1 <html><body> 2 <style> 3 4 body, h1, h2, h3, div, span, p, pre, a { 5 margin: 0; 6 padding: 0; 7 border: 0; 8 font-weight: inherit; 9 font-style: inherit; 10 font-size: 100%; 11 font-family: inherit; 12 vertical-align: baseline; 13 } 14 15 body { 16 font-size: 13px; 17 padding: 1em; 18 } 19 20 h1 { 21 font-size: 26px; 22 margin-bottom: 1em; 23 } 24 25 h2 { 26 font-size: 24px; 27 margin-bottom: 1em; 28 } 29 30 h3 { 31 font-size: 20px; 32 margin-bottom: 1em; 33 margin-top: 1em; 34 } 35 36 pre, code { 37 line-height: 1.5; 38 font-family: Monaco, 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', 'Lucida Console', monospace; 39 } 40 41 pre { 42 margin-top: 0.5em; 43 } 44 45 h1, h2, h3, p { 46 font-family: Arial, sans serif; 47 } 48 49 h1, h2, h3 { 50 border-bottom: solid #CCC 1px; 51 } 52 53 .toc_element { 54 margin-top: 0.5em; 55 } 56 57 .firstline { 58 margin-left: 2 em; 59 } 60 61 .method { 62 margin-top: 1em; 63 border: solid 1px #CCC; 64 padding: 1em; 65 background: #EEE; 66 } 67 68 .details { 69 font-weight: bold; 70 font-size: 14px; 71 } 72 73 </style> 74 75 <h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.annotations.html">annotations</a></h1> 76 <h2>Instance Methods</h2> 77 <p class="toc_element"> 78 <code><a href="#batchCreate">batchCreate(body, x__xgafv=None)</a></code></p> 79 <p class="firstline">Creates one or more new annotations atomically. All annotations must</p> 80 <p class="toc_element"> 81 <code><a href="#create">create(body, x__xgafv=None)</a></code></p> 82 <p class="firstline">Creates a new annotation. Caller must have WRITE permission</p> 83 <p class="toc_element"> 84 <code><a href="#delete">delete(annotationId, x__xgafv=None)</a></code></p> 85 <p class="firstline">Deletes an annotation. Caller must have WRITE permission for</p> 86 <p class="toc_element"> 87 <code><a href="#get">get(annotationId, x__xgafv=None)</a></code></p> 88 <p class="firstline">Gets an annotation. Caller must have READ permission</p> 89 <p class="toc_element"> 90 <code><a href="#search">search(body, x__xgafv=None)</a></code></p> 91 <p class="firstline">Searches for annotations that match the given criteria. Results are</p> 92 <p class="toc_element"> 93 <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p> 94 <p class="firstline">Retrieves the next page of results.</p> 95 <p class="toc_element"> 96 <code><a href="#update">update(annotationId, body, updateMask=None, x__xgafv=None)</a></code></p> 97 <p class="firstline">Updates an annotation. Caller must have</p> 98 <h3>Method Details</h3> 99 <div class="method"> 100 <code class="details" id="batchCreate">batchCreate(body, x__xgafv=None)</code> 101 <pre>Creates one or more new annotations atomically. All annotations must 102 belong to the same annotation set. Caller must have WRITE 103 permission for this annotation set. For optimal performance, batch 104 positionally adjacent annotations together. 105 106 If the request has a systemic issue, such as an attempt to write to 107 an inaccessible annotation set, the entire RPC will fail accordingly. For 108 lesser data issues, when possible an error will be isolated to the 109 corresponding batch entry in the response; the remaining well formed 110 annotations will be created normally. 111 112 For details on the requirements for each individual annotation resource, 113 see 114 CreateAnnotation. 115 116 Args: 117 body: object, The request body. (required) 118 The object takes the form of: 119 120 { 121 "requestId": "A String", # A unique request ID which enables the server to detect duplicated requests. 122 # If provided, duplicated requests will result in the same response; if not 123 # provided, duplicated requests may result in duplicated data. For a given 124 # annotation set, callers should not reuse `request_id`s when writing 125 # different batches of annotations - behavior in this case is undefined. 126 # A common approach is to use a UUID. For batch jobs where worker crashes are 127 # a possibility, consider using some unique variant of a worker or run ID. 128 "annotations": [ # The annotations to be created. At most 4096 can be specified in a single 129 # request. 130 { # An annotation describes a region of reference genome. The value of an 131 # annotation may be one of several canonical types, supplemented by arbitrary 132 # info tags. An annotation is not inherently associated with a specific 133 # sample or individual (though a client could choose to use annotations in 134 # this way). Example canonical annotation types are `GENE` and 135 # `VARIANT`. 136 "info": { # A map of additional read alignment information. This must be of the form 137 # map<string, string[]> (string key mapping to a list of string values). 138 "a_key": [ 139 "", 140 ], 141 }, 142 "referenceId": "A String", # The ID of the Google Genomics reference associated with this range. 143 "end": "A String", # The end position of the range on the reference, 0-based exclusive. 144 "name": "A String", # The display name of this annotation. 145 "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of 146 # the reference genome may be transcribed as RNA. An alternative splicing 147 # pattern would be represented as a separate transcript object. This field 148 # is only set for annotations of type `TRANSCRIPT`. 149 # reference genome may be transcribed as RNA. 150 "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine 151 # the exact ranges of coding sequence, intersect this range with those of the 152 # exons, if any. If there are any 153 # exons, the 154 # codingSequence must start 155 # and end within them. 156 # 157 # Note that in some cases, the reference genome will not exactly match the 158 # observed mRNA transcript e.g. due to variance in the source genome from 159 # reference. In these cases, 160 # exon.frame will not necessarily 161 # match the expected reference reading frame and coding exon reference bases 162 # cannot necessarily be concatenated to produce the original transcript mRNA. 163 "start": "A String", # The start of the coding sequence on this annotation's reference sequence, 164 # 0-based inclusive. Note that this position is relative to the reference 165 # start, and *not* the containing annotation start. 166 "end": "A String", # The end of the coding sequence on this annotation's reference sequence, 167 # 0-based exclusive. Note that this position is relative to the reference 168 # start, and *not* the containing annotation start. 169 }, 170 "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose 171 # this transcript. This field should be unset for genomes where transcript 172 # splicing does not occur, for example prokaryotes. 173 # 174 # Introns are regions of the transcript that are not included in the 175 # spliced RNA product. Though not explicitly modeled here, intron ranges can 176 # be deduced; all regions of this transcript that are not exons are introns. 177 # 178 # Exonic sequences do not necessarily code for a translational product 179 # (amino acids). Only the regions of exons bounded by the 180 # codingSequence correspond 181 # to coding DNA sequence. 182 # 183 # Exons are ordered by start position and may not overlap. 