| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 1 | <html><body> |
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| 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> |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 79 | <p class="firstline">Creates one or more new annotations atomically. All annotations must</p> |
| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 80 | <p class="toc_element"> |
| 81 | <code><a href="#create">create(body, x__xgafv=None)</a></code></p> |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 82 | <p class="firstline">Creates a new annotation. Caller must have WRITE permission</p> |
| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 83 | <p class="toc_element"> |
| 84 | <code><a href="#delete">delete(annotationId, x__xgafv=None)</a></code></p> |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 85 | <p class="firstline">Deletes an annotation. Caller must have WRITE permission for</p> |
| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 86 | <p class="toc_element"> |
| 87 | <code><a href="#get">get(annotationId, x__xgafv=None)</a></code></p> |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 88 | <p class="firstline">Gets an annotation. Caller must have READ permission</p> |
| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 89 | <p class="toc_element"> |
| 90 | <code><a href="#search">search(body, x__xgafv=None)</a></code></p> |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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> |
| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 95 | <p class="toc_element"> |
| 96 | <code><a href="#update">update(annotationId, body, updateMask=None, x__xgafv=None)</a></code></p> |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 97 | <p class="firstline">Updates an annotation. Caller must have</p> |
| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 98 | <h3>Method Details</h3> |
| 99 | <div class="method"> |
| 100 | <code class="details" id="batchCreate">batchCreate(body, x__xgafv=None)</code> |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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. |
| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 115 | |
| 116 | Args: |
| 117 | body: object, The request body. (required) |
| 118 | The object takes the form of: |
| 119 | |
| 120 | { |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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). |
| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | }, |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | ], |
| Sai Cheemalapati | e833b79 | 2017-03-24 15:06:46 -0700 | [diff] [blame] | 206 | "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 207 | }, |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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 | ], |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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/ |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 236 | "omimId": "A String", # The OMIM id for this condition. |
| 237 | # Search for these IDs at http://omim.org/ |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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. |
| Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 255 | "id": "A String", # The server-generated annotation ID, unique across all annotations. |
| 256 | }, |
| 257 | ], |
| 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 |
| 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 |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 289 | # in the package `google.rpc` that can be used for common error conditions. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 312 | # have a `Status` message for error reporting. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | }, |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | ], |
| Sai Cheemalapati | e833b79 | 2017-03-24 15:06:46 -0700 | [diff] [blame] | 411 | "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 412 | }, |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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 | ], |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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/ |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 441 | "omimId": "A String", # The OMIM id for this condition. |
| 442 | # Search for these IDs at http://omim.org/ |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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. |
| 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. |
| 461 | }, |
| 462 | }, |
| 463 | ], |
| 464 | }</pre> |
| 465 | </div> |
| 466 | |
| 467 | <div class="method"> |
| 468 | <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: |
| 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. |
| 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] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | }, |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | ], |
| Sai Cheemalapati | e833b79 | 2017-03-24 15:06:46 -0700 | [diff] [blame] | 572 | "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 573 | }, |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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 | ], |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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/ |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 602 | "omimId": "A String", # The OMIM id for this condition. |
| 603 | # Search for these IDs at http://omim.org/ |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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. |
| 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] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | }, |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | ], |
| Sai Cheemalapati | e833b79 | 2017-03-24 15:06:46 -0700 | [diff] [blame] | 708 | "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 709 | }, |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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 | ], |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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/ |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 738 | "omimId": "A String", # The OMIM id for this condition. |
| 739 | # Search for these IDs at http://omim.org/ |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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. |
| 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. |
| 758 | }</pre> |
| 759 | </div> |
| 760 | |
| 761 | <div class="method"> |
| 762 | <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] | 785 | }</pre> |
| 786 | </div> |
| 787 | |
| 788 | <div class="method"> |
| 789 | <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] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | }, |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | ], |
| Sai Cheemalapati | e833b79 | 2017-03-24 15:06:46 -0700 | [diff] [blame] | 879 | "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 880 | }, |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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 | ], |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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/ |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 909 | "omimId": "A String", # The OMIM id for this condition. |
| 910 | # Search for these IDs at http://omim.org/ |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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. |
| 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. |
| 929 | }</pre> |
| 930 | </div> |
| 931 | |
| 932 | <div class="method"> |
| 933 | <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. |
| Sai Cheemalapati | e833b79 | 2017-03-24 15:06:46 -0700 | [diff] [blame] | 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. |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | }, |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | ], |
| Sai Cheemalapati | e833b79 | 2017-03-24 15:06:46 -0700 | [diff] [blame] | 1060 | "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 1061 | }, |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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 | ], |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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/ |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 1090 | "omimId": "A String", # The OMIM id for this condition. |
| 1091 | # Search for these IDs at http://omim.org/ |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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. |
| 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. |
| 1110 | }, |
| 1111 | ], |
| 1112 | }</pre> |
| 1113 | </div> |
| 1114 | |
| 1115 | <div class="method"> |
| Sai Cheemalapati | c30d2b5 | 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. |
| 1126 | </pre> |
| 1127 | </div> |
| 1128 | |
| 1129 | <div class="method"> |
| Jon Wayne Parrott | 0a471d3 | 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] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | }, |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | ], |
| Sai Cheemalapati | e833b79 | 2017-03-24 15:06:46 -0700 | [diff] [blame] | 1215 | "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 1216 | }, |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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 | ], |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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/ |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 1245 | "omimId": "A String", # The OMIM id for this condition. |
| 1246 | # Search for these IDs at http://omim.org/ |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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. |
| 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 |
| 1268 | name, |
| 1269 | variant, |
| 1270 | transcript, and |
| 1271 | 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] | 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. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | }, |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 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 | ], |
| Sai Cheemalapati | e833b79 | 2017-03-24 15:06:46 -0700 | [diff] [blame] | 1357 | "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame] | 1358 | }, |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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 | ], |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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/ |
| Sai Cheemalapati | 4ba8c23 | 2017-06-06 18:46:08 -0400 | [diff] [blame] | 1387 | "omimId": "A String", # The OMIM id for this condition. |
| 1388 | # Search for these IDs at http://omim.org/ |
| Thomas Coffee | 2f24537 | 2017-03-27 10:39:26 -0700 | [diff] [blame] | 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. |
| 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. |
| 1407 | }</pre> |
| 1408 | </div> |
| 1409 | |
| 1410 | </body></html> |