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| <h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.annotations.html">annotations</a></h1> |
| <h2>Instance Methods</h2> |
| <p class="toc_element"> |
| <code><a href="#batchCreate">batchCreate(body, x__xgafv=None)</a></code></p> |
| <p class="firstline">Creates one or more new annotations atomically. All annotations must</p> |
| <p class="toc_element"> |
| <code><a href="#create">create(body, x__xgafv=None)</a></code></p> |
| <p class="firstline">Creates a new annotation. Caller must have WRITE permission</p> |
| <p class="toc_element"> |
| <code><a href="#delete">delete(annotationId, x__xgafv=None)</a></code></p> |
| <p class="firstline">Deletes an annotation. Caller must have WRITE permission for</p> |
| <p class="toc_element"> |
| <code><a href="#get">get(annotationId, x__xgafv=None)</a></code></p> |
| <p class="firstline">Gets an annotation. Caller must have READ permission</p> |
| <p class="toc_element"> |
| <code><a href="#search">search(body, x__xgafv=None)</a></code></p> |
| <p class="firstline">Searches for annotations that match the given criteria. Results are</p> |
| <p class="toc_element"> |
| <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p> |
| <p class="firstline">Retrieves the next page of results.</p> |
| <p class="toc_element"> |
| <code><a href="#update">update(annotationId, body, updateMask=None, x__xgafv=None)</a></code></p> |
| <p class="firstline">Updates an annotation. Caller must have</p> |
| <h3>Method Details</h3> |
| <div class="method"> |
| <code class="details" id="batchCreate">batchCreate(body, x__xgafv=None)</code> |
| <pre>Creates one or more new annotations atomically. All annotations must |
| belong to the same annotation set. Caller must have WRITE |
| permission for this annotation set. For optimal performance, batch |
| positionally adjacent annotations together. |
| |
| If the request has a systemic issue, such as an attempt to write to |
| an inaccessible annotation set, the entire RPC will fail accordingly. For |
| lesser data issues, when possible an error will be isolated to the |
| corresponding batch entry in the response; the remaining well formed |
| annotations will be created normally. |
| |
| For details on the requirements for each individual annotation resource, |
| see |
| CreateAnnotation. |
| |
| Args: |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { |
| "requestId": "A String", # A unique request ID which enables the server to detect duplicated requests. |
| # If provided, duplicated requests will result in the same response; if not |
| # provided, duplicated requests may result in duplicated data. For a given |
| # annotation set, callers should not reuse `request_id`s when writing |
| # different batches of annotations - behavior in this case is undefined. |
| # A common approach is to use a UUID. For batch jobs where worker crashes are |
| # a possibility, consider using some unique variant of a worker or run ID. |
| "annotations": [ # The annotations to be created. At most 4096 can be specified in a single |
| # request. |
| { # An annotation describes a region of reference genome. The value of an |
| # annotation may be one of several canonical types, supplemented by arbitrary |
| # info tags. An annotation is not inherently associated with a specific |
| # sample or individual (though a client could choose to use annotations in |
| # this way). Example canonical annotation types are `GENE` and |
| # `VARIANT`. |
| "info": { # A map of additional read alignment information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "referenceId": "A String", # The ID of the Google Genomics reference associated with this range. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. |
| "name": "A String", # The display name of this annotation. |
| "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of |
| # the reference genome may be transcribed as RNA. An alternative splicing |
| # pattern would be represented as a separate transcript object. This field |
| # is only set for annotations of type `TRANSCRIPT`. |
| # reference genome may be transcribed as RNA. |
| "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine |
| # the exact ranges of coding sequence, intersect this range with those of the |
| # exons, if any. If there are any |
| # exons, the |
| # codingSequence must start |
| # and end within them. |
| # |
| # Note that in some cases, the reference genome will not exactly match the |
| # observed mRNA transcript e.g. due to variance in the source genome from |
| # reference. In these cases, |
| # exon.frame will not necessarily |
| # match the expected reference reading frame and coding exon reference bases |
| # cannot necessarily be concatenated to produce the original transcript mRNA. |
| "start": "A String", # The start of the coding sequence on this annotation's reference sequence, |
| # 0-based inclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| "end": "A String", # The end of the coding sequence on this annotation's reference sequence, |
| # 0-based exclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| }, |
| "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose |
| # this transcript. This field should be unset for genomes where transcript |
| # splicing does not occur, for example prokaryotes. |
| # |
| # Introns are regions of the transcript that are not included in the |
| # spliced RNA product. Though not explicitly modeled here, intron ranges can |
| # be deduced; all regions of this transcript that are not exons are introns. |
| # |
| # Exonic sequences do not necessarily code for a translational product |
| # (amino acids). Only the regions of exons bounded by the |
| # codingSequence correspond |
| # to coding DNA sequence. |
| # |
| # Exons are ordered by start position and may not overlap. |
| { |
| "start": "A String", # The start position of the exon on this annotation's reference sequence, |
| # 0-based inclusive. Note that this is relative to the reference start, and |
| # **not** the containing annotation start. |
| "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates |
| # the offset of the first coding base of the exon within the reading frame |
| # of the coding DNA sequence, if any. This field is dependent on the |
| # strandedness of this annotation (see |
| # Annotation.reverse_strand). |
| # For forward stranded annotations, this offset is relative to the |
| # exon.start. For reverse |
| # strand annotations, this offset is relative to the |
| # exon.end `- 1`. |
| # |
| # Unset if this exon does not intersect the coding sequence. Upon creation |
| # of a transcript, the frame must be populated for all or none of the |
| # coding exons. |
| "end": "A String", # The end position of the exon on this annotation's reference sequence, |
| # 0-based exclusive. Note that this is relative to the reference start, and |
| # *not* the containing annotation start. |
| }, |
| ], |
| "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| }, |
| "variant": { # A variant annotation, which describes the effect of a variant on the |
| # genome, the coding sequence, and/or higher level consequences at the |
| # organism level e.g. pathogenicity. This field is only set for annotations |
| # of type `VARIANT`. |
| "type": "A String", # Type has been adapted from ClinVar's list of variant types. |
| "effect": "A String", # Effect of the variant on the coding sequence. |
| "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These |
| # should be provided when the variant is created. |
| "A String", |
| ], |
| "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles |
| # exist at this location, create a separate variant for each one, as they |
| # may represent distinct conditions. |
| "clinicalSignificance": "A String", # Describes the clinical significance of a variant. |
| # It is adapted from the ClinVar controlled vocabulary for clinical |
| # significance described at: |
| # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ |
| "conditions": [ # The set of conditions associated with this variant. |
| # A condition describes the way a variant influences human health. |
| { |
| "externalIds": [ # The set of external IDs for this condition. |
| { |
| "sourceName": "A String", # The name of the source of this data. |
| "id": "A String", # The id used by the source of this data. |
| }, |
| ], |
| "conceptId": "A String", # The MedGen concept id associated with this gene. |
| # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ |
| "omimId": "A String", # The OMIM id for this condition. |
| # Search for these IDs at http://omim.org/ |
| "names": [ # A set of names for the condition. |
| "A String", |
| ], |
| }, |
| ], |
| "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should |
| # be provided when the variant is created. |
| }, |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. |
| "annotationSetId": "A String", # The annotation set to which this annotation belongs. |
| "referenceName": "A String", # The display name corresponding to the reference specified by |
| # `referenceId`, for example `chr1`, `1`, or `chrX`. |
| "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward |
| # strand. Note that regardless of this field, the start/end position of the |
| # range always refer to the forward strand. |
| "type": "A String", # The data type for this annotation. Must match the containing annotation |
| # set's type. |
| "id": "A String", # The server-generated annotation ID, unique across all annotations. |
| }, |
| ], |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { |
| "entries": [ # The resulting per-annotation entries, ordered consistently with the |
| # original request. |
| { |
| "status": { # The `Status` type defines a logical error model that is suitable for different # The creation status. |
| # programming environments, including REST APIs and RPC APIs. It is used by |
| # [gRPC](https://github.com/grpc). The error model is designed to be: |
| # |
| # - Simple to use and understand for most users |
| # - Flexible enough to meet unexpected needs |
| # |
| # # Overview |
| # |
| # The `Status` message contains three pieces of data: error code, error message, |
| # and error details. The error code should be an enum value of |
| # google.rpc.Code, but it may accept additional error codes if needed. The |
| # error message should be a developer-facing English message that helps |
| # developers *understand* and *resolve* the error. If a localized user-facing |
| # error message is needed, put the localized message in the error details or |
| # localize it in the client. The optional error details may contain arbitrary |
| # information about the error. There is a predefined set of error detail types |
| # in the package `google.rpc` that can be used for common error conditions. |
| # |
| # # Language mapping |
| # |
| # The `Status` message is the logical representation of the error model, but it |
| # is not necessarily the actual wire format. When the `Status` message is |
| # exposed in different client libraries and different wire protocols, it can be |
| # mapped differently. For example, it will likely be mapped to some exceptions |
| # in Java, but more likely mapped to some error codes in C. |
| # |
| # # Other uses |
| # |
| # The error model and the `Status` message can be used in a variety of |
| # environments, either with or without APIs, to provide a |
| # consistent developer experience across different environments. |
| # |
| # Example uses of this error model include: |
| # |
| # - Partial errors. If a service needs to return partial errors to the client, |
| # it may embed the `Status` in the normal response to indicate the partial |
| # errors. |
| # |
| # - Workflow errors. A typical workflow has multiple steps. Each step may |
| # have a `Status` message for error reporting. |
| # |
| # - Batch operations. If a client uses batch request and batch response, the |
| # `Status` message should be used directly inside batch response, one for |
| # each error sub-response. |
| # |
| # - Asynchronous operations. If an API call embeds asynchronous operation |
| # results in its response, the status of those operations should be |
| # represented directly using the `Status` message. |
| # |
| # - Logging. If some API errors are stored in logs, the message `Status` could |
| # be used directly after any stripping needed for security/privacy reasons. |
| "message": "A String", # A developer-facing error message, which should be in English. Any |
| # user-facing error message should be localized and sent in the |
| # google.rpc.Status.details field, or localized by the client. |
| "code": 42, # The status code, which should be an enum value of google.rpc.Code. |
| "details": [ # A list of messages that carry the error details. There will be a |
| # common set of message types for APIs to use. |
| { |
| "a_key": "", # Properties of the object. Contains field @type with type URL. |
| }, |
| ], |
| }, |
| "annotation": { # An annotation describes a region of reference genome. The value of an # The created annotation, if creation was successful. |
| # annotation may be one of several canonical types, supplemented by arbitrary |
| # info tags. An annotation is not inherently associated with a specific |
| # sample or individual (though a client could choose to use annotations in |
| # this way). Example canonical annotation types are `GENE` and |
| # `VARIANT`. |
| "info": { # A map of additional read alignment information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "referenceId": "A String", # The ID of the Google Genomics reference associated with this range. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. |
| "name": "A String", # The display name of this annotation. |
| "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of |
| # the reference genome may be transcribed as RNA. An alternative splicing |
| # pattern would be represented as a separate transcript object. This field |
| # is only set for annotations of type `TRANSCRIPT`. |
| # reference genome may be transcribed as RNA. |
| "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine |
| # the exact ranges of coding sequence, intersect this range with those of the |
| # exons, if any. If there are any |
| # exons, the |
| # codingSequence must start |
| # and end within them. |
| # |
| # Note that in some cases, the reference genome will not exactly match the |
| # observed mRNA transcript e.g. due to variance in the source genome from |
| # reference. In these cases, |
| # exon.frame will not necessarily |
| # match the expected reference reading frame and coding exon reference bases |
| # cannot necessarily be concatenated to produce the original transcript mRNA. |
| "start": "A String", # The start of the coding sequence on this annotation's reference sequence, |
| # 0-based inclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| "end": "A String", # The end of the coding sequence on this annotation's reference sequence, |
| # 0-based exclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| }, |
| "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose |
| # this transcript. This field should be unset for genomes where transcript |
| # splicing does not occur, for example prokaryotes. |
| # |
| # Introns are regions of the transcript that are not included in the |
| # spliced RNA product. Though not explicitly modeled here, intron ranges can |
| # be deduced; all regions of this transcript that are not exons are introns. |
| # |
| # Exonic sequences do not necessarily code for a translational product |
| # (amino acids). Only the regions of exons bounded by the |
| # codingSequence correspond |
| # to coding DNA sequence. |
| # |
| # Exons are ordered by start position and may not overlap. |
| { |
| "start": "A String", # The start position of the exon on this annotation's reference sequence, |