184 { 185 "start": "A String", # The start position of the exon on this annotation's reference sequence, 186 # 0-based inclusive. Note that this is relative to the reference start, and 187 # **not** the containing annotation start. 188 "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates 189 # the offset of the first coding base of the exon within the reading frame 190 # of the coding DNA sequence, if any. This field is dependent on the 191 # strandedness of this annotation (see 192 # Annotation.reverse_strand). 193 # For forward stranded annotations, this offset is relative to the 194 # exon.start. For reverse 195 # strand annotations, this offset is relative to the 196 # exon.end `- 1`. 197 # 198 # Unset if this exon does not intersect the coding sequence. Upon creation 199 # of a transcript, the frame must be populated for all or none of the 200 # coding exons. 201 "end": "A String", # The end position of the exon on this annotation's reference sequence, 202 # 0-based exclusive. Note that this is relative to the reference start, and 203 # *not* the containing annotation start. 204 }, 205 ], 206 "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. 207 }, 208 "variant": { # A variant annotation, which describes the effect of a variant on the 209 # genome, the coding sequence, and/or higher level consequences at the 210 # organism level e.g. pathogenicity. This field is only set for annotations 211 # of type `VARIANT`. 212 "type": "A String", # Type has been adapted from ClinVar's list of variant types. 213 "effect": "A String", # Effect of the variant on the coding sequence. 214 "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These 215 # should be provided when the variant is created. 216 "A String", 217 ], 218 "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles 219 # exist at this location, create a separate variant for each one, as they 220 # may represent distinct conditions. 221 "clinicalSignificance": "A String", # Describes the clinical significance of a variant. 222 # It is adapted from the ClinVar controlled vocabulary for clinical 223 # significance described at: 224 # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 225 "conditions": [ # The set of conditions associated with this variant. 226 # A condition describes the way a variant influences human health. 227 { 228 "externalIds": [ # The set of external IDs for this condition. 229 { 230 "sourceName": "A String", # The name of the source of this data. 231 "id": "A String", # The id used by the source of this data. 232 }, 233 ], 234 "conceptId": "A String", # The MedGen concept id associated with this gene. 235 # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ 236 "omimId": "A String", # The OMIM id for this condition. 237 # Search for these IDs at http://omim.org/ 238 "names": [ # A set of names for the condition. 239 "A String", 240 ], 241 }, 242 ], 243 "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should 244 # be provided when the variant is created. 245 }, 246 "start": "A String", # The start position of the range on the reference, 0-based inclusive. 247 "annotationSetId": "A String", # The annotation set to which this annotation belongs. 248 "referenceName": "A String", # The display name corresponding to the reference specified by 249 # `referenceId`, for example `chr1`, `1`, or `chrX`. 250 "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward 251 # strand. Note that regardless of this field, the start/end position of the 252 # range always refer to the forward strand. 253 "type": "A String", # The data type for this annotation. Must match the containing annotation 254 # set's type. 255 "id": "A String", # The server-generated annotation ID, unique across all annotations. 256 }, 257 ], 258 } 259 260 x__xgafv: string, V1 error format. 261 Allowed values 262 1 - v1 error format 263 2 - v2 error format 264 265 Returns: 266 An object of the form: 267 268 { 269 "entries": [ # The resulting per-annotation entries, ordered consistently with the 270 # original request. 271 { 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 278 # 279 # # Overview 280 # 281 # 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` that can be used for common error conditions. 290 # 291 # # Language mapping 292 # 293 # 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. 298 # 299 # # Other uses 300 # 301 # 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. 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. 327 "code": 42, # The status code, which should be an enum value of google.rpc.Code. 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. 330 { 331 "a_key": "", # Properties of the object. Contains field @type with type URL. 332 }, 333 ], 334 }, 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). 343 "a_key": [ 344 "", 345 ], 346 }, 347 "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. 350 "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of 351 # the reference genome may be transcribed as RNA. An alternative splicing 352 # pattern would be represented as a separate transcript object. This field 353 # is only set for annotations of type `TRANSCRIPT`. 354 # reference genome may be transcribed as RNA. 355 "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine 356 # the exact ranges of coding sequence, intersect this range with those of the 357 # exons, if any. If there are any 358 # exons, the 359 # codingSequence must start 360 # and end within them. 361 # 362 # Note that in some cases, the reference genome will not exactly match the 363 # observed mRNA transcript e.g. due to variance in the source genome from 364 # reference. In these cases, 365 # exon.frame will not necessarily 366 # match the expected reference reading frame and coding exon reference bases 367 # cannot necessarily be concatenated to produce the original transcript mRNA. 368 "start": "A String", # The start of the coding sequence on this annotation's reference sequence, 369 # 0-based inclusive. Note that this position is relative to the reference 370 # start, and *not* the containing annotation start. 371 "end": "A String", # The end of the coding sequence on this annotation's reference sequence, 372 # 0-based exclusive. Note that this position is relative to the reference 373 # start, and *not* the containing annotation start. 374 }, 375 "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose 376 # this transcript. This field should be unset for genomes where transcript 377 # splicing does not occur, for example prokaryotes. 378 # 379 # Introns are regions of the transcript that are not included in the 380 # spliced RNA product. Though not explicitly modeled here, intron ranges can 381 # be deduced; all regions of this transcript that are not exons are introns. 382 # 383 # Exonic sequences do not necessarily code for a translational product 384 # (amino acids). Only the regions of exons bounded by the 385 # codingSequence correspond 386 # to coding DNA sequence. 387 # 388 # Exons are ordered by start position and may not overlap. 389 { 390 "start": "A String", # The start position of the exon on this annotation's reference sequence, 391 # 0-based inclusive. Note that this is relative to the reference start, and 392 # **not** the containing annotation start. 