google_api_genomics v0.5.0 API Reference
Modules
API calls for all endpoints tagged Annotations
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API calls for all endpoints tagged Annotationsets
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API calls for all endpoints tagged Callsets
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API calls for all endpoints tagged Datasets
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API calls for all endpoints tagged Operations
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API calls for all endpoints tagged Readgroupsets
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API calls for all endpoints tagged Reads
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API calls for all endpoints tagged References
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API calls for all endpoints tagged Referencesets
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API calls for all endpoints tagged Variants
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API calls for all endpoints tagged Variantsets
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Handle Tesla connections for GoogleApi.Genomics.V1.
Helper functions for deserializing responses into models.
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`.
An annotation set is a logical grouping of annotations that share consistent type information and provenance. Examples of annotation sets include 'all genes from refseq', and 'all variant annotations from ClinVar'.
Attributes
- annotations ([Annotation]): The annotations to be created. At most 4096 can be specified in a single request. Defaults to:
null
. - requestId (String.t): A unique request ID which enables the server to detect duplicated requests. If provided, duplicated requests will result in the same response; if not provided, duplicated requests may result in duplicated data. For a given annotation set, callers should not reuse `request_id`s when writing different batches of annotations - behavior in this case is undefined. A common approach is to use a UUID. For batch jobs where worker crashes are a possibility, consider using some unique variant of a worker or run ID. Defaults to:
null
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Associates `members` with a `role`.
A call set is a collection of variant calls, typically for one sample. It belongs to a variant set.
The request message for Operations.CancelOperation.
A single CIGAR operation.
Attributes
- conceptId (String.t): The MedGen concept id associated with this gene. Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/ Defaults to:
null
. - externalIds ([ExternalId]): The set of external IDs for this condition. Defaults to:
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. - names ([String.t]): A set of names for the condition. Defaults to:
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. - omimId (String.t): The OMIM id for this condition. Search for these IDs at http://omim.org/ Defaults to:
null
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Attributes
- end (String.t): 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. Defaults to:
null
. - start (String.t): 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. Defaults to:
null
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Describes a Compute Engine resource that is being managed by a running pipeline.
An event generated when a container is forcibly terminated by the worker. Currently, this only occurs when the container outlives the timeout specified by the user.
An event generated when a container starts.
An event generated when a container exits.
A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence.
A Dataset is a collection of genomic data.
An event generated whenever a resource limitation or transient error delays execution of a pipeline that was otherwise ready to run.
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 `{}`.
Carries information about events that occur during pipeline execution.
Attributes
- end (String.t): 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. Defaults to:
null
. - frame (integer()): 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. Defaults to:
null
. - start (String.t): 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. Defaults to:
null
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Attributes
- instrumentModel (String.t): The instrument model used as part of this experiment. This maps to sequencing technology in the SAM spec. Defaults to:
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. - libraryId (String.t): A client-supplied library identifier; a library is a collection of DNA fragments which have been prepared for sequencing from a sample. This field is important for quality control as error or bias can be introduced during sample preparation. Defaults to:
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. - platformUnit (String.t): The platform unit used as part of this experiment, for example flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the @RG PU field in the SAM spec. Defaults to:
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. - sequencingCenter (String.t): The sequencing center used as part of this experiment. Defaults to:
null
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The read group set export request.
The variant data export request.
Represents an expression text. Example: title: "User account presence" description: "Determines whether the request has a user account" expression: "size(request.user) > 0"
An event generated when the execution of a pipeline has failed. Note that other events can continue to occur after this event.
Request message for `GetIamPolicy` method.
The read group set import request.
The read group set import response.
The variant data import request.
The variant data import response.
A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference.