| # 0-based inclusive. Note that this is relative to the reference start, and |
| # **not** the containing annotation start. |
| "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates |
| # the offset of the first coding base of the exon within the reading frame |
| # of the coding DNA sequence, if any. This field is dependent on the |
| # strandedness of this annotation (see |
| # Annotation.reverse_strand). |
| # For forward stranded annotations, this offset is relative to the |
| # exon.start. For reverse |
| # strand annotations, this offset is relative to the |
| # exon.end `- 1`. |
| # |
| # Unset if this exon does not intersect the coding sequence. Upon creation |
| # of a transcript, the frame must be populated for all or none of the |
| # coding exons. |
| "end": "A String", # The end position of the exon on this annotation's reference sequence, |
| # 0-based exclusive. Note that this is relative to the reference start, and |
| # *not* the containing annotation start. |
| }, |
| ], |
| "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| }, |
| "variant": { # A variant annotation, which describes the effect of a variant on the |
| # genome, the coding sequence, and/or higher level consequences at the |
| # organism level e.g. pathogenicity. This field is only set for annotations |
| # of type `VARIANT`. |
| "type": "A String", # Type has been adapted from ClinVar's list of variant types. |
| "effect": "A String", # Effect of the variant on the coding sequence. |
| "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These |
| # should be provided when the variant is created. |
| "A String", |
| ], |
| "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles |
| # exist at this location, create a separate variant for each one, as they |
| # may represent distinct conditions. |
| "clinicalSignificance": "A String", # Describes the clinical significance of a variant. |
| # It is adapted from the ClinVar controlled vocabulary for clinical |
| # significance described at: |
| # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ |
| "conditions": [ # The set of conditions associated with this variant. |
| # A condition describes the way a variant influences human health. |
| { |
| "externalIds": [ # The set of external IDs for this condition. |
| { |
| "sourceName": "A String", # The name of the source of this data. |
| "id": "A String", # The id used by the source of this data. |
| }, |
| ], |
| "conceptId": "A String", # The MedGen concept id associated with this gene. |
| # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ |
| "omimId": "A String", # The OMIM id for this condition. |
| # Search for these IDs at http://omim.org/ |
| "names": [ # A set of names for the condition. |
| "A String", |
| ], |
| }, |
| ], |
| "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should |
| # be provided when the variant is created. |
| }, |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. |
| "annotationSetId": "A String", # The annotation set to which this annotation belongs. |
| "referenceName": "A String", # The display name corresponding to the reference specified by |
| # `referenceId`, for example `chr1`, `1`, or `chrX`. |
| "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward |
| # strand. Note that regardless of this field, the start/end position of the |
| # range always refer to the forward strand. |
| "type": "A String", # The data type for this annotation. Must match the containing annotation |
| # set's type. |
| "id": "A String", # The server-generated annotation ID, unique across all annotations. |
| }, |
| }, |
| ], |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="create">create(body, x__xgafv=None)</code> |
| <pre>Creates a new annotation. Caller must have WRITE permission |
| for the associated annotation set. |
| |
| The following fields are required: |
| |
| * annotationSetId |
| * referenceName or |
| referenceId |
| |
| ### Transcripts |
| |
| For annotations of type TRANSCRIPT, the following fields of |
| transcript must be provided: |
| |
| * exons.start |
| * exons.end |
| |
| All other fields may be optionally specified, unless documented as being |
| server-generated (for example, the `id` field). The annotated |
| range must be no longer than 100Mbp (mega base pairs). See the |
| Annotation resource |
| for additional restrictions on each field. |
| |
| Args: |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { # An annotation describes a region of reference genome. The value of an |
| # annotation may be one of several canonical types, supplemented by arbitrary |
| # info tags. An annotation is not inherently associated with a specific |
| # sample or individual (though a client could choose to use annotations in |
| # this way). Example canonical annotation types are `GENE` and |
| # `VARIANT`. |
| "info": { # A map of additional read alignment information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "referenceId": "A String", # The ID of the Google Genomics reference associated with this range. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. |
| "name": "A String", # The display name of this annotation. |
| "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of |
| # the reference genome may be transcribed as RNA. An alternative splicing |
| # pattern would be represented as a separate transcript object. This field |
| # is only set for annotations of type `TRANSCRIPT`. |
| # reference genome may be transcribed as RNA. |
| "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine |
| # the exact ranges of coding sequence, intersect this range with those of the |
| # exons, if any. If there are any |
| # exons, the |
| # codingSequence must start |
| # and end within them. |
| # |
| # Note that in some cases, the reference genome will not exactly match the |
| # observed mRNA transcript e.g. due to variance in the source genome from |
| # reference. In these cases, |
| # exon.frame will not necessarily |
| # match the expected reference reading frame and coding exon reference bases |
| # cannot necessarily be concatenated to produce the original transcript mRNA. |
| "start": "A String", # The start of the coding sequence on this annotation's reference sequence, |
| # 0-based inclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| "end": "A String", # The end of the coding sequence on this annotation's reference sequence, |
| # 0-based exclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| }, |
| "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose |
| # this transcript. This field should be unset for genomes where transcript |
| # splicing does not occur, for example prokaryotes. |
| # |
| # Introns are regions of the transcript that are not included in the |
| # spliced RNA product. Though not explicitly modeled here, intron ranges can |
| # be deduced; all regions of this transcript that are not exons are introns. |
| # |
| # Exonic sequences do not necessarily code for a translational product |
| # (amino acids). Only the regions of exons bounded by the |
| # codingSequence correspond |
| # to coding DNA sequence. |
| # |
| # Exons are ordered by start position and may not overlap. |
| { |
| "start": "A String", # The start position of the exon on this annotation's reference sequence, |
| # 0-based inclusive. Note that this is relative to the reference start, and |
| # **not** the containing annotation start. |
| "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates |
| # the offset of the first coding base of the exon within the reading frame |
| # of the coding DNA sequence, if any. This field is dependent on the |
| # strandedness of this annotation (see |
| # Annotation.reverse_strand). |
| # For forward stranded annotations, this offset is relative to the |
| # exon.start. For reverse |
| # strand annotations, this offset is relative to the |
| # exon.end `- 1`. |
| # |
| # Unset if this exon does not intersect the coding sequence. Upon creation |