393 "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates 394 # the offset of the first coding base of the exon within the reading frame 395 # of the coding DNA sequence, if any. This field is dependent on the 396 # strandedness of this annotation (see 397 # Annotation.reverse_strand). 398 # For forward stranded annotations, this offset is relative to the 399 # exon.start. For reverse 400 # strand annotations, this offset is relative to the 401 # exon.end `- 1`. 402 # 403 # Unset if this exon does not intersect the coding sequence. Upon creation 404 # of a transcript, the frame must be populated for all or none of the 405 # coding exons. 406 "end": "A String", # The end position of the exon on this annotation's reference sequence, 407 # 0-based exclusive. Note that this is relative to the reference start, and 408 # *not* the containing annotation start. 409 }, 410 ], 411 "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. 412 }, 413 "variant": { # A variant annotation, which describes the effect of a variant on the 414 # genome, the coding sequence, and/or higher level consequences at the 415 # organism level e.g. pathogenicity. This field is only set for annotations 416 # of type `VARIANT`. 417 "type": "A String", # Type has been adapted from ClinVar's list of variant types. 418 "effect": "A String", # Effect of the variant on the coding sequence. 419 "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These 420 # should be provided when the variant is created. 421 "A String", 422 ], 423 "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles 424 # exist at this location, create a separate variant for each one, as they 425 # may represent distinct conditions. 426 "clinicalSignificance": "A String", # Describes the clinical significance of a variant. 427 # It is adapted from the ClinVar controlled vocabulary for clinical 428 # significance described at: 429 # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 430 "conditions": [ # The set of conditions associated with this variant. 431 # A condition describes the way a variant influences human health. 432 { 433 "externalIds": [ # The set of external IDs for this condition. 434 { 435 "sourceName": "A String", # The name of the source of this data. 436 "id": "A String", # The id used by the source of this data. 437 }, 438 ], 439 "conceptId": "A String", # The MedGen concept id associated with this gene. 440 # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ 441 "omimId": "A String", # The OMIM id for this condition. 442 # Search for these IDs at http://omim.org/ 443 "names": [ # A set of names for the condition. 444 "A String", 445 ], 446 }, 447 ], 448 "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should 449 # be provided when the variant is created. 450 }, 451 "start": "A String", # The start position of the range on the reference, 0-based inclusive. 452 "annotationSetId": "A String", # The annotation set to which this annotation belongs. 453 "referenceName": "A String", # The display name corresponding to the reference specified by 454 # `referenceId`, for example `chr1`, `1`, or `chrX`. 455 "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward 456 # strand. Note that regardless of this field, the start/end position of the 457 # range always refer to the forward strand. 458 "type": "A String", # The data type for this annotation. Must match the containing annotation 459 # set's type. 460 "id": "A String", # The server-generated annotation ID, unique across all annotations. 461 }, 462 }, 463 ], 464 }</pre> 465 </div> 466 467 <div class="method"> 468 <code class="details" id="create">create(body, x__xgafv=None)</code> 469 <pre>Creates a new annotation. Caller must have WRITE permission 470 for the associated annotation set. 471 472 The following fields are required: 473 474 * annotationSetId 475 * referenceName or 476 referenceId 477 478 ### Transcripts 479 480 For annotations of type TRANSCRIPT, the following fields of 481 transcript must be provided: 482 483 * exons.start 484 * exons.end 485 486 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. 491 492 Args: 493 body: object, The request body. (required) 494 The object takes the form of: 495 496 { # 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). 504 "a_key": [ 505 "", 506 ], 507 }, 508 "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. 511 "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of 512 # the reference genome may be transcribed as RNA. An alternative splicing 513 # pattern would be represented as a separate transcript object. This field 514 # is only set for annotations of type `TRANSCRIPT`. 515 # reference genome may be transcribed as RNA. 516 "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine 517 # the exact ranges of coding sequence, intersect this range with those of the 518 # exons, if any. If there are any 519 # exons, the 520 # codingSequence must start 521 # and end within them. 522 # 523 # Note that in some cases, the reference genome will not exactly match the 524 # observed mRNA transcript e.g. due to variance in the source genome from 525 # reference. In these cases, 526 # exon.frame will not necessarily 527 # match the expected reference reading frame and coding exon reference bases 528 # cannot necessarily be concatenated to produce the original transcript mRNA. 529 "start": "A String", # The start of the coding sequence on this annotation's reference sequence, 530 # 0-based inclusive. Note that this position is relative to the reference 531 # start, and *not* the containing annotation start. 532 "end": "A String", # The end of the coding sequence on this annotation's reference sequence, 533 # 0-based exclusive. Note that this position is relative to the reference 534 # start, and *not* the containing annotation start. 535 }, 536 "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose 537 # this transcript. This field should be unset for genomes where transcript 538 # splicing does not occur, for example prokaryotes. 539 # 540 # Introns are regions of the transcript that are not included in the 541 # spliced RNA product. Though not explicitly modeled here, intron ranges can 542 # be deduced; all regions of this transcript that are not exons are introns. 543 # 544 # Exonic sequences do not necessarily code for a translational product 545 # (amino acids). Only the regions of exons bounded by the 546 # codingSequence correspond 547 # to coding DNA sequence. 548 # 549 # Exons are ordered by start position and may not overlap. 550 { 551 "start": "A String", # The start position of the exon on this annotation's reference sequence, 552 # 0-based inclusive. Note that this is relative to the reference start, and 553 # **not** the containing annotation start. 554 "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates 555 # the offset of the first coding base of the exon within the reading frame 556 # of the coding DNA sequence, if any. This field is dependent on the 557 # strandedness of this annotation (see 558 # Annotation.reverse_strand). 559 # For forward stranded annotations, this offset is relative to the 560 # exon.start. For reverse 561 # strand annotations, this offset is relative to the 562 # exon.end `- 1`. 563 # 564 # Unset if this exon does not intersect the coding sequence. Upon creation 565 # of a transcript, the frame must be populated for all or none of the 566 # coding exons. 