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

},

],

}

x__xgafv: string, V1 error format.

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Allowed values

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1 - v1 error format

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2 - v2 error format

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Returns:

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An object of the form:

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{

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

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# original request.

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{

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

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

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

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#

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# - Simple to use and understand for most users

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# - Flexible enough to meet unexpected needs

#

# # Overview

#

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

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

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

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

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

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

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

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

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

#

# # Language mapping

#

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

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

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

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

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# 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

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

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# consistent developer experience across different environments.

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#

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# Example uses of this error model include:

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#

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

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

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# errors.

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#

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

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

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#

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

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

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# each error sub-response.

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#

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

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

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# represented directly using the `Status` message.

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#

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

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

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

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

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

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

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

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# common set of message types for APIs to use.

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{

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

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},

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],

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},

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

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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

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# 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": [

"",

],

},

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

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# set's type.

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

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

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{

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

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{

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

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

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},

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],

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

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

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

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

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

"A String",

],

},

],

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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

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# should be provided when the variant is created.

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"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

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# may represent distinct conditions.

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

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# It is adapted from the ClinVar controlled vocabulary for clinical

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# significance described at:

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

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

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

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# be provided when the variant is created.

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},

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

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

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

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

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

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

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# range always refer to the forward strand.

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

},

},

],

}</pre>

</div>

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

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

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for the associated annotation set.

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The following fields are required:

* annotationSetId

* referenceName or

referenceId

### Transcripts

For annotations of type TRANSCRIPT, the following fields of

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transcript must be provided:

* exons.start

* exons.end

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

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

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

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Annotation resource

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for additional restrictions on each field.

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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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{ # 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

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# 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": [

"",

],

},

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

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# set's type.

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

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

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{

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

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{

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

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

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},

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],

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

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

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

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

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

"A String",

],

},

],

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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

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# should be provided when the variant is created.

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"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

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# may represent distinct conditions.

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

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# It is adapted from the ClinVar controlled vocabulary for clinical

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# significance described at:

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

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

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

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# be provided when the variant is created.

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},

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

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

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

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

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

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

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# range always refer to the forward strand.

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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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#

591

# 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.

595

#

596

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

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{

598

"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.

601

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

602

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

603

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

604

# strandedness of this annotation (see

605

# Annotation.reverse_strand).

606

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

607

# exon.start. For reverse

608

# strand annotations, this offset is relative to the

609

# exon.end `- 1`.

610

#

611

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

612

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

613

# coding exons.

614

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

615

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

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# *not* the containing annotation start.

617

},

618

],

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

622

}

623

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x__xgafv: string, V1 error format.

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Allowed values

626

1 - v1 error format

627

2 - v2 error format

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Returns:

630

An object of the form:

631

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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

635

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

636

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

637

# `VARIANT`.

638

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

639

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

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"a_key": [

"",

],

},

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

645

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

646

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

Sai Cheemalapati

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

[diff] [blame]

647

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

648

# set's type.

649

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

650

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

651

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

652

# of type `VARIANT`.

653

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

654

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

Jon Wayne Parrott

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

[diff] [blame]

655

{

Jon Wayne Parrott

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

[diff] [blame]

656

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

657

{

658

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

659

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

660

},

661

],

Sai Cheemalapati

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

[diff] [blame]

662

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

663

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

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

664

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

665

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

Jon Wayne Parrott

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

[diff] [blame]

666

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

"A String",

],

},

],

Sai Cheemalapati

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

[diff] [blame]

671

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

672

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

673

# should be provided when the variant is created.

674

"A String",

675

],

676

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

677

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

678

# may represent distinct conditions.

679

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

680

# It is adapted from the ClinVar controlled vocabulary for clinical

681

# significance described at:

682

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

683

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

684

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

685

# be provided when the variant is created.

Jon Wayne Parrott

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

[diff] [blame]

686

},

687

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

688

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

Sai Cheemalapati

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

[diff] [blame]

689

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

690

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

691

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

692

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

693

# range always refer to the forward strand.

694

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

695

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

696

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

697

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

698

# reference genome may be transcribed as RNA.

699

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

700

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

701

# exons, if any. If there are any

702

# exons, the

703

# codingSequence must start

704

# and end within them.

705

#

706

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

707

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

708

# reference. In these cases,

709

# exon.frame will not necessarily

710

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

711

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

712

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

713

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

714

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

715

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

716

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

717

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

718

},

Sai Cheemalapati

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

[diff] [blame]

