

# significance described at:

1189

# http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/

1190

"type": "A String", # Type has been adapted from ClinVar's list of variant types.

1191

"geneId": "A String", # Google annotation ID of the gene affected by this variant. This should

1192

# be provided when the variant is created.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1193

},

1194

"start": "A String", # The start position of the range on the reference, 0-based inclusive.

1195

"annotationSetId": "A String", # The annotation set to which this annotation belongs.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1196

"referenceName": "A String", # The display name corresponding to the reference specified by

1197

# `referenceId`, for example `chr1`, `1`, or `chrX`.

1198

"reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward

1199

# strand. Note that regardless of this field, the start/end position of the

1200

# range always refer to the forward strand.

1201

"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of

1202

# the reference genome may be transcribed as RNA. An alternative splicing

1203

# pattern would be represented as a separate transcript object. This field

1204

# is only set for annotations of type `TRANSCRIPT`.

1205

# reference genome may be transcribed as RNA.

1206

"codingSequence": { # The range of the coding sequence for this transcript, if any. To determine

1207

# the exact ranges of coding sequence, intersect this range with those of the

1208

# exons, if any. If there are any

1209

# exons, the

1210

# codingSequence must start

1211

# and end within them.

1212

#

1213

# Note that in some cases, the reference genome will not exactly match the

1214

# observed mRNA transcript e.g. due to variance in the source genome from

1215

# reference. In these cases,

1216

# exon.frame will not necessarily

1217

# match the expected reference reading frame and coding exon reference bases

1218

# cannot necessarily be concatenated to produce the original transcript mRNA.

1219

"start": "A String", # The start of the coding sequence on this annotation's reference sequence,

1220

# 0-based inclusive. Note that this position is relative to the reference

1221

# start, and *not* the containing annotation start.

1222

"end": "A String", # The end of the coding sequence on this annotation's reference sequence,

1223

# 0-based exclusive. Note that this position is relative to the reference

1224

# start, and *not* the containing annotation start.

1225

},

1226

"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.

1227

"exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose

1228

# this transcript. This field should be unset for genomes where transcript

1229

# splicing does not occur, for example prokaryotes.

1230

#

1231

# Introns are regions of the transcript that are not included in the

1232

# spliced RNA product. Though not explicitly modeled here, intron ranges can

1233

# be deduced; all regions of this transcript that are not exons are introns.

1234

#

1235

# Exonic sequences do not necessarily code for a translational product

1236

# (amino acids). Only the regions of exons bounded by the

1237

# codingSequence correspond

1238

# to coding DNA sequence.

1239

#

1240

# Exons are ordered by start position and may not overlap.

1241

{

1242

"start": "A String", # The start position of the exon on this annotation's reference sequence,

1243

# 0-based inclusive. Note that this is relative to the reference start, and

1244

# **not** the containing annotation start.

1245

"frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates

1246

# the offset of the first coding base of the exon within the reading frame

1247

# of the coding DNA sequence, if any. This field is dependent on the

1248

# strandedness of this annotation (see

1249

# Annotation.reverse_strand).

1250

# For forward stranded annotations, this offset is relative to the

1251

# exon.start. For reverse

1252

# strand annotations, this offset is relative to the

1253

# exon.end `- 1`.

1254

#

1255

# Unset if this exon does not intersect the coding sequence. Upon creation

1256

# of a transcript, the frame must be populated for all or none of the

1257

# coding exons.

1258

"end": "A String", # The end position of the exon on this annotation's reference sequence,

1259

# 0-based exclusive. Note that this is relative to the reference start, and

1260

# *not* the containing annotation start.

1261

},

1262

],

1263

},

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1264

"id": "A String", # The server-generated annotation ID, unique across all annotations.

1265

}

1266

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1267

updateMask: string, An optional mask specifying which fields to update. Mutable fields are

name,

variant,

transcript, and

info. If unspecified, all mutable

1272

fields will be updated.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1273

x__xgafv: string, V1 error format.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1274

Allowed values

1275

1 - v1 error format

1276

2 - v2 error format

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1277

1278

Returns:

1279

An object of the form:

1280

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1281

{ # An annotation describes a region of reference genome. The value of an

1282

# annotation may be one of several canonical types, supplemented by arbitrary

1283

# info tags. An annotation is not inherently associated with a specific

1284

# sample or individual (though a client could choose to use annotations in

1285

# this way). Example canonical annotation types are `GENE` and

1286

# `VARIANT`.

1287

"info": { # A map of additional read alignment information. This must be of the form

1288

# map<string, string[]> (string key mapping to a list of string values).

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

"a_key": [

"",

],

},

"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.

1294

"end": "A String", # The end position of the range on the reference, 0-based exclusive.

1295

"name": "A String", # The display name of this annotation.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1296

"type": "A String", # The data type for this annotation. Must match the containing annotation

1297

# set's type.

1298

"variant": { # A variant annotation, which describes the effect of a variant on the

1299

# genome, the coding sequence, and/or higher level consequences at the

1300

# organism level e.g. pathogenicity. This field is only set for annotations

1301

# of type `VARIANT`.

1302

"conditions": [ # The set of conditions associated with this variant.

1303

# A condition describes the way a variant influences human health.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1304

{

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1305

"externalIds": [ # The set of external IDs for this condition.

1306

{

1307

"sourceName": "A String", # The name of the source of this data.

1308

"id": "A String", # The id used by the source of this data.

1309

},

1310

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1311

"omimId": "A String", # The OMIM id for this condition.

1312

# Search for these IDs at http://omim.org/

1313

"conceptId": "A String", # The MedGen concept id associated with this gene.

1314

# Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1315

"names": [ # A set of names for the condition.

"A String",

],

},

],

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1320

"effect": "A String", # Effect of the variant on the coding sequence.

1321

"transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These

1322

# should be provided when the variant is created.

1323

"A String",

1324

],

1325

"alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles

1326

# exist at this location, create a separate variant for each one, as they

1327

# may represent distinct conditions.

1328

"clinicalSignificance": "A String", # Describes the clinical significance of a variant.

1329

# It is adapted from the ClinVar controlled vocabulary for clinical

1330

# significance described at:

1331

# http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/

1332

"type": "A String", # Type has been adapted from ClinVar's list of variant types.

1333

"geneId": "A String", # Google annotation ID of the gene affected by this variant. This should

1334

# be provided when the variant is created.

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1335

},

1336

"start": "A String", # The start position of the range on the reference, 0-based inclusive.

1337

"annotationSetId": "A String", # The annotation set to which this annotation belongs.

Sai Cheemalapati

c30d2b5

2017-03-13 12:12:03 -0400

[diff] [blame^]

1338

"referenceName": "A String", # The display name corresponding to the reference specified by

1339

# `referenceId`, for example `chr1`, `1`, or `chrX`.

1340

"reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward

1341

# strand. Note that regardless of this field, the start/end position of the

1342

# range always refer to the forward strand.

1343

"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of

1344

# the reference genome may be transcribed as RNA. An alternative splicing

1345

# pattern would be represented as a separate transcript object. This field

1346

# is only set for annotations of type `TRANSCRIPT`.

1347

# reference genome may be transcribed as RNA.

1348

"codingSequence": { # The range of the coding sequence for this transcript, if any. To determine

1349

# the exact ranges of coding sequence, intersect this range with those of the

1350

# exons, if any. If there are any

1351

# exons, the

1352

# codingSequence must start

1353

# and end within them.

1354

#

1355

# Note that in some cases, the reference genome will not exactly match the

1356

# observed mRNA transcript e.g. due to variance in the source genome from

1357

# reference. In these cases,

1358

# exon.frame will not necessarily

1359

# match the expected reference reading frame and coding exon reference bases

1360

# cannot necessarily be concatenated to produce the original transcript mRNA.

1361

"start": "A String", # The start of the coding sequence on this annotation's reference sequence,

1362

# 0-based inclusive. Note that this position is relative to the reference

1363

# start, and *not* the containing annotation start.

1364

"end": "A String", # The end of the coding sequence on this annotation's reference sequence,

1365

# 0-based exclusive. Note that this position is relative to the reference

1366

# start, and *not* the containing annotation start.

1367

},

1368

"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.

1369

"exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose

1370

# this transcript. This field should be unset for genomes where transcript

1371

# splicing does not occur, for example prokaryotes.

1372

#

1373

# Introns are regions of the transcript that are not included in the

1374

# spliced RNA product. Though not explicitly modeled here, intron ranges can

1375

# be deduced; all regions of this transcript that are not exons are introns.

1376

#

1377

# Exonic sequences do not necessarily code for a translational product

1378

# (amino acids). Only the regions of exons bounded by the

1379

# codingSequence correspond

1380

# to coding DNA sequence.

1381

#

1382

# Exons are ordered by start position and may not overlap.

1383

{

1384

"start": "A String", # The start position of the exon on this annotation's reference sequence,

1385

# 0-based inclusive. Note that this is relative to the reference start, and

1386

# **not** the containing annotation start.

1387

"frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates

1388

# the offset of the first coding base of the exon within the reading frame

1389

# of the coding DNA sequence, if any. This field is dependent on the

1390

# strandedness of this annotation (see

1391

# Annotation.reverse_strand).

1392

# For forward stranded annotations, this offset is relative to the

1393

# exon.start. For reverse

1394

# strand annotations, this offset is relative to the

1395

# exon.end `- 1`.

1396

#

1397

# Unset if this exon does not intersect the coding sequence. Upon creation

1398

# of a transcript, the frame must be populated for all or none of the

1399

# coding exons.

1400

"end": "A String", # The end position of the exon on this annotation's reference sequence,

1401

# 0-based exclusive. Note that this is relative to the reference start, and

1402

# *not* the containing annotation start.

1403

},

1404

],

1405

},

Jon Wayne Parrott

0a471d3

2016-05-19 10:54:38 -0700

[diff] [blame]

1406

"id": "A String", # The server-generated annotation ID, unique across all annotations.

}</pre>

</div>

</body></html>