567 "end": "A String", # The end position of the exon on this annotation's reference sequence, 568 # 0-based exclusive. Note that this is relative to the reference start, and 569 # *not* the containing annotation start. 570 }, 571 ], 572 "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. 573 }, 574 "variant": { # A variant annotation, which describes the effect of a variant on the 575 # genome, the coding sequence, and/or higher level consequences at the 576 # organism level e.g. pathogenicity. This field is only set for annotations 577 # of type `VARIANT`. 578 "type": "A String", # Type has been adapted from ClinVar's list of variant types. 579 "effect": "A String", # Effect of the variant on the coding sequence. 580 "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These 581 # should be provided when the variant is created. 582 "A String", 583 ], 584 "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles 585 # exist at this location, create a separate variant for each one, as they 586 # may represent distinct conditions. 587 "clinicalSignificance": "A String", # Describes the clinical significance of a variant. 588 # It is adapted from the ClinVar controlled vocabulary for clinical 589 # significance described at: 590 # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 591 "conditions": [ # The set of conditions associated with this variant. 592 # A condition describes the way a variant influences human health. 593 { 594 "externalIds": [ # The set of external IDs for this condition. 595 { 596 "sourceName": "A String", # The name of the source of this data. 597 "id": "A String", # The id used by the source of this data. 598 }, 599 ], 600 "conceptId": "A String", # The MedGen concept id associated with this gene. 601 # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ 602 "omimId": "A String", # The OMIM id for this condition. 603 # Search for these IDs at http://omim.org/ 604 "names": [ # A set of names for the condition. 605 "A String", 606 ], 607 }, 608 ], 609 "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should 610 # be provided when the variant is created. 611 }, 612 "start": "A String", # The start position of the range on the reference, 0-based inclusive. 613 "annotationSetId": "A String", # The annotation set to which this annotation belongs. 614 "referenceName": "A String", # The display name corresponding to the reference specified by 615 # `referenceId`, for example `chr1`, `1`, or `chrX`. 616 "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward 617 # strand. Note that regardless of this field, the start/end position of the 618 # range always refer to the forward strand. 619 "type": "A String", # The data type for this annotation. Must match the containing annotation 620 # set's type. 621 "id": "A String", # The server-generated annotation ID, unique across all annotations. 622 } 623 624 x__xgafv: string, V1 error format. 625 Allowed values 626 1 - v1 error format 627 2 - v2 error format 628 629 Returns: 630 An object of the form: 631 632 { # 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). 640 "a_key": [ 641 "", 642 ], 643 }, 644 "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. 647 "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of 648 # the reference genome may be transcribed as RNA. An alternative splicing 649 # pattern would be represented as a separate transcript object. This field 650 # is only set for annotations of type `TRANSCRIPT`. 651 # reference genome may be transcribed as RNA. 652 "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine 653 # the exact ranges of coding sequence, intersect this range with those of the 654 # exons, if any. If there are any 655 # exons, the 656 # codingSequence must start 657 # and end within them. 658 # 659 # Note that in some cases, the reference genome will not exactly match the 660 # observed mRNA transcript e.g. due to variance in the source genome from 661 # reference. In these cases, 662 # exon.frame will not necessarily 663 # match the expected reference reading frame and coding exon reference bases 664 # cannot necessarily be concatenated to produce the original transcript mRNA. 665 "start": "A String", # The start of the coding sequence on this annotation's reference sequence, 666 # 0-based inclusive. Note that this position is relative to the reference 667 # start, and *not* the containing annotation start. 668 "end": "A String", # The end of the coding sequence on this annotation's reference sequence, 669 # 0-based exclusive. Note that this position is relative to the reference 670 # start, and *not* the containing annotation start. 671 }, 672 "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose 673 # this transcript. This field should be unset for genomes where transcript 674 # splicing does not occur, for example prokaryotes. 675 # 676 # Introns are regions of the transcript that are not included in the 677 # spliced RNA product. Though not explicitly modeled here, intron ranges can 678 # be deduced; all regions of this transcript that are not exons are introns. 679 # 680 # Exonic sequences do not necessarily code for a translational product 681 # (amino acids). Only the regions of exons bounded by the 682 # codingSequence correspond 683 # to coding DNA sequence. 684 # 685 # Exons are ordered by start position and may not overlap. 686 { 687 "start": "A String", # The start position of the exon on this annotation's reference sequence, 688 # 0-based inclusive. Note that this is relative to the reference start, and 689 # **not** the containing annotation start. 690 "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates 691 # the offset of the first coding base of the exon within the reading frame 692 # of the coding DNA sequence, if any. This field is dependent on the 693 # strandedness of this annotation (see 694 # Annotation.reverse_strand). 695 # For forward stranded annotations, this offset is relative to the 696 # exon.start. For reverse 697 # strand annotations, this offset is relative to the 698 # exon.end `- 1`. 699 # 700 # Unset if this exon does not intersect the coding sequence. Upon creation 701 # of a transcript, the frame must be populated for all or none of the 702 # coding exons. 703 "end": "A String", # The end position of the exon on this annotation's reference sequence, 704 # 0-based exclusive. Note that this is relative to the reference start, and 705 # *not* the containing annotation start. 706 }, 707 ], 708 "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. 709 }, 710 "variant": { # A variant annotation, which describes the effect of a variant on the 711 # genome, the coding sequence, and/or higher level consequences at the 712 # organism level e.g. pathogenicity. This field is only set for annotations 713 # of type `VARIANT`. 714 "type": "A String", # Type has been adapted from ClinVar's list of variant types. 715 "effect": "A String", # Effect of the variant on the coding sequence. 716 "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These 717 # should be provided when the variant is created. 718 "A String", 719 ], 720 "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles 721 # exist at this location, create a separate variant for each one, as they 722 # may represent distinct conditions. 