719

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

720

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

721

# splicing does not occur, for example prokaryotes.

722

#

723

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

724

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

725

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

726

#

727

# Exonic sequences do not necessarily code for a translational product

728

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

729

# codingSequence correspond

730

# to coding DNA sequence.

731

#

732

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

733

{

734

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

735

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

736

# **not** the containing annotation start.

737

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

738

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

739

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

740

# strandedness of this annotation (see

741

# Annotation.reverse_strand).

742

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

743

# exon.start. For reverse

744

# strand annotations, this offset is relative to the

745

# exon.end `- 1`.

746

#

747

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

748

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

749

# coding exons.

750

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

751

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

752

# *not* the containing annotation start.

753

},

754

],

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

755

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

Sai Cheemalapati

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

[diff] [blame]

756

},

Jon Wayne Parrott

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

[diff] [blame]

757

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

}</pre>

</div>

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

Sai Cheemalapati

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

[diff] [blame]

763

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

764

the associated annotation set.

Jon Wayne Parrott

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

[diff] [blame]

765

766

Args:

767

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

768

x__xgafv: string, V1 error format.

Sai Cheemalapati

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

[diff] [blame]

769

Allowed values

770

1 - v1 error format

771

2 - v2 error format

Jon Wayne Parrott

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

[diff] [blame]

772

773

Returns:

774

An object of the form:

775

Sai Cheemalapati

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

[diff] [blame]

776

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

777

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

778

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

779

#

780

# service Foo {

781

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

782

# }

783

#

784

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

Jon Wayne Parrott

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

[diff] [blame]

}</pre>

</div>

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

Sai Cheemalapati

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

[diff] [blame]

790

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

791

for the associated annotation set.

Jon Wayne Parrott

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

[diff] [blame]

792

793

Args:

794

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

795

x__xgafv: string, V1 error format.

Sai Cheemalapati

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

[diff] [blame]

796

Allowed values

797

1 - v1 error format

798

2 - v2 error format

Jon Wayne Parrott

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

[diff] [blame]

799

800

Returns:

801

An object of the form:

802

Sai Cheemalapati

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

[diff] [blame]

803

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

804

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

805

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

806

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

807

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

808

# `VARIANT`.

809

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

810

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

Jon Wayne Parrott

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

[diff] [blame]

"a_key": [

"",

],

},

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

816

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

817

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

Sai Cheemalapati

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

[diff] [blame]

818

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

819

# set's type.

820

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

821

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

822

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

823

# of type `VARIANT`.

824

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

825

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

Jon Wayne Parrott

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

[diff] [blame]

826

{

Jon Wayne Parrott

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

[diff] [blame]

827

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

828

{

829

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

830

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

831

},

832

],

Sai Cheemalapati

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

[diff] [blame]

833

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

834

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

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

835

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

836

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

Jon Wayne Parrott

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

[diff] [blame]

837

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

"A String",

],

},

],

Sai Cheemalapati

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

[diff] [blame]

842

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

843

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

844

# should be provided when the variant is created.

845

"A String",

846

],

847

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

848

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

849

# may represent distinct conditions.

850

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

851

# It is adapted from the ClinVar controlled vocabulary for clinical

852

# significance described at:

853

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

854

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

855

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

856

# be provided when the variant is created.

Jon Wayne Parrott

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

[diff] [blame]

857

},

858

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

859

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

Sai Cheemalapati

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

[diff] [blame]

860

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

861

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

862

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

863

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

864

# range always refer to the forward strand.

865

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

866

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

867

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

868

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

869

# reference genome may be transcribed as RNA.

870

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

871

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

872

# exons, if any. If there are any

873

# exons, the

874

# codingSequence must start

875

# and end within them.

876

#

877

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

878

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

879

# reference. In these cases,

880

# exon.frame will not necessarily

881

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

882

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

883

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

884

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

885

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

886

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

887

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

888

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

889

},

Sai Cheemalapati

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

[diff] [blame]