Attributes
- nextPageToken (String.t): 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. Defaults to:
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. - offset (String.t): The offset position (0-based) of the given `sequence` from the start of this `Reference`. This value will differ for each page in a paginated request. Defaults to:
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. - sequence (String.t): A substring of the bases that make up this reference. Defaults to:
null
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Attributes
- bucketWidth (String.t): The length of each coverage bucket in base pairs. Note that buckets at the end of a reference sequence may be shorter. This value is omitted if the bucket width is infinity (the default behaviour, with no range or `targetBucketWidth`). Defaults to:
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. - coverageBuckets ([CoverageBucket]): The coverage buckets. The list of buckets is sparse; a bucket with 0 overlapping reads is not returned. A bucket never crosses more than one reference sequence. Each bucket has width `bucketWidth`, unless its end is the end of the reference sequence. Defaults to:
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. - nextPageToken (String.t): 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. Defaults to:
null
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The dataset list response.
The response message for Operations.ListOperations.
This resource represents a long-running operation that is the result of a network API call.
An event that occurred during an Operation.
Metadata describing an Operation.
Defines an Identity and Access Management (IAM) policy. It is used to specify access control policies for Cloud Platform resources. A `Policy` consists of a list of `bindings`. A `binding` binds a list of `members` to a `role`, where the members can be user accounts, Google groups, Google domains, and service accounts. A `role` is a named list of permissions defined by IAM. JSON Example { "bindings": [ { "role": "roles/owner", "members": [ "user:mike@example.com", "group:admins@example.com", "domain:google.com", "serviceAccount:my-other-app@appspot.gserviceaccount.com" ] }, { "role": "roles/viewer", "members": ["user:sean@example.com"] } ] } YAML Example bindings: - members: - user:mike@example.com - group:admins@example.com - domain:google.com - serviceAccount:my-other-app@appspot.gserviceaccount.com role: roles/owner - members: - user:sean@example.com role: roles/viewer For a description of IAM and its features, see the IAM developer's guide.
An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand.
Attributes
- commandLine (String.t): The command line used to run this program. Defaults to:
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. - id (String.t): The user specified locally unique ID of the program. Used along with `prevProgramId` to define an ordering between programs. Defaults to:
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. - name (String.t): The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'. Defaults to:
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. - prevProgramId (String.t): The ID of the program run before this one. Defaults to:
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. - version (String.t): The version of the program run. Defaults to:
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An event generated when the worker starts pulling an image.
An event generated when the worker stops pulling an image.
A 0-based half-open genomic coordinate range for search requests.
A read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set. ### Reverse-stranded reads Mapped reads (reads having a non-null `alignment`) can be aligned to either the forward or the reverse strand of their associated reference. Strandedness of a mapped read is encoded by `alignment.position.reverseStrand`. If we consider the reference to be a forward-stranded coordinate space of `[0, reference.length)` with `0` as the left-most position and `reference.length` as the right-most position, reads are always aligned left to right. That is, `alignment.position.position` always refers to the left-most reference coordinate and `alignment.cigar` describes the alignment of this read to the reference from left to right. All per-base fields such as `alignedSequence` and `alignedQuality` share this same left-to-right orientation; this is true of reads which are aligned to either strand. For reverse-stranded reads, this means that `alignedSequence` is the reverse complement of the bases that were originally reported by the sequencing machine. ### Generating a reference-aligned sequence string When interacting with mapped reads, it's often useful to produce a string representing the local alignment of the read to reference. The following pseudocode demonstrates one way of doing this: out = "" offset = 0 for c in read.alignment.cigar { switch c.operation { case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset:offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", "INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c.operationLength) break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD": break } } return out ### Converting to SAM's CIGAR string The following pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this is a lossy conversion (`cigar.referenceSequence` is lost). cigarMap = { "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH": "X", } cigarStr = "" for c in read.alignment.cigar { cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr
A read group is all the data that's processed the same way by the sequencer.
A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way. A read group set belongs to one dataset. A read group belongs to one read group set. * A read belongs to one read group.
A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets.
ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
A reference set is a set of references which typically comprise a reference assembly for a species, such as `GRCh38` which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references.
The response to the RunPipeline method, returned in the operation's result field on success.
Runtime metadata that will be populated in the runtimeMetadata field of the Operation associated with a RunPipeline execution.