723 "clinicalSignificance": "A String", # Describes the clinical significance of a variant. 724 # It is adapted from the ClinVar controlled vocabulary for clinical 725 # significance described at: 726 # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 727 "conditions": [ # The set of conditions associated with this variant. 728 # A condition describes the way a variant influences human health. 729 { 730 "externalIds": [ # The set of external IDs for this condition. 731 { 732 "sourceName": "A String", # The name of the source of this data. 733 "id": "A String", # The id used by the source of this data. 734 }, 735 ], 736 "conceptId": "A String", # The MedGen concept id associated with this gene. 737 # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ 738 "omimId": "A String", # The OMIM id for this condition. 739 # Search for these IDs at http://omim.org/ 740 "names": [ # A set of names for the condition. 741 "A String", 742 ], 743 }, 744 ], 745 "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should 746 # be provided when the variant is created. 747 }, 748 "start": "A String", # The start position of the range on the reference, 0-based inclusive. 749 "annotationSetId": "A String", # The annotation set to which this annotation belongs. 750 "referenceName": "A String", # The display name corresponding to the reference specified by 751 # `referenceId`, for example `chr1`, `1`, or `chrX`. 752 "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward 753 # strand. Note that regardless of this field, the start/end position of the 754 # range always refer to the forward strand. 755 "type": "A String", # The data type for this annotation. Must match the containing annotation 756 # set's type. 757 "id": "A String", # The server-generated annotation ID, unique across all annotations. 758 }</pre> 759 </div> 760 761 <div class="method"> 762 <code class="details" id="delete">delete(annotationId, x__xgafv=None)</code> 763 <pre>Deletes an annotation. Caller must have WRITE permission for 764 the associated annotation set. 765 766 Args: 767 annotationId: string, The ID of the annotation to be deleted. (required) 768 x__xgafv: string, V1 error format. 769 Allowed values 770 1 - v1 error format 771 2 - v2 error format 772 773 Returns: 774 An object of the form: 775 776 { # 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 `{}`. 785 }</pre> 786 </div> 787 788 <div class="method"> 789 <code class="details" id="get">get(annotationId, x__xgafv=None)</code> 790 <pre>Gets an annotation. Caller must have READ permission 791 for the associated annotation set. 792 793 Args: 794 annotationId: string, The ID of the annotation to be retrieved. (required) 795 x__xgafv: string, V1 error format. 796 Allowed values 797 1 - v1 error format 798 2 - v2 error format 799 800 Returns: 801 An object of the form: 802 803 { # 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). 811 "a_key": [ 812 "", 813 ], 814 }, 815 "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. 818 "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of 819 # the reference genome may be transcribed as RNA. An alternative splicing 820 # pattern would be represented as a separate transcript object. This field 821 # is only set for annotations of type `TRANSCRIPT`. 822 # reference genome may be transcribed as RNA. 823 "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine 824 # the exact ranges of coding sequence, intersect this range with those of the 825 # exons, if any. If there are any 826 # exons, the 827 # codingSequence must start 828 # and end within them. 829 # 830 # Note that in some cases, the reference genome will not exactly match the 831 # observed mRNA transcript e.g. due to variance in the source genome from 832 # reference. In these cases, 833 # exon.frame will not necessarily 834 # match the expected reference reading frame and coding exon reference bases 835 # cannot necessarily be concatenated to produce the original transcript mRNA. 836 "start": "A String", # The start of the coding sequence on this annotation's reference sequence, 837 # 0-based inclusive. Note that this position is relative to the reference 838 # start, and *not* the containing annotation start. 839 "end": "A String", # The end of the coding sequence on this annotation's reference sequence, 840 # 0-based exclusive. Note that this position is relative to the reference 841 # start, and *not* the containing annotation start. 842 }, 843 "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose 844 # this transcript. This field should be unset for genomes where transcript 845 # splicing does not occur, for example prokaryotes. 846 # 847 # Introns are regions of the transcript that are not included in the 848 # spliced RNA product. Though not explicitly modeled here, intron ranges can 849 # be deduced; all regions of this transcript that are not exons are introns. 850 # 851 # Exonic sequences do not necessarily code for a translational product 852 # (amino acids). Only the regions of exons bounded by the 853 # codingSequence correspond 854 # to coding DNA sequence. 855 # 856 # Exons are ordered by start position and may not overlap. 857 { 858 "start": "A String", # The start position of the exon on this annotation's reference sequence, 859 # 0-based inclusive. Note that this is relative to the reference start, and 860 # **not** the containing annotation start. 861 "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates 862 # the offset of the first coding base of the exon within the reading frame 863 # of the coding DNA sequence, if any. This field is dependent on the 864 # strandedness of this annotation (see 865 # Annotation.reverse_strand). 866 # For forward stranded annotations, this offset is relative to the 867 # exon.start. For reverse 868 # strand annotations, this offset is relative to the 869 # exon.end `- 1`. 870 # 871 # Unset if this exon does not intersect the coding sequence. Upon creation 872 # of a transcript, the frame must be populated for all or none of the 873 # coding exons. 874 "end": "A String", # The end position of the exon on this annotation's reference sequence, 875 # 0-based exclusive. Note that this is relative to the reference start, and 876 # *not* the containing annotation start. 877 }, 878 ], 879 "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. 880 }, 881 "variant": { # A variant annotation, which describes the effect of a variant on the 882 # genome, the coding sequence, and/or higher level consequences at the 883 # organism level e.g. pathogenicity. This field is only set for annotations 884 # of type `VARIANT`. 885 "type": "A String", # Type has been adapted from ClinVar's list of variant types. 886 "effect": "A String", # Effect of the variant on the coding sequence. 887 "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These 888 # should be provided when the variant is created. 889 "A String", 890 ], 891 "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles 892 # exist at this location, create a separate variant for each one, as they 893 # may represent distinct conditions. 894 "clinicalSignificance": "A String", # Describes the clinical significance of a variant. 