890

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

891

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

892

# splicing does not occur, for example prokaryotes.

893

#

894

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

895

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

896

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

897

#

898

# Exonic sequences do not necessarily code for a translational product

899

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

900

# codingSequence correspond

901

# to coding DNA sequence.

902

#

903

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

904

{

905

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

906

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

907

# **not** the containing annotation start.

908

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

909

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

910

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

911

# strandedness of this annotation (see

912

# Annotation.reverse_strand).

913

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

914

# exon.start. For reverse

915

# strand annotations, this offset is relative to the

916

# exon.end `- 1`.

917

#

918

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

919

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

920

# coding exons.

921

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

922

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

923

# *not* the containing annotation start.

924

},

925

],

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

926

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

Sai Cheemalapati

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

[diff] [blame]

927

},

Jon Wayne Parrott

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

[diff] [blame]

928

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

}</pre>

</div>

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

Sai Cheemalapati

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

[diff] [blame]

934

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

935

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

936

Annotations with equivalent genomic coordinates are returned in an

937

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

938

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

939

across their respective streams of paginated responses. Caller must have

940

READ permission for the queried annotation sets.

Jon Wayne Parrott

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

[diff] [blame]

941

942

Args:

943

body: object, The request body. (required)

944

The object takes the form of:

945

946

{

947

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

Sai Cheemalapati

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

[diff] [blame]

948

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

949

# referenceId or

950

# referenceName

951

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

952

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

953

# defaults to 256. The maximum value is 2048.

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

954

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

955

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

956

# `nextPageToken` from the previous response.

Sai Cheemalapati

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

[diff] [blame]

957

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

958

# `READ` access to these annotation sets.

959

# All queried annotation sets must have the same type.

Jon Wayne Parrott

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

[diff] [blame]

960

"A String",

961

],

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

962

"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.

Sai Cheemalapati

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

[diff] [blame]

967

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

968

# with this query.

Jon Wayne Parrott

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

[diff] [blame]

969

}

970

971

x__xgafv: string, V1 error format.

Sai Cheemalapati

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

[diff] [blame]

972

Allowed values

973

1 - v1 error format

974

2 - v2 error format

Jon Wayne Parrott

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

[diff] [blame]

975

976

Returns:

977

An object of the form:

978

979

{

Sai Cheemalapati

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

[diff] [blame]

980

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

981

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

982

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

Jon Wayne Parrott

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

[diff] [blame]

983

"annotations": [ # The matching annotations.

Sai Cheemalapati

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

[diff] [blame]

984

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

985

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

986

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

987

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

988

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

989

# `VARIANT`.

990

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

991

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

Jon Wayne Parrott

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

[diff] [blame]

"a_key": [

"",

],

},

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

997

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

998

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

Sai Cheemalapati

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

[diff] [blame]

999

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

1000

# set's type.

1001

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

1002

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

1003

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

1004

# of type `VARIANT`.

1005

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

1006

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

Jon Wayne Parrott

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

[diff] [blame]

1007

{

Jon Wayne Parrott

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

[diff] [blame]

1008

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

1009

{

1010

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

1011

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

1012

},

1013

],

Sai Cheemalapati

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

[diff] [blame]

1014

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

1015

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

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

1016

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

1017

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

Jon Wayne Parrott

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

[diff] [blame]

1018

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

"A String",

],

},

],

Sai Cheemalapati

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

[diff] [blame]

1023

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

1024

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

1025

# should be provided when the variant is created.

1026

"A String",

1027

],

1028

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

1029

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

1030

# may represent distinct conditions.

1031

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

1032

# It is adapted from the ClinVar controlled vocabulary for clinical

1033

# significance described at:

1034

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

1035

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

1036

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

1037

# be provided when the variant is created.

Jon Wayne Parrott

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

[diff] [blame]

1038

},

1039

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

1040

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

Sai Cheemalapati

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

[diff] [blame]

1041

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

1042

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

1043

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

1044

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

1045

# range always refer to the forward strand.

1046

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

1047

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

1048

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

1049

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

1050

# reference genome may be transcribed as RNA.

1051

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

1052

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

1053

# exons, if any. If there are any

1054

# exons, the

1055

# codingSequence must start

1056

# and end within them.

1057

#

1058

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

1059

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

1060

# reference. In these cases,

1061

# exon.frame will not necessarily

1062

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

1063

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

1064

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

1065

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

1066

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

1067

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

1068

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

1069

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

1070

},

Sai Cheemalapati

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

[diff] [blame]

1071

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

1072

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

1073

# splicing does not occur, for example prokaryotes.

1074

#

1075

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

1076

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

1077

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

1078

#

1079

# Exonic sequences do not necessarily code for a translational product

1080

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

1081

# codingSequence correspond

1082

# to coding DNA sequence.

1083

#

1084

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

1085

{

1086

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

1087

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

1088

# **not** the containing annotation start.

1089

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

1090

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

1091

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

1092

# strandedness of this annotation (see

1093

# Annotation.reverse_strand).

1094

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

1095

# exon.start. For reverse

1096

# strand annotations, this offset is relative to the

1097

# exon.end `- 1`.

1098

#

1099

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

1100

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

1101

# coding exons.

1102

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

1103

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

1104

# *not* the containing annotation start.

1105

},

1106

],

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

1107

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

Sai Cheemalapati

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

[diff] [blame]

1108

},

Jon Wayne Parrott

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

[diff] [blame]

1109

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

},

],

}</pre>

</div>

Sai Cheemalapati

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

[diff] [blame]

1116

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

1117

<pre>Retrieves the next page of results.

1118

1119

Args:

1120

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

1121

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

1122

1123

Returns:

1124

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

1125

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

</pre>

</div>

Jon Wayne Parrott

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

[diff] [blame]

1130

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

Sai Cheemalapati

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

[diff] [blame]

1131

<pre>Updates an annotation. Caller must have

1132

WRITE permission for the associated dataset.

Jon Wayne Parrott

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

[diff] [blame]

1133

1134

Args:

1135

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

1136

body: object, The request body. (required)

1137

The object takes the form of:

1138

Sai Cheemalapati

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

[diff] [blame]

1139

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

1140

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

1141

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

1142

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

1143

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

1144

# `VARIANT`.

1145

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

1146

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

Jon Wayne Parrott

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

[diff] [blame]

"a_key": [

"",

],

},

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

1152

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

1153

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

Sai Cheemalapati

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

[diff] [blame]

1154

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

1155

# set's type.

1156

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

1157

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

1158

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

1159

# of type `VARIANT`.

1160

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

1161

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

Jon Wayne Parrott

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

[diff] [blame]

1162

{

Jon Wayne Parrott

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

[diff] [blame]

1163

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

1164

{

1165

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

1166

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

1167

},

1168

],

Sai Cheemalapati

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

[diff] [blame]

1169

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

1170

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

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

1171

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

1172

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

Jon Wayne Parrott

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

[diff] [blame]

1173

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

"A String",

],

},

],

Sai Cheemalapati

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

[diff] [blame]

1178

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

1179

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

1180

# should be provided when the variant is created.

1181

"A String",

1182

],

1183

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

1184

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

1185

# may represent distinct conditions.

1186

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

1187

# It is adapted from the ClinVar controlled vocabulary for clinical

1188

# significance described at:

1189

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

1190

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

1191

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

1192

# be provided when the variant is created.

Jon Wayne Parrott

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

[diff] [blame]

1193

},

1194

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

1195

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

Sai Cheemalapati

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

[diff] [blame]

1196

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

1197

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

1198

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

1199

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

1200

# range always refer to the forward strand.

1201

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

1202

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

1203

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

1204

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

1205

# reference genome may be transcribed as RNA.

1206

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

1207

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

1208

# exons, if any. If there are any

1209

# exons, the

1210

# codingSequence must start

1211

# and end within them.

1212

#

1213

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

1214

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

1215

# reference. In these cases,

1216

# exon.frame will not necessarily

1217

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

1218

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

1219

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

1220

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

1221

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

1222

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

1223

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

1224

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

1225

},

Sai Cheemalapati

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

[diff] [blame]

