Returns the coveragebuckets Resource.
delete(readGroupSetId, x__xgafv=None)
Deletes a read group set.
export(readGroupSetId, body, x__xgafv=None)
Exports a read group set to a BAM file in Google Cloud Storage.
get(readGroupSetId, x__xgafv=None)
Gets a read group set by ID.
Creates read group sets by asynchronously importing the provided
patch(readGroupSetId, body, updateMask=None, x__xgafv=None)
Updates a read group set.
Searches for read group sets matching the criteria.
search_next(previous_request, previous_response)
Retrieves the next page of results.
delete(readGroupSetId, x__xgafv=None)
Deletes a read group set. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Args: readGroupSetId: string, The ID of the read group set to be deleted. The caller must have WRITE permissions to the dataset associated with this read group set. (required) x__xgafv: string, V1 error format. Allowed values 1 - v1 error format 2 - v2 error format Returns: An object of the form: { # A generic empty message that you can re-use to avoid defining duplicated # empty messages in your APIs. A typical example is to use it as the request # or the response type of an API method. For instance: # # service Foo { # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); # } # # The JSON representation for `Empty` is empty JSON object `{}`. }
export(readGroupSetId, body, x__xgafv=None)
Exports a read group set to a BAM file in Google Cloud Storage. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. See ImportReadGroupSets for caveats. Args: readGroupSetId: string, Required. The ID of the read group set to export. The caller must have READ access to this read group set. (required) body: object, The request body. (required) The object takes the form of: { # The read group set export request. "projectId": "A String", # Required. The Google Cloud project ID that owns this # export. The caller must have WRITE access to this project. "referenceNames": [ # The reference names to export. If this is not specified, all reference # sequences, including unmapped reads, are exported. # Use `*` to export only unmapped reads. "A String", ], "exportUri": "A String", # Required. A Google Cloud Storage URI for the exported BAM file. # The currently authenticated user must have write access to the new file. # An error will be returned if the URI already contains data. } x__xgafv: string, V1 error format. Allowed values 1 - v1 error format 2 - v2 error format Returns: An object of the form: { # This resource represents a long-running operation that is the result of a # network API call. "metadata": { # An OperationMetadata object. This will always be returned with the Operation. "a_key": "", # Properties of the object. Contains field @type with type URL. }, "error": { # The `Status` type defines a logical error model that is suitable for different # The error result of the operation in case of failure or cancellation. # programming environments, including REST APIs and RPC APIs. It is used by # [gRPC](https://github.com/grpc). The error model is designed to be: # # - Simple to use and understand for most users # - Flexible enough to meet unexpected needs # # # Overview # # The `Status` message contains three pieces of data: error code, error message, # and error details. The error code should be an enum value of # google.rpc.Code, but it may accept additional error codes if needed. The # error message should be a developer-facing English message that helps # developers *understand* and *resolve* the error. If a localized user-facing # error message is needed, put the localized message in the error details or # localize it in the client. The optional error details may contain arbitrary # information about the error. There is a predefined set of error detail types # in the package `google.rpc` that can be used for common error conditions. # # # Language mapping # # The `Status` message is the logical representation of the error model, but it # is not necessarily the actual wire format. When the `Status` message is # exposed in different client libraries and different wire protocols, it can be # mapped differently. For example, it will likely be mapped to some exceptions # in Java, but more likely mapped to some error codes in C. # # # Other uses # # The error model and the `Status` message can be used in a variety of # environments, either with or without APIs, to provide a # consistent developer experience across different environments. # # Example uses of this error model include: # # - Partial errors. If a service needs to return partial errors to the client, # it may embed the `Status` in the normal response to indicate the partial # errors. # # - Workflow errors. A typical workflow has multiple steps. Each step may # have a `Status` message for error reporting. # # - Batch operations. If a client uses batch request and batch response, the # `Status` message should be used directly inside batch response, one for # each error sub-response. # # - Asynchronous operations. If an API call embeds asynchronous operation # results in its response, the status of those operations should be # represented directly using the `Status` message. # # - Logging. If some API errors are stored in logs, the message `Status` could # be used directly after any stripping needed for security/privacy reasons. "message": "A String", # A developer-facing error message, which should be in English. Any # user-facing error message should be localized and sent in the # google.rpc.Status.details field, or localized by the client. "code": 42, # The status code, which should be an enum value of google.rpc.Code. "details": [ # A list of messages that carry the error details. There will be a # common set of message types for APIs to use. { "a_key": "", # Properties of the object. Contains field @type with type URL. }, ], }, "done": True or False, # If the value is `false`, it means the operation is still in progress. # If true, the operation is completed, and either `error` or `response` is # available. "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned. "a_key": "", # Properties of the object. Contains field @type with type URL. }, "name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw` }