895 # It is adapted from the ClinVar controlled vocabulary for clinical 896 # significance described at: 897 # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 898 "conditions": [ # The set of conditions associated with this variant. 899 # A condition describes the way a variant influences human health. 900 { 901 "externalIds": [ # The set of external IDs for this condition. 902 { 903 "sourceName": "A String", # The name of the source of this data. 904 "id": "A String", # The id used by the source of this data. 905 }, 906 ], 907 "conceptId": "A String", # The MedGen concept id associated with this gene. 908 # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ 909 "omimId": "A String", # The OMIM id for this condition. 910 # Search for these IDs at http://omim.org/ 911 "names": [ # A set of names for the condition. 912 "A String", 913 ], 914 }, 915 ], 916 "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should 917 # be provided when the variant is created. 918 }, 919 "start": "A String", # The start position of the range on the reference, 0-based inclusive. 920 "annotationSetId": "A String", # The annotation set to which this annotation belongs. 921 "referenceName": "A String", # The display name corresponding to the reference specified by 922 # `referenceId`, for example `chr1`, `1`, or `chrX`. 923 "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward 924 # strand. Note that regardless of this field, the start/end position of the 925 # range always refer to the forward strand. 926 "type": "A String", # The data type for this annotation. Must match the containing annotation 927 # set's type. 928 "id": "A String", # The server-generated annotation ID, unique across all annotations. 929 }</pre> 930 </div> 931 932 <div class="method"> 933 <code class="details" id="search">search(body, x__xgafv=None)</code> 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. 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. 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 955 # specified, 956 # referenceId or 957 # referenceName 958 # 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. 962 "A String", 963 ], 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. 969 } 970 971 x__xgafv: string, V1 error format. 972 Allowed values 973 1 - v1 error format 974 2 - v2 error format 975 976 Returns: 977 An object of the form: 978 979 { 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. 983 "annotations": [ # The matching annotations. 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). 992 "a_key": [ 993 "", 994 ], 995 }, 996 "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. 999 "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of 1000 # the reference genome may be transcribed as RNA. An alternative splicing 1001 # pattern would be represented as a separate transcript object. This field 1002 # is only set for annotations of type `TRANSCRIPT`. 1003 # reference genome may be transcribed as RNA. 1004 "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine 1005 # the exact ranges of coding sequence, intersect this range with those of the 1006 # exons, if any. If there are any 1007 # exons, the 1008 # codingSequence must start 1009 # and end within them. 1010 # 1011 # Note that in some cases, the reference genome will not exactly match the 1012 # observed mRNA transcript e.g. due to variance in the source genome from 1013 # reference. In these cases, 1014 # exon.frame will not necessarily 1015 # match the expected reference reading frame and coding exon reference bases 1016 # cannot necessarily be concatenated to produce the original transcript mRNA. 1017 "start": "A String", # The start of the coding sequence on this annotation's reference sequence, 1018 # 0-based inclusive. Note that this position is relative to the reference 1019 # start, and *not* the containing annotation start. 1020 "end": "A String", # The end of the coding sequence on this annotation's reference sequence, 1021 # 0-based exclusive. Note that this position is relative to the reference 1022 # start, and *not* the containing annotation start. 1023 }, 1024 "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose 1025 # this transcript. This field should be unset for genomes where transcript 1026 # splicing does not occur, for example prokaryotes. 1027 # 1028 # Introns are regions of the transcript that are not included in the 1029 # spliced RNA product. Though not explicitly modeled here, intron ranges can 1030 # be deduced; all regions of this transcript that are not exons are introns. 1031 # 1032 # Exonic sequences do not necessarily code for a translational product 1033 # (amino acids). Only the regions of exons bounded by the 1034 # codingSequence correspond 1035 # to coding DNA sequence. 1036 # 1037 # Exons are ordered by start position and may not overlap. 1038 { 1039 "start": "A String", # The start position of the exon on this annotation's reference sequence, 1040 # 0-based inclusive. Note that this is relative to the reference start, and 1041 # **not** the containing annotation start. 1042 "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates 1043 # the offset of the first coding base of the exon within the reading frame 1044 # of the coding DNA sequence, if any. This field is dependent on the 1045 # strandedness of this annotation (see 1046 # Annotation.reverse_strand). 1047 # For forward stranded annotations, this offset is relative to the 1048 # exon.start. For reverse 1049 # strand annotations, this offset is relative to the 1050 # exon.end `- 1`. 1051 # 1052 # Unset if this exon does not intersect the coding sequence. Upon creation 1053 # of a transcript, the frame must be populated for all or none of the 1054 # coding exons. 1055 "end": "A String", # The end position of the exon on this annotation's reference sequence, 1056 # 0-based exclusive. Note that this is relative to the reference start, and 1057 # *not* the containing annotation start. 1058 }, 1059 ], 1060 "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. 1061 }, 1062 "variant": { # A variant annotation, which describes the effect of a variant on the 1063 # genome, the coding sequence, and/or higher level consequences at the 1064 # organism level e.g. pathogenicity. This field is only set for annotations 1065 # of type `VARIANT`. 1066 "type": "A String", # Type has been adapted from ClinVar's list of variant types. 1067 "effect": "A String", # Effect of the variant on the coding sequence. 1068 "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These 1069 # should be provided when the variant is created. 1070 "A String", 1071 ], 1072 "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles 1073 # exist at this location, create a separate variant for each one, as they 1074 # may represent distinct conditions. 1075 "clinicalSignificance": "A String", # Describes the clinical significance of a variant. 1076 # It is adapted from the ClinVar controlled vocabulary for clinical 1077 # significance described at: 1078 # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 1079 "conditions": [ # The set of conditions associated with this variant. 1080 # A condition describes the way a variant influences human health. 1081 { 1082 "externalIds": [ # The set of external IDs for this condition. 