1226

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

1227

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

1228

# splicing does not occur, for example prokaryotes.

1229

#

1230

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

1231

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

1232

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

1233

#

1234

# Exonic sequences do not necessarily code for a translational product

1235

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

1236

# codingSequence correspond

1237

# to coding DNA sequence.

1238

#

1239

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

1240

{

1241

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

1242

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

1243

# **not** the containing annotation start.

1244

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

1245

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

1246

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

1247

# strandedness of this annotation (see

1248

# Annotation.reverse_strand).

1249

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

1250

# exon.start. For reverse

1251

# strand annotations, this offset is relative to the

1252

# exon.end `- 1`.

1253

#

1254

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

1255

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

1256

# coding exons.

1257

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

1258

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

1259

# *not* the containing annotation start.

1260

},

1261

],

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

1262

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

Sai Cheemalapati

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

[diff] [blame]

1263

},

Jon Wayne Parrott

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

[diff] [blame]

1264

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

1265

}

1266

Sai Cheemalapati

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

[diff] [blame]

1267

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

name,

variant,

transcript, and

info. If unspecified, all mutable

1272

fields will be updated.

Jon Wayne Parrott

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

[diff] [blame]

1273

x__xgafv: string, V1 error format.

Sai Cheemalapati

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

[diff] [blame]

1274

Allowed values

1275

1 - v1 error format

1276

2 - v2 error format

Jon Wayne Parrott

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

[diff] [blame]

1277

1278

Returns:

1279

An object of the form:

1280

Sai Cheemalapati

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

[diff] [blame]

1281

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

1282

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

1283

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

1284

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

1285

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

1286

# `VARIANT`.

1287

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

1288

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

Jon Wayne Parrott

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

[diff] [blame]

"a_key": [

"",

],

},

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

1294

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

1295

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

Sai Cheemalapati

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

[diff] [blame]

1296

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

1297

# set's type.

1298

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

1299

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

1300

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

1301

# of type `VARIANT`.

1302

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

1303

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

Jon Wayne Parrott

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

[diff] [blame]

1304

{

Jon Wayne Parrott

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

[diff] [blame]

1305

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

1306

{

1307

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

1308

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

1309

},

1310

],

Sai Cheemalapati

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

[diff] [blame]

1311

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

1312

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

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

1313

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

1314

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

Jon Wayne Parrott

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

[diff] [blame]

1315

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

"A String",

],

},

],

Sai Cheemalapati

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

[diff] [blame]

1320

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

1321

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

1322

# should be provided when the variant is created.

1323

"A String",

1324

],

1325

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

1326

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

1327

# may represent distinct conditions.

1328

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

1329

# It is adapted from the ClinVar controlled vocabulary for clinical

1330

# significance described at:

1331

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

1332

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

1333

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

1334

# be provided when the variant is created.

Jon Wayne Parrott

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

[diff] [blame]

1335

},

1336

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

1337

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

Sai Cheemalapati

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

[diff] [blame]

1338

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

1339

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

1340

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

1341

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

1342

# range always refer to the forward strand.

1343

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

1344

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

1345

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

1346

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

1347

# reference genome may be transcribed as RNA.

1348

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

1349

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

1350

# exons, if any. If there are any

1351

# exons, the

1352

# codingSequence must start

1353

# and end within them.

1354

#

1355

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

1356

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

1357

# reference. In these cases,

1358

# exon.frame will not necessarily

1359

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

1360

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

1361

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

1362

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

1363

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

1364

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

1365

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

1366

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

1367

},

Sai Cheemalapati

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

[diff] [blame]

1368

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

1369

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

1370

# splicing does not occur, for example prokaryotes.

1371

#

1372

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

1373

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

1374

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

1375

#

1376

# Exonic sequences do not necessarily code for a translational product

1377

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

1378

# codingSequence correspond

1379

# to coding DNA sequence.

1380

#

1381

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

1382

{

1383

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

1384

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

1385

# **not** the containing annotation start.

1386

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

1387

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

1388

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

1389

# strandedness of this annotation (see

1390

# Annotation.reverse_strand).

1391

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

1392

# exon.start. For reverse

1393

# strand annotations, this offset is relative to the

1394

# exon.end `- 1`.

1395

#

1396

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

1397

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

1398

# coding exons.

1399

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

1400

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

1401

# *not* the containing annotation start.

1402

},

1403

],

Sai Cheemalapati

2017-03-24 15:06:46 -0700

[diff] [blame^]

1404

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

Sai Cheemalapati

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

[diff] [blame]

1405

},

Jon Wayne Parrott