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<h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.annotations.html">annotations</a></h1>
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<h2>Instance Methods</h2>
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<p class="toc_element">
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<code><a href="#batchCreate">batchCreate(body, x__xgafv=None)</a></code></p>
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<p class="firstline">Creates one or more new annotations atomically. All annotations must</p>
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<p class="toc_element">
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<code><a href="#create">create(body, x__xgafv=None)</a></code></p>
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<p class="firstline">Creates a new annotation. Caller must have WRITE permission</p>
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<p class="toc_element">
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<code><a href="#delete">delete(annotationId, x__xgafv=None)</a></code></p>
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<p class="firstline">Deletes an annotation. Caller must have WRITE permission for</p>
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<p class="toc_element">
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<code><a href="#get">get(annotationId, x__xgafv=None)</a></code></p>
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<p class="firstline">Gets an annotation. Caller must have READ permission</p>
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<p class="toc_element">
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<code><a href="#search">search(body, x__xgafv=None)</a></code></p>
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<p class="firstline">Searches for annotations that match the given criteria. Results are</p>
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<p class="toc_element">
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<code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p>
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<p class="firstline">Retrieves the next page of results.</p>
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<p class="toc_element">
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<code><a href="#update">update(annotationId, body, updateMask=None, x__xgafv=None)</a></code></p>
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<p class="firstline">Updates an annotation. Caller must have</p>
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<h3>Method Details</h3>
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<div class="method">
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<code class="details" id="batchCreate">batchCreate(body, x__xgafv=None)</code>
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<pre>Creates one or more new annotations atomically. All annotations must
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belong to the same annotation set. Caller must have WRITE
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permission for this annotation set. For optimal performance, batch
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positionally adjacent annotations together.
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|
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If the request has a systemic issue, such as an attempt to write to
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an inaccessible annotation set, the entire RPC will fail accordingly. For
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lesser data issues, when possible an error will be isolated to the
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corresponding batch entry in the response; the remaining well formed
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annotations will be created normally.
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For details on the requirements for each individual annotation resource,
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see
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CreateAnnotation.
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Args:
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body: object, The request body. (required)
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The object takes the form of:
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{
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"requestId": "A String", # A unique request ID which enables the server to detect duplicated requests.
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# If provided, duplicated requests will result in the same response; if not
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# provided, duplicated requests may result in duplicated data. For a given
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# annotation set, callers should not reuse `request_id`s when writing
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# different batches of annotations - behavior in this case is undefined.
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# A common approach is to use a UUID. For batch jobs where worker crashes are
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# a possibility, consider using some unique variant of a worker or run ID.
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"annotations": [ # The annotations to be created. At most 4096 can be specified in a single
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# request.
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{ # An annotation describes a region of reference genome. The value of an
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# annotation may be one of several canonical types, supplemented by arbitrary
|
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# info tags. An annotation is not inherently associated with a specific
|
|
# sample or individual (though a client could choose to use annotations in
|
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# this way). Example canonical annotation types are `GENE` and
|
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# `VARIANT`.
|
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"info": { # A map of additional read alignment information. This must be of the form
|
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# map<string, string[]> (string key mapping to a list of string values).
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"a_key": [
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"",
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],
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},
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"referenceId": "A String", # The ID of the Google Genomics reference associated with this range.
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|
"end": "A String", # The end position of the range on the reference, 0-based exclusive.
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"name": "A String", # The display name of this annotation.
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"transcript": { # A transcript represents the assertion that a particular region of the # A transcript value represents the assertion that a particular region of
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# the reference genome may be transcribed as RNA. An alternative splicing
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# pattern would be represented as a separate transcript object. This field
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# is only set for annotations of type `TRANSCRIPT`.
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# reference genome may be transcribed as RNA.
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"codingSequence": { # The range of the coding sequence for this transcript, if any. To determine
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# the exact ranges of coding sequence, intersect this range with those of the
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# exons, if any. If there are any
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# exons, the
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# codingSequence must start
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# and end within them.
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#
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# Note that in some cases, the reference genome will not exactly match the
|
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# observed mRNA transcript e.g. due to variance in the source genome from
|
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# reference. In these cases,
|
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# exon.frame will not necessarily
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# match the expected reference reading frame and coding exon reference bases
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# cannot necessarily be concatenated to produce the original transcript mRNA.
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"start": "A String", # The start of the coding sequence on this annotation's reference sequence,
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# 0-based inclusive. Note that this position is relative to the reference
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# start, and *not* the containing annotation start.
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"end": "A String", # The end of the coding sequence on this annotation's reference sequence,
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# 0-based exclusive. Note that this position is relative to the reference
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# start, and *not* the containing annotation start.
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},
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"exons": [ # The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose
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# this transcript. This field should be unset for genomes where transcript
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# splicing does not occur, for example prokaryotes.
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#
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# Introns are regions of the transcript that are not included in the
|
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# spliced RNA product. Though not explicitly modeled here, intron ranges can
|
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# be deduced; all regions of this transcript that are not exons are introns.
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#
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# Exonic sequences do not necessarily code for a translational product
|
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# (amino acids). Only the regions of exons bounded by the
|
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# codingSequence correspond
|
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# to coding DNA sequence.
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#
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# Exons are ordered by start position and may not overlap.
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{
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"start": "A String", # The start position of the exon on this annotation's reference sequence,
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# 0-based inclusive. Note that this is relative to the reference start, and
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# **not** the containing annotation start.
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"frame": 42, # The frame of this exon. Contains a value of 0, 1, or 2, which indicates
|
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# the offset of the first coding base of the exon within the reading frame
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# of the coding DNA sequence, if any. This field is dependent on the
|
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# strandedness of this annotation (see
|
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# Annotation.reverse_strand).
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# For forward stranded annotations, this offset is relative to the
|
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# exon.start. For reverse
|
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# strand annotations, this offset is relative to the
|
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# exon.end `- 1`.
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#
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# Unset if this exon does not intersect the coding sequence. Upon creation
|
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# of a transcript, the frame must be populated for all or none of the
|
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# coding exons.
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"end": "A String", # The end position of the exon on this annotation's reference sequence,
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# 0-based exclusive. Note that this is relative to the reference start, and
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# *not* the containing annotation start.
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},
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],
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"geneId": "A String", # The annotation ID of the gene from which this transcript is transcribed.
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},
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"variant": { # A variant annotation, which describes the effect of a variant on the
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# genome, the coding sequence, and/or higher level consequences at the
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# organism level e.g. pathogenicity. This field is only set for annotations
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# of type `VARIANT`.
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"type": "A String", # Type has been adapted from ClinVar's list of variant types.
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"effect": "A String", # Effect of the variant on the coding sequence.
|
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"transcriptIds": [ # Google annotation IDs of the transcripts affected by this variant. These
|
|
# should be provided when the variant is created.
|
|
"A String",
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],
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"alternateBases": "A String", # The alternate allele for this variant. If multiple alternate alleles
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# 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.
|
|
},
|
|
],
|
|
}
|
|
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|
x__xgafv: string, V1 error format.
|
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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>
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</body></html> |