| # of a transcript, the frame must be populated for all or none of the |
| # coding exons. |
| "end": "A String", # The end position of the exon on this annotation's reference sequence, |
| # 0-based exclusive. Note that this is relative to the reference start, and |
| # *not* the containing annotation start. |
| }, |
| ], |
| "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| }, |
| "variant": { # A variant annotation, which describes the effect of a variant on the |
| # genome, the coding sequence, and/or higher level consequences at the |
| # organism level e.g. pathogenicity. This field is only set for annotations |
| # of type `VARIANT`. |
| "type": "A String", # Type has been adapted from ClinVar's list of variant types. |
| "effect": "A String", # Effect of the variant on the coding sequence. |
| "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These |
| # should be provided when the variant is created. |
| "A String", |
| ], |
| "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles |
| # exist at this location, create a separate variant for each one, as they |
| # may represent distinct conditions. |
| "clinicalSignificance": "A String", # Describes the clinical significance of a variant. |
| # It is adapted from the ClinVar controlled vocabulary for clinical |
| # significance described at: |
| # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ |
| "conditions": [ # The set of conditions associated with this variant. |
| # A condition describes the way a variant influences human health. |
| { |
| "externalIds": [ # The set of external IDs for this condition. |
| { |
| "sourceName": "A String", # The name of the source of this data. |
| "id": "A String", # The id used by the source of this data. |
| }, |
| ], |
| "conceptId": "A String", # The MedGen concept id associated with this gene. |
| # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ |
| "omimId": "A String", # The OMIM id for this condition. |
| # Search for these IDs at http://omim.org/ |
| "names": [ # A set of names for the condition. |
| "A String", |
| ], |
| }, |
| ], |
| "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should |
| # be provided when the variant is created. |
| }, |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. |
| "annotationSetId": "A String", # The annotation set to which this annotation belongs. |
| "referenceName": "A String", # The display name corresponding to the reference specified by |
| # `referenceId`, for example `chr1`, `1`, or `chrX`. |
| "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward |
| # strand. Note that regardless of this field, the start/end position of the |
| # range always refer to the forward strand. |
| "type": "A String", # The data type for this annotation. Must match the containing annotation |
| # set's type. |
| "id": "A String", # The server-generated annotation ID, unique across all annotations. |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # An annotation describes a region of reference genome. The value of an |
| # annotation may be one of several canonical types, supplemented by arbitrary |
| # info tags. An annotation is not inherently associated with a specific |
| # sample or individual (though a client could choose to use annotations in |
| # this way). Example canonical annotation types are `GENE` and |
| # `VARIANT`. |
| "info": { # A map of additional read alignment information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "referenceId": "A String", # The ID of the Google Genomics reference associated with this range. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. |
| "name": "A String", # The display name of this annotation. |
| "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of |
| # the reference genome may be transcribed as RNA. An alternative splicing |
| # pattern would be represented as a separate transcript object. This field |
| # is only set for annotations of type `TRANSCRIPT`. |
| # reference genome may be transcribed as RNA. |
| "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine |
| # the exact ranges of coding sequence, intersect this range with those of the |
| # exons, if any. If there are any |
| # exons, the |
| # codingSequence must start |
| # and end within them. |
| # |
| # Note that in some cases, the reference genome will not exactly match the |
| # observed mRNA transcript e.g. due to variance in the source genome from |
| # reference. In these cases, |
| # exon.frame will not necessarily |
| # match the expected reference reading frame and coding exon reference bases |
| # cannot necessarily be concatenated to produce the original transcript mRNA. |
| "start": "A String", # The start of the coding sequence on this annotation's reference sequence, |
| # 0-based inclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| "end": "A String", # The end of the coding sequence on this annotation's reference sequence, |
| # 0-based exclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| }, |
| "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose |
| # this transcript. This field should be unset for genomes where transcript |
| # splicing does not occur, for example prokaryotes. |
| # |
| # Introns are regions of the transcript that are not included in the |
| # spliced RNA product. Though not explicitly modeled here, intron ranges can |
| # be deduced; all regions of this transcript that are not exons are introns. |
| # |
| # Exonic sequences do not necessarily code for a translational product |
| # (amino acids). Only the regions of exons bounded by the |
| # codingSequence correspond |
| # to coding DNA sequence. |
| # |
| # Exons are ordered by start position and may not overlap. |
| { |
| "start": "A String", # The start position of the exon on this annotation's reference sequence, |
| # 0-based inclusive. Note that this is relative to the reference start, and |
| # **not** the containing annotation start. |
| "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates |
| # the offset of the first coding base of the exon within the reading frame |
| # of the coding DNA sequence, if any. This field is dependent on the |
| # strandedness of this annotation (see |
| # Annotation.reverse_strand). |
| # For forward stranded annotations, this offset is relative to the |
| # exon.start. For reverse |
| # strand annotations, this offset is relative to the |
| # exon.end `- 1`. |
| # |
| # Unset if this exon does not intersect the coding sequence. Upon creation |
| # of a transcript, the frame must be populated for all or none of the |
| # coding exons. |
| "end": "A String", # The end position of the exon on this annotation's reference sequence, |
| # 0-based exclusive. Note that this is relative to the reference start, and |
| # *not* the containing annotation start. |
| }, |
| ], |
| "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| }, |
| "variant": { # A variant annotation, which describes the effect of a variant on the |
| # genome, the coding sequence, and/or higher level consequences at the |
| # organism level e.g. pathogenicity. This field is only set for annotations |
| # of type `VARIANT`. |
| "type": "A String", # Type has been adapted from ClinVar's list of variant types. |
| "effect": "A String", # Effect of the variant on the coding sequence. |
| "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These |
| # should be provided when the variant is created. |
| "A String", |
| ], |
| "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles |
| # exist at this location, create a separate variant for each one, as they |
| # may represent distinct conditions. |
| "clinicalSignificance": "A String", # Describes the clinical significance of a variant. |
| # It is adapted from the ClinVar controlled vocabulary for clinical |
| # significance described at: |
| # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ |
| "conditions": [ # The set of conditions associated with this variant. |