1083 { 1084 "sourceName": "A String", # The name of the source of this data. 1085 "id": "A String", # The id used by the source of this data. 1086 }, 1087 ], 1088 "conceptId": "A String", # The MedGen concept id associated with this gene. 1089 # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ 1090 "omimId": "A String", # The OMIM id for this condition. 1091 # Search for these IDs at http://omim.org/ 1092 "names": [ # A set of names for the condition. 1093 "A String", 1094 ], 1095 }, 1096 ], 1097 "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should 1098 # be provided when the variant is created. 1099 }, 1100 "start": "A String", # The start position of the range on the reference, 0-based inclusive. 1101 "annotationSetId": "A String", # The annotation set to which this annotation belongs. 1102 "referenceName": "A String", # The display name corresponding to the reference specified by 1103 # `referenceId`, for example `chr1`, `1`, or `chrX`. 1104 "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward 1105 # strand. Note that regardless of this field, the start/end position of the 1106 # range always refer to the forward strand. 1107 "type": "A String", # The data type for this annotation. Must match the containing annotation 1108 # set's type. 1109 "id": "A String", # The server-generated annotation ID, unique across all annotations. 1110 }, 1111 ], 1112 }</pre> 1113 </div> 1114 1115 <div class="method"> 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. 1126 </pre> 1127 </div> 1128 1129 <div class="method"> 1130 <code class="details" id="update">update(annotationId, body, updateMask=None, x__xgafv=None)</code> 1131 <pre>Updates an annotation. Caller must have 1132 WRITE permission for the associated dataset. 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 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). 1147 "a_key": [ 1148 "", 1149 ], 1150 }, 1151 "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. 1154 "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of 1155 # the reference genome may be transcribed as RNA. An alternative splicing 1156 # pattern would be represented as a separate transcript object. This field 1157 # is only set for annotations of type `TRANSCRIPT`. 1158 # reference genome may be transcribed as RNA. 1159 "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine 1160 # the exact ranges of coding sequence, intersect this range with those of the 1161 # exons, if any. If there are any 1162 # exons, the 1163 # codingSequence must start 1164 # and end within them. 1165 # 1166 # Note that in some cases, the reference genome will not exactly match the 1167 # observed mRNA transcript e.g. due to variance in the source genome from 1168 # reference. In these cases, 1169 # exon.frame will not necessarily 1170 # match the expected reference reading frame and coding exon reference bases 1171 # cannot necessarily be concatenated to produce the original transcript mRNA. 1172 "start": "A String", # The start of the coding sequence on this annotation's reference sequence, 1173 # 0-based inclusive. Note that this position is relative to the reference 1174 # start, and *not* the containing annotation start. 1175 "end": "A String", # The end of the coding sequence on this annotation's reference sequence, 1176 # 0-based exclusive. Note that this position is relative to the reference 1177 # start, and *not* the containing annotation start. 1178 }, 1179 "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose 1180 # this transcript. This field should be unset for genomes where transcript 1181 # splicing does not occur, for example prokaryotes. 1182 # 1183 # Introns are regions of the transcript that are not included in the 1184 # spliced RNA product. Though not explicitly modeled here, intron ranges can 1185 # be deduced; all regions of this transcript that are not exons are introns. 1186 # 1187 # Exonic sequences do not necessarily code for a translational product 1188 # (amino acids). Only the regions of exons bounded by the 1189 # codingSequence correspond 1190 # to coding DNA sequence. 1191 # 1192 # Exons are ordered by start position and may not overlap. 1193 { 1194 "start": "A String", # The start position of the exon on this annotation's reference sequence, 1195 # 0-based inclusive. Note that this is relative to the reference start, and 1196 # **not** the containing annotation start. 1197 "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates 1198 # the offset of the first coding base of the exon within the reading frame 1199 # of the coding DNA sequence, if any. This field is dependent on the 1200 # strandedness of this annotation (see 1201 # Annotation.reverse_strand). 1202 # For forward stranded annotations, this offset is relative to the 1203 # exon.start. For reverse 1204 # strand annotations, this offset is relative to the 1205 # exon.end `- 1`. 1206 # 1207 # Unset if this exon does not intersect the coding sequence. Upon creation 1208 # of a transcript, the frame must be populated for all or none of the 1209 # coding exons. 1210 "end": "A String", # The end position of the exon on this annotation's reference sequence, 1211 # 0-based exclusive. Note that this is relative to the reference start, and 1212 # *not* the containing annotation start. 1213 }, 1214 ], 1215 "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. 1216 }, 1217 "variant": { # A variant annotation, which describes the effect of a variant on the 1218 # genome, the coding sequence, and/or higher level consequences at the 1219 # organism level e.g. pathogenicity. This field is only set for annotations 1220 # of type `VARIANT`. 1221 "type": "A String", # Type has been adapted from ClinVar's list of variant types. 1222 "effect": "A String", # Effect of the variant on the coding sequence. 1223 "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These 1224 # should be provided when the variant is created. 1225 "A String", 1226 ], 1227 "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles 1228 # exist at this location, create a separate variant for each one, as they 1229 # may represent distinct conditions. 1230 "clinicalSignificance": "A String", # Describes the clinical significance of a variant. 1231 # It is adapted from the ClinVar controlled vocabulary for clinical 1232 # significance described at: 1233 # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 1234 "conditions": [ # The set of conditions associated with this variant. 1235 # A condition describes the way a variant influences human health. 1236 { 1237 "externalIds": [ # The set of external IDs for this condition. 1238 { 1239 "sourceName": "A String", # The name of the source of this data. 1240 "id": "A String", # The id used by the source of this data. 1241 }, 1242 ], 1243 "conceptId": "A String", # The MedGen concept id associated with this gene. 1244 # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ 1245 "omimId": "A String", # The OMIM id for this condition. 1246 # Search for these IDs at http://omim.org/ 1247 "names": [ # A set of names for the condition. 1248 "A String", 1249 ], 1250 }, 1251 ], 1252 "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should 1253 # be provided when the variant is created. 1254 }, 1255 "start": "A String", # The start position of the range on the reference, 0-based inclusive. 