Attributes
- datasetIds ([String.t]): Required. The dataset IDs to search within. Caller must have `READ` access to these datasets. Defaults to:
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. - name (String.t): Only return annotations sets for which a substring of the name matches this string (case insensitive). Defaults to:
null
. - pageSize (integer()): The maximum number of results to return in a single page. If unspecified, defaults to 128. The maximum value is 1024. Defaults to:
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. - pageToken (String.t): 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. Defaults to:
null
. - referenceSetId (String.t): If specified, only annotation sets associated with the given reference set are returned. Defaults to:
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. types ([String.t]): If specified, only annotation sets that have any of these types are returned. Defaults to:
null
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Attributes
- annotationSets ([AnnotationSet]): The matching annotation sets. Defaults to:
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. - nextPageToken (String.t): 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. Defaults to:
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Attributes
- annotationSetIds ([String.t]): 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. Defaults to:
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. - end (String.t): 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. Defaults to:
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. - pageSize (integer()): The maximum number of results to return in a single page. If unspecified, defaults to 256. The maximum value is 2048. Defaults to:
null
. - pageToken (String.t): 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. Defaults to:
null
. - referenceId (String.t): The ID of the reference to query. Defaults to:
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. - referenceName (String.t): The name of the reference to query, within the reference set associated with this query. Defaults to:
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. - start (String.t): The start position of the range on the reference, 0-based inclusive. If specified, referenceId or referenceName must be specified. Defaults to 0. Defaults to:
null
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Attributes
- annotations ([Annotation]): The matching annotations. Defaults to:
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. - nextPageToken (String.t): 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. Defaults to:
null
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The call set search request.
The call set search response.
The read group set search request.
The read group set search response.
The read search request.
The read search response.
Attributes
- accessions ([String.t]): If present, return reference sets for which a prefix of any of sourceAccessions match any of these strings. Accession numbers typically have a main number and a version, for example `NC_000001.11`. Defaults to:
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. - assemblyId (String.t): If present, return reference sets for which a substring of their `assemblyId` matches this string (case insensitive). Defaults to:
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. - md5checksums ([String.t]): If present, return reference sets for which the md5checksum matches exactly. Defaults to:
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. - pageSize (integer()): The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 4096. Defaults to:
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. - pageToken (String.t): 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. Defaults to:
null
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Attributes
- nextPageToken (String.t): 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. Defaults to:
null
. - referenceSets ([ReferenceSet]): The matching references sets. Defaults to:
null
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Attributes
- accessions ([String.t]): If present, return references for which a prefix of any of sourceAccessions match any of these strings. Accession numbers typically have a main number and a version, for example `GCF_000001405.26`. Defaults to:
null
. - md5checksums ([String.t]): If present, return references for which the md5checksum matches exactly. Defaults to:
null
. - pageSize (integer()): The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 4096. Defaults to:
null
. - pageToken (String.t): 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. Defaults to:
null
. - referenceSetId (String.t): If present, return only references which belong to this reference set. Defaults to:
null
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Attributes
- nextPageToken (String.t): 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. Defaults to:
null
. - references ([Reference]): The matching references. Defaults to:
null
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The search variant sets request.
The search variant sets response.
The variant search request.
The variant search response.
Request message for `SetIamPolicy` method.
The `Status` type defines a logical error model that is suitable for different programming environments, including REST APIs and RPC APIs. It is used by gRPC. Each `Status` message contains three pieces of data: error code, error message, and error details. You can find out more about this error model and how to work with it in the API Design Guide.
Request message for `TestIamPermissions` method.
Response message for `TestIamPermissions` method.
A transcript represents the assertion that a particular region of the reference genome may be transcribed as RNA.
An event generated when the execution of a container results in a non-zero exit status that was not otherwise ignored. Execution will continue, but only actions that are flagged as `ALWAYS_RUN` will be executed. Other actions will be skipped.
A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample.
Attributes
- alternateBases (String.t): 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. Defaults to:
null
. clinicalSignificance (String.t): 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/ Defaults to:
null
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A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.
A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
An event generated after a worker VM has been assigned to run the pipeline.
An event generated when the worker VM that was assigned to the pipeline has been released (deleted).
Helper functions for building Tesla requests.