| # A condition describes the way a variant influences human health. |
| { |
| "externalIds": [ # The set of external IDs for this condition. |
| { |
| "sourceName": "A String", # The name of the source of this data. |
| "id": "A String", # The id used by the source of this data. |
| }, |
| ], |
| "conceptId": "A String", # The MedGen concept id associated with this gene. |
| # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ |
| "omimId": "A String", # The OMIM id for this condition. |
| # Search for these IDs at http://omim.org/ |
| "names": [ # A set of names for the condition. |
| "A String", |
| ], |
| }, |
| ], |
| "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should |
| # be provided when the variant is created. |
| }, |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. |
| "annotationSetId": "A String", # The annotation set to which this annotation belongs. |
| "referenceName": "A String", # The display name corresponding to the reference specified by |
| # `referenceId`, for example `chr1`, `1`, or `chrX`. |
| "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward |
| # strand. Note that regardless of this field, the start/end position of the |
| # range always refer to the forward strand. |
| "type": "A String", # The data type for this annotation. Must match the containing annotation |
| # set's type. |
| "id": "A String", # The server-generated annotation ID, unique across all annotations. |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="delete">delete(annotationId, x__xgafv=None)</code> |
| <pre>Deletes an annotation. Caller must have WRITE permission for |
| the associated annotation set. |
| |
| Args: |
| annotationId: string, The ID of the annotation to be deleted. (required) |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # A generic empty message that you can re-use to avoid defining duplicated |
| # empty messages in your APIs. A typical example is to use it as the request |
| # or the response type of an API method. For instance: |
| # |
| # service Foo { |
| # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); |
| # } |
| # |
| # The JSON representation for `Empty` is empty JSON object `{}`. |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="get">get(annotationId, x__xgafv=None)</code> |
| <pre>Gets an annotation. Caller must have READ permission |
| for the associated annotation set. |
| |
| Args: |
| annotationId: string, The ID of the annotation to be retrieved. (required) |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # An annotation describes a region of reference genome. The value of an |
| # annotation may be one of several canonical types, supplemented by arbitrary |
| # info tags. An annotation is not inherently associated with a specific |
| # sample or individual (though a client could choose to use annotations in |
| # this way). Example canonical annotation types are `GENE` and |
| # `VARIANT`. |
| "info": { # A map of additional read alignment information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "referenceId": "A String", # The ID of the Google Genomics reference associated with this range. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. |
| "name": "A String", # The display name of this annotation. |
| "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of |
| # the reference genome may be transcribed as RNA. An alternative splicing |
| # pattern would be represented as a separate transcript object. This field |
| # is only set for annotations of type `TRANSCRIPT`. |
| # reference genome may be transcribed as RNA. |
| "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine |
| # the exact ranges of coding sequence, intersect this range with those of the |
| # exons, if any. If there are any |
| # exons, the |
| # codingSequence must start |
| # and end within them. |
| # |
| # Note that in some cases, the reference genome will not exactly match the |
| # observed mRNA transcript e.g. due to variance in the source genome from |
| # reference. In these cases, |
| # exon.frame will not necessarily |
| # match the expected reference reading frame and coding exon reference bases |
| # cannot necessarily be concatenated to produce the original transcript mRNA. |
| "start": "A String", # The start of the coding sequence on this annotation's reference sequence, |
| # 0-based inclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| "end": "A String", # The end of the coding sequence on this annotation's reference sequence, |
| # 0-based exclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| }, |
| "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose |
| # this transcript. This field should be unset for genomes where transcript |
| # splicing does not occur, for example prokaryotes. |
| # |
| # Introns are regions of the transcript that are not included in the |
| # spliced RNA product. Though not explicitly modeled here, intron ranges can |
| # be deduced; all regions of this transcript that are not exons are introns. |
| # |
| # Exonic sequences do not necessarily code for a translational product |
| # (amino acids). Only the regions of exons bounded by the |
| # codingSequence correspond |
| # to coding DNA sequence. |
| # |
| # Exons are ordered by start position and may not overlap. |
| { |
| "start": "A String", # The start position of the exon on this annotation's reference sequence, |
| # 0-based inclusive. Note that this is relative to the reference start, and |
| # **not** the containing annotation start. |
| "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates |
| # the offset of the first coding base of the exon within the reading frame |
| # of the coding DNA sequence, if any. This field is dependent on the |
| # strandedness of this annotation (see |
| # Annotation.reverse_strand). |
| # For forward stranded annotations, this offset is relative to the |
| # exon.start. For reverse |
| # strand annotations, this offset is relative to the |
| # exon.end `- 1`. |
| # |
| # Unset if this exon does not intersect the coding sequence. Upon creation |
| # of a transcript, the frame must be populated for all or none of the |
| # coding exons. |
| "end": "A String", # The end position of the exon on this annotation's reference sequence, |
| # 0-based exclusive. Note that this is relative to the reference start, and |
| # *not* the containing annotation start. |
| }, |
| ], |
| "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| }, |
| "variant": { # A variant annotation, which describes the effect of a variant on the |
| # genome, the coding sequence, and/or higher level consequences at the |
| # organism level e.g. pathogenicity. This field is only set for annotations |
| # of type `VARIANT`. |
| "type": "A String", # Type has been adapted from ClinVar's list of variant types. |
| "effect": "A String", # Effect of the variant on the coding sequence. |
| "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These |
| # should be provided when the variant is created. |
| "A String", |
| ], |
| "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles |
| # exist at this location, create a separate variant for each one, as they |
| # may represent distinct conditions. |
| "clinicalSignificance": "A String", # Describes the clinical significance of a variant. |
| # It is adapted from the ClinVar controlled vocabulary for clinical |
| # significance described at: |
| # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ |
| "conditions": [ # The set of conditions associated with this variant. |
| # A condition describes the way a variant influences human health. |
| { |
| "externalIds": [ # The set of external IDs for this condition. |
| { |
| "sourceName": "A String", # The name of the source of this data. |
| "id": "A String", # The id used by the source of this data. |
| }, |
| ], |
| "conceptId": "A String", # The MedGen concept id associated with this gene. |
| # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ |
| "omimId": "A String", # The OMIM id for this condition. |
| # Search for these IDs at http://omim.org/ |
| "names": [ # A set of names for the condition. |
| "A String", |
| ], |
| }, |
| ], |
| "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should |
| # be provided when the variant is created. |
| }, |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. |
| "annotationSetId": "A String", # The annotation set to which this annotation belongs. |
| "referenceName": "A String", # The display name corresponding to the reference specified by |
| # `referenceId`, for example `chr1`, `1`, or `chrX`. |
| "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward |
| # strand. Note that regardless of this field, the start/end position of the |
| # range always refer to the forward strand. |
| "type": "A String", # The data type for this annotation. Must match the containing annotation |
| # set's type. |
| "id": "A String", # The server-generated annotation ID, unique across all annotations. |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="search">search(body, x__xgafv=None)</code> |
| <pre>Searches for annotations that match the given criteria. Results are |
| ordered by genomic coordinate (by reference sequence, then position). |
| Annotations with equivalent genomic coordinates are returned in an |
| unspecified order. This order is consistent, such that two queries for the |
| same content (regardless of page size) yield annotations in the same order |
| across their respective streams of paginated responses. Caller must have |
| READ permission for the queried annotation sets. |
| |
| Args: |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { |
| "referenceId": "A String", # The ID of the reference to query. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. If |
| # referenceId or |
| # referenceName |
| # must be specified, Defaults to the length of the reference. |
| "pageSize": 42, # The maximum number of results to return in a single page. If unspecified, |
| # defaults to 256. The maximum value is 2048. |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. If |
| # specified, |
| # referenceId or |
| # referenceName |
| # must be specified. Defaults to 0. |
| "annotationSetIds": [ # Required. The annotation sets to search within. The caller must have |
| # `READ` access to these annotation sets. |
| # All queried annotation sets must have the same type. |
| "A String", |
| ], |
| "pageToken": "A String", # The continuation token, which is used to page through large result sets. |
| # To get the next page of results, set this parameter to the value of |
| # `nextPageToken` from the previous response. |
| "referenceName": "A String", # The name of the reference to query, within the reference set associated |
| # with this query. |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { |
| "nextPageToken": "A String", # The continuation token, which is used to page through large result sets. |
| # Provide this value in a subsequent request to return the next page of |
| # results. This field will be empty if there aren't any additional results. |
| "annotations": [ # The matching annotations. |
| { # An annotation describes a region of reference genome. The value of an |
| # annotation may be one of several canonical types, supplemented by arbitrary |
| # info tags. An annotation is not inherently associated with a specific |
| # sample or individual (though a client could choose to use annotations in |
| # this way). Example canonical annotation types are `GENE` and |
| # `VARIANT`. |
| "info": { # A map of additional read alignment information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "referenceId": "A String", # The ID of the Google Genomics reference associated with this range. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. |
| "name": "A String", # The display name of this annotation. |
| "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of |
| # the reference genome may be transcribed as RNA. An alternative splicing |
| # pattern would be represented as a separate transcript object. This field |
| # is only set for annotations of type `TRANSCRIPT`. |
| # reference genome may be transcribed as RNA. |
| "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine |
| # the exact ranges of coding sequence, intersect this range with those of the |
| # exons, if any. If there are any |
| # exons, the |
| # codingSequence must start |
| # and end within them. |
| # |
| # Note that in some cases, the reference genome will not exactly match the |
| # observed mRNA transcript e.g. due to variance in the source genome from |
| # reference. In these cases, |
| # exon.frame will not necessarily |
| # match the expected reference reading frame and coding exon reference bases |
| # cannot necessarily be concatenated to produce the original transcript mRNA. |
| "start": "A String", # The start of the coding sequence on this annotation's reference sequence, |
| # 0-based inclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| "end": "A String", # The end of the coding sequence on this annotation's reference sequence, |
| # 0-based exclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| }, |
| "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose |
| # this transcript. This field should be unset for genomes where transcript |
| # splicing does not occur, for example prokaryotes. |
| # |
| # Introns are regions of the transcript that are not included in the |
| # spliced RNA product. Though not explicitly modeled here, intron ranges can |
| # be deduced; all regions of this transcript that are not exons are introns. |
| # |
| # Exonic sequences do not necessarily code for a translational product |
| # (amino acids). Only the regions of exons bounded by the |
| # codingSequence correspond |
| # to coding DNA sequence. |
| # |
| # Exons are ordered by start position and may not overlap. |
| { |
| "start": "A String", # The start position of the exon on this annotation's reference sequence, |
| # 0-based inclusive. Note that this is relative to the reference start, and |
| # **not** the containing annotation start. |
| "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates |
| # the offset of the first coding base of the exon within the reading frame |
| # of the coding DNA sequence, if any. This field is dependent on the |
| # strandedness of this annotation (see |
| # Annotation.reverse_strand). |
| # For forward stranded annotations, this offset is relative to the |
| # exon.start. For reverse |
| # strand annotations, this offset is relative to the |
| # exon.end `- 1`. |
| # |
| # Unset if this exon does not intersect the coding sequence. Upon creation |
| # of a transcript, the frame must be populated for all or none of the |
| # coding exons. |
| "end": "A String", # The end position of the exon on this annotation's reference sequence, |
| # 0-based exclusive. Note that this is relative to the reference start, and |
| # *not* the containing annotation start. |
| }, |
| ], |
| "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| }, |
| "variant": { # A variant annotation, which describes the effect of a variant on the |
| # genome, the coding sequence, and/or higher level consequences at the |
| # organism level e.g. pathogenicity. This field is only set for annotations |
| # of type `VARIANT`. |
| "type": "A String", # Type has been adapted from ClinVar's list of variant types. |
| "effect": "A String", # Effect of the variant on the coding sequence. |
| "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These |
| # should be provided when the variant is created. |
| "A String", |
| ], |
| "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles |
| # exist at this location, create a separate variant for each one, as they |
| # may represent distinct conditions. |
| "clinicalSignificance": "A String", # Describes the clinical significance of a variant. |
| # It is adapted from the ClinVar controlled vocabulary for clinical |
| # significance described at: |
| # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ |
| "conditions": [ # The set of conditions associated with this variant. |
| # A condition describes the way a variant influences human health. |
| { |
| "externalIds": [ # The set of external IDs for this condition. |
| { |
| "sourceName": "A String", # The name of the source of this data. |
| "id": "A String", # The id used by the source of this data. |
| }, |
| ], |
| "conceptId": "A String", # The MedGen concept id associated with this gene. |
| # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ |
| "omimId": "A String", # The OMIM id for this condition. |
| # Search for these IDs at http://omim.org/ |
| "names": [ # A set of names for the condition. |
| "A String", |
| ], |
| }, |
| ], |
| "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should |
| # be provided when the variant is created. |
| }, |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. |
| "annotationSetId": "A String", # The annotation set to which this annotation belongs. |
| "referenceName": "A String", # The display name corresponding to the reference specified by |
| # `referenceId`, for example `chr1`, `1`, or `chrX`. |
| "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward |
| # strand. Note that regardless of this field, the start/end position of the |
| # range always refer to the forward strand. |
| "type": "A String", # The data type for this annotation. Must match the containing annotation |
| # set's type. |
| "id": "A String", # The server-generated annotation ID, unique across all annotations. |
| }, |
| ], |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="search_next">search_next(previous_request, previous_response)</code> |
| <pre>Retrieves the next page of results. |
| |
| Args: |
| previous_request: The request for the previous page. (required) |
| previous_response: The response from the request for the previous page. (required) |
| |
| Returns: |
| A request object that you can call 'execute()' on to request the next |
| page. Returns None if there are no more items in the collection. |
| </pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="update">update(annotationId, body, updateMask=None, x__xgafv=None)</code> |
| <pre>Updates an annotation. Caller must have |
| WRITE permission for the associated dataset. |
| |
| Args: |
| annotationId: string, The ID of the annotation to be updated. (required) |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { # An annotation describes a region of reference genome. The value of an |
| # annotation may be one of several canonical types, supplemented by arbitrary |
| # info tags. An annotation is not inherently associated with a specific |
| # sample or individual (though a client could choose to use annotations in |
| # this way). Example canonical annotation types are `GENE` and |
| # `VARIANT`. |
| "info": { # A map of additional read alignment information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "referenceId": "A String", # The ID of the Google Genomics reference associated with this range. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. |
| "name": "A String", # The display name of this annotation. |
| "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of |
| # the reference genome may be transcribed as RNA. An alternative splicing |
| # pattern would be represented as a separate transcript object. This field |
| # is only set for annotations of type `TRANSCRIPT`. |
| # reference genome may be transcribed as RNA. |
| "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine |
| # the exact ranges of coding sequence, intersect this range with those of the |
| # exons, if any. If there are any |
| # exons, the |
| # codingSequence must start |
| # and end within them. |
| # |
| # Note that in some cases, the reference genome will not exactly match the |
| # observed mRNA transcript e.g. due to variance in the source genome from |
| # reference. In these cases, |
| # exon.frame will not necessarily |
| # match the expected reference reading frame and coding exon reference bases |
| # cannot necessarily be concatenated to produce the original transcript mRNA. |
| "start": "A String", # The start of the coding sequence on this annotation's reference sequence, |
| # 0-based inclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| "end": "A String", # The end of the coding sequence on this annotation's reference sequence, |
| # 0-based exclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| }, |
| "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose |
| # this transcript. This field should be unset for genomes where transcript |
| # splicing does not occur, for example prokaryotes. |
| # |
| # Introns are regions of the transcript that are not included in the |
| # spliced RNA product. Though not explicitly modeled here, intron ranges can |
| # be deduced; all regions of this transcript that are not exons are introns. |
| # |
| # Exonic sequences do not necessarily code for a translational product |
| # (amino acids). Only the regions of exons bounded by the |
| # codingSequence correspond |
| # to coding DNA sequence. |
| # |
| # Exons are ordered by start position and may not overlap. |
| { |
| "start": "A String", # The start position of the exon on this annotation's reference sequence, |
| # 0-based inclusive. Note that this is relative to the reference start, and |
| # **not** the containing annotation start. |
| "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates |
| # the offset of the first coding base of the exon within the reading frame |
| # of the coding DNA sequence, if any. This field is dependent on the |
| # strandedness of this annotation (see |
| # Annotation.reverse_strand). |
| # For forward stranded annotations, this offset is relative to the |
| # exon.start. For reverse |
| # strand annotations, this offset is relative to the |
| # exon.end `- 1`. |
| # |
| # Unset if this exon does not intersect the coding sequence. Upon creation |
| # of a transcript, the frame must be populated for all or none of the |
| # coding exons. |
| "end": "A String", # The end position of the exon on this annotation's reference sequence, |
| # 0-based exclusive. Note that this is relative to the reference start, and |
| # *not* the containing annotation start. |
| }, |
| ], |
| "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| }, |
| "variant": { # A variant annotation, which describes the effect of a variant on the |
| # genome, the coding sequence, and/or higher level consequences at the |
| # organism level e.g. pathogenicity. This field is only set for annotations |
| # of type `VARIANT`. |
| "type": "A String", # Type has been adapted from ClinVar's list of variant types. |
| "effect": "A String", # Effect of the variant on the coding sequence. |
| "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These |
| # should be provided when the variant is created. |
| "A String", |
| ], |
| "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles |
| # exist at this location, create a separate variant for each one, as they |
| # may represent distinct conditions. |
| "clinicalSignificance": "A String", # Describes the clinical significance of a variant. |
| # It is adapted from the ClinVar controlled vocabulary for clinical |
| # significance described at: |
| # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ |
| "conditions": [ # The set of conditions associated with this variant. |
| # A condition describes the way a variant influences human health. |
| { |
| "externalIds": [ # The set of external IDs for this condition. |
| { |
| "sourceName": "A String", # The name of the source of this data. |
| "id": "A String", # The id used by the source of this data. |
| }, |
| ], |
| "conceptId": "A String", # The MedGen concept id associated with this gene. |
| # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ |
| "omimId": "A String", # The OMIM id for this condition. |
| # Search for these IDs at http://omim.org/ |
| "names": [ # A set of names for the condition. |
| "A String", |
| ], |
| }, |
| ], |
| "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should |
| # be provided when the variant is created. |
| }, |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. |
| "annotationSetId": "A String", # The annotation set to which this annotation belongs. |
| "referenceName": "A String", # The display name corresponding to the reference specified by |
| # `referenceId`, for example `chr1`, `1`, or `chrX`. |
| "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward |
| # strand. Note that regardless of this field, the start/end position of the |
| # range always refer to the forward strand. |
| "type": "A String", # The data type for this annotation. Must match the containing annotation |
| # set's type. |
| "id": "A String", # The server-generated annotation ID, unique across all annotations. |
| } |
| |
| updateMask: string, An optional mask specifying which fields to update. Mutable fields are |
| name, |
| variant, |
| transcript, and |
| info. If unspecified, all mutable |
| fields will be updated. |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # An annotation describes a region of reference genome. The value of an |
| # annotation may be one of several canonical types, supplemented by arbitrary |
| # info tags. An annotation is not inherently associated with a specific |
| # sample or individual (though a client could choose to use annotations in |
| # this way). Example canonical annotation types are `GENE` and |
| # `VARIANT`. |
| "info": { # A map of additional read alignment information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "referenceId": "A String", # The ID of the Google Genomics reference associated with this range. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. |
| "name": "A String", # The display name of this annotation. |
| "transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of |
| # the reference genome may be transcribed as RNA. An alternative splicing |
| # pattern would be represented as a separate transcript object. This field |
| # is only set for annotations of type `TRANSCRIPT`. |
| # reference genome may be transcribed as RNA. |
| "codingSequence": { # The range of the coding sequence for this transcript, if any. To determine |
| # the exact ranges of coding sequence, intersect this range with those of the |
| # exons, if any. If there are any |
| # exons, the |
| # codingSequence must start |
| # and end within them. |
| # |
| # Note that in some cases, the reference genome will not exactly match the |
| # observed mRNA transcript e.g. due to variance in the source genome from |
| # reference. In these cases, |
| # exon.frame will not necessarily |
| # match the expected reference reading frame and coding exon reference bases |
| # cannot necessarily be concatenated to produce the original transcript mRNA. |
| "start": "A String", # The start of the coding sequence on this annotation's reference sequence, |
| # 0-based inclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| "end": "A String", # The end of the coding sequence on this annotation's reference sequence, |
| # 0-based exclusive. Note that this position is relative to the reference |
| # start, and *not* the containing annotation start. |
| }, |
| "exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose |
| # this transcript. This field should be unset for genomes where transcript |
| # splicing does not occur, for example prokaryotes. |
| # |
| # Introns are regions of the transcript that are not included in the |
| # spliced RNA product. Though not explicitly modeled here, intron ranges can |
| # be deduced; all regions of this transcript that are not exons are introns. |
| # |
| # Exonic sequences do not necessarily code for a translational product |
| # (amino acids). Only the regions of exons bounded by the |
| # codingSequence correspond |
| # to coding DNA sequence. |
| # |
| # Exons are ordered by start position and may not overlap. |
| { |
| "start": "A String", # The start position of the exon on this annotation's reference sequence, |
| # 0-based inclusive. Note that this is relative to the reference start, and |
| # **not** the containing annotation start. |
| "frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates |
| # the offset of the first coding base of the exon within the reading frame |
| # of the coding DNA sequence, if any. This field is dependent on the |
| # strandedness of this annotation (see |
| # Annotation.reverse_strand). |
| # For forward stranded annotations, this offset is relative to the |
| # exon.start. For reverse |
| # strand annotations, this offset is relative to the |
| # exon.end `- 1`. |
| # |
| # Unset if this exon does not intersect the coding sequence. Upon creation |
| # of a transcript, the frame must be populated for all or none of the |
| # coding exons. |
| "end": "A String", # The end position of the exon on this annotation's reference sequence, |
| # 0-based exclusive. Note that this is relative to the reference start, and |
| # *not* the containing annotation start. |
| }, |
| ], |
| "geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed. |
| }, |
| "variant": { # A variant annotation, which describes the effect of a variant on the |
| # genome, the coding sequence, and/or higher level consequences at the |
| # organism level e.g. pathogenicity. This field is only set for annotations |
| # of type `VARIANT`. |
| "type": "A String", # Type has been adapted from ClinVar's list of variant types. |
| "effect": "A String", # Effect of the variant on the coding sequence. |
| "transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These |
| # should be provided when the variant is created. |
| "A String", |
| ], |
| "alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles |
| # exist at this location, create a separate variant for each one, as they |
| # may represent distinct conditions. |
| "clinicalSignificance": "A String", # Describes the clinical significance of a variant. |
| # It is adapted from the ClinVar controlled vocabulary for clinical |
| # significance described at: |
| # http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ |
| "conditions": [ # The set of conditions associated with this variant. |
| # A condition describes the way a variant influences human health. |
| { |
| "externalIds": [ # The set of external IDs for this condition. |
| { |
| "sourceName": "A String", # The name of the source of this data. |
| "id": "A String", # The id used by the source of this data. |
| }, |
| ], |
| "conceptId": "A String", # The MedGen concept id associated with this gene. |
| # Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ |
| "omimId": "A String", # The OMIM id for this condition. |
| # Search for these IDs at http://omim.org/ |
| "names": [ # A set of names for the condition. |
| "A String", |
| ], |
| }, |
| ], |
| "geneId": "A String", # Google annotation ID of the gene affected by this variant. This should |
| # be provided when the variant is created. |
| }, |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. |
| "annotationSetId": "A String", # The annotation set to which this annotation belongs. |
| "referenceName": "A String", # The display name corresponding to the reference specified by |
| # `referenceId`, for example `chr1`, `1`, or `chrX`. |
| "reverseStrand": True or False, # Whether this range refers to the reverse strand, as opposed to the forward |
| # strand. Note that regardless of this field, the start/end position of the |
| # range always refer to the forward strand. |
| "type": "A String", # The data type for this annotation. Must match the containing annotation |
| # set's type. |
| "id": "A String", # The server-generated annotation ID, unique across all annotations. |
| }</pre> |
| </div> |
| |
| </body></html> |