1256 "annotationSetId": "A String", # The annotation set to which this annotation belongs. 1257 "referenceName": "A String", # The display name corresponding to the reference specified by 1258 # `referenceId`, for example `chr1`, `1`, or `chrX`. 1259 "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward 1260 # strand. Note that regardless of this field, the start/end position of the 1261 # range always refer to the forward strand. 1262 "type": "A String", # The data type for this annotation. Must match the containing annotation 1263 # set's type. 1264 "id": "A String", # The server-generated annotation ID, unique across all annotations. 1265 } 1266 1267 updateMask: string, An optional mask specifying which fields to update. Mutable fields are 1268 name, 1269 variant, 1270 transcript, and 1271 info. If unspecified, all mutable 1272 fields will be updated. 1273 x__xgafv: string, V1 error format. 1274 Allowed values 1275 1 - v1 error format 1276 2 - v2 error format 1277 1278 Returns: 1279 An object of the form: 1280 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). 1289 "a_key": [ 1290 "", 1291 ], 1292 }, 1293 "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. 1296 "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of 1297 # the reference genome may be transcribed as RNA. An alternative splicing 1298 # pattern would be represented as a separate transcript object. This field 1299 # is only set for annotations of type `TRANSCRIPT`. 1300 # reference genome may be transcribed as RNA. 1301 "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine 1302 # the exact ranges of coding sequence, intersect this range with those of the 1303 # exons, if any. If there are any 1304 # exons, the 1305 # codingSequence must start 1306 # and end within them. 1307 # 1308 # Note that in some cases, the reference genome will not exactly match the 1309 # observed mRNA transcript e.g. due to variance in the source genome from 1310 # reference. In these cases, 1311 # exon.frame will not necessarily 1312 # match the expected reference reading frame and coding exon reference bases 1313 # cannot necessarily be concatenated to produce the original transcript mRNA. 1314 "start": "A String", # The start of the coding sequence on this annotation's reference sequence, 1315 # 0-based inclusive. Note that this position is relative to the reference 1316 # start, and *not* the containing annotation start. 1317 "end": "A String", # The end of the coding sequence on this annotation's reference sequence, 1318 # 0-based exclusive. Note that this position is relative to the reference 1319 # start, and *not* the containing annotation start. 1320 }, 1321 "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose 1322 # this transcript. This field should be unset for genomes where transcript 1323 # splicing does not occur, for example prokaryotes. 1324 # 1325 # Introns are regions of the transcript that are not included in the 1326 # spliced RNA product. Though not explicitly modeled here, intron ranges can 1327 # be deduced; all regions of this transcript that are not exons are introns. 1328 # 1329 # Exonic sequences do not necessarily code for a translational product 1330 # (amino acids). Only the regions of exons bounded by the 1331 # codingSequence correspond 1332 # to coding DNA sequence. 1333 # 1334 # Exons are ordered by start position and may not overlap. 1335 { 1336 "start": "A String", # The start position of the exon on this annotation's reference sequence, 1337 # 0-based inclusive. Note that this is relative to the reference start, and 1338 # **not** the containing annotation start. 1339 "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates 1340 # the offset of the first coding base of the exon within the reading frame 1341 # of the coding DNA sequence, if any. This field is dependent on the 1342 # strandedness of this annotation (see 1343 # Annotation.reverse_strand). 1344 # For forward stranded annotations, this offset is relative to the 1345 # exon.start. For reverse 1346 # strand annotations, this offset is relative to the 1347 # exon.end `- 1`. 1348 # 1349 # Unset if this exon does not intersect the coding sequence. Upon creation 1350 # of a transcript, the frame must be populated for all or none of the 1351 # coding exons. 1352 "end": "A String", # The end position of the exon on this annotation's reference sequence, 1353 # 0-based exclusive. Note that this is relative to the reference start, and 1354 # *not* the containing annotation start. 1355 }, 1356 ], 1357 "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. 1358 }, 1359 "variant": { # A variant annotation, which describes the effect of a variant on the 1360 # genome, the coding sequence, and/or higher level consequences at the 1361 # organism level e.g. pathogenicity. This field is only set for annotations 1362 # of type `VARIANT`. 1363 "type": "A String", # Type has been adapted from ClinVar's list of variant types. 1364 "effect": "A String", # Effect of the variant on the coding sequence. 1365 "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These 1366 # should be provided when the variant is created. 1367 "A String", 1368 ], 1369 "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles 1370 # exist at this location, create a separate variant for each one, as they 1371 # may represent distinct conditions. 1372 "clinicalSignificance": "A String", # Describes the clinical significance of a variant. 1373 # It is adapted from the ClinVar controlled vocabulary for clinical 1374 # significance described at: 1375 # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 1376 "conditions": [ # The set of conditions associated with this variant. 1377 # A condition describes the way a variant influences human health. 1378 { 1379 "externalIds": [ # The set of external IDs for this condition. 1380 { 1381 "sourceName": "A String", # The name of the source of this data. 1382 "id": "A String", # The id used by the source of this data. 1383 }, 1384 ], 1385 "conceptId": "A String", # The MedGen concept id associated with this gene. 1386 # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ 1387 "omimId": "A String", # The OMIM id for this condition. 1388 # Search for these IDs at http://omim.org/ 1389 "names": [ # A set of names for the condition. 1390 "A String", 1391 ], 1392 }, 1393 ], 1394 "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should 1395 # be provided when the variant is created. 1396 }, 1397 "start": "A String", # The start position of the range on the reference, 0-based inclusive. 1398 "annotationSetId": "A String", # The annotation set to which this annotation belongs. 1399 "referenceName": "A String", # The display name corresponding to the reference specified by 1400 # `referenceId`, for example `chr1`, `1`, or `chrX`. 1401 "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward 1402 # strand. Note that regardless of this field, the start/end position of the 1403 # range always refer to the forward strand. 1404 "type": "A String", # The data type for this annotation. Must match the containing annotation 1405 # set's type. 1406 "id": "A String", # The server-generated annotation ID, unique across all annotations. 1407 }</pre> 1408 </div> 1409 1410 </body></html>