get(readGroupSetId, x__xgafv=None)
Gets a read group set by ID. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Args: readGroupSetId: string, The ID of the read group set. (required) x__xgafv: string, V1 error format. Allowed values 1 - v1 error format 2 - v2 error format Returns: An object of the form: { # 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. # # For more genomics resource definitions, see [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) "info": { # A map of additional read group set information. "a_key": [ "", ], }, "name": "A String", # The read group set name. By default this will be initialized to the sample # name of the sequenced data contained in this set. "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read # group set. { # A read group is all the data that's processed the same way by the sequencer. "info": { # A map of additional read group information. This must be of the form # map(string key mapping to a list of string values). "a_key": [ "", ], }, "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length # the sequenced DNA fragment from end-to-end, not including the adapters. "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. "programs": [ # The programs used to generate this read group. Programs are always # identical for all read groups within a read group set. For this reason, # only the first read group in a returned set will have this field # populated. { "prevProgramId": "A String", # The ID of the program run before this one. "commandLine": "A String", # The command line used to run this program. "version": "A String", # The version of the program run. "id": "A String", # The user specified locally unique ID of the program. Used along with # `prevProgramId` to define an ordering between programs. "name": "A String", # The display name of the program. This is typically the colloquial name of # the tool used, for example 'bwa' or 'picard'. }, ], "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. "experiment": { # The experiment used to generate this read group. "sequencingCenter": "A String", # The sequencing center used as part of this experiment. "libraryId": "A String", # 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. "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to # sequencing technology in the SAM spec. "platformUnit": "A String", # 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. }, "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. "id": "A String", # The server-generated read group ID, unique for all read groups. # Note: This is different than the @RG ID field in the SAM spec. For that # value, see name. "datasetId": "A String", # The dataset to which this read group belongs. "description": "A String", # A free-form text description of this read group. }, ], "filename": "A String", # The filename of the original source file for this read group set, if any. "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. "id": "A String", # The server-generated read group set ID, unique for all read group sets. "datasetId": "A String", # The dataset to which this read group set belongs. }
import_(body, x__xgafv=None)
Creates read group sets by asynchronously importing the provided information. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) The caller must have WRITE permissions to the dataset. ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import - Tags will be converted to strings - tag types are not preserved - Comments (`@CO`) in the input file header will not be preserved - Original header order of references (`@SQ`) will not be preserved - Any reverse stranded unmapped reads will be reverse complemented, and their qualities (also the "BQ" and "OQ" tags, if any) will be reversed - Unmapped reads will be stripped of positional information (reference name and position) Args: body: object, The request body. (required) The object takes the form of: { # The read group set import request. "partitionStrategy": "A String", # The partition strategy describes how read groups are partitioned into read # group sets. "sourceUris": [ # A list of URIs pointing at [BAM # files](https://samtools.github.io/hts-specs/SAMv1.pdf) # in Google Cloud Storage. # Those URIs can include wildcards (*), but do not add or remove # matching files before import has completed. # # Note that Google Cloud Storage object listing is only eventually # consistent: files added may be not be immediately visible to # everyone. Thus, if using a wildcard it is preferable not to start # the import immediately after the files are created. "A String", ], "referenceSetId": "A String", # The reference set to which the imported read group sets are aligned to, if # any. The reference names of this reference set must be a superset of those # found in the imported file headers. If no reference set id is provided, a # best effort is made to associate with a matching reference set. "datasetId": "A String", # Required. The ID of the dataset these read group sets will belong to. The # caller must have WRITE permissions to this dataset. } x__xgafv: string, V1 error format. Allowed values 1 - v1 error format 2 - v2 error format Returns: An object of the form: { # This resource represents a long-running operation that is the result of a # network API call. "metadata": { # An OperationMetadata object. This will always be returned with the Operation. "a_key": "", # Properties of the object. Contains field @type with type URL. }, "error": { # The `Status` type defines a logical error model that is suitable for different # The error result of the operation in case of failure or cancellation. # programming environments, including REST APIs and RPC APIs. It is used by # [gRPC](https://github.com/grpc). The error model is designed to be: # # - Simple to use and understand for most users # - Flexible enough to meet unexpected needs # # # Overview # # The `Status` message contains three pieces of data: error code, error message, # and error details. The error code should be an enum value of # google.rpc.Code, but it may accept additional error codes if needed. The # error message should be a developer-facing English message that helps # developers *understand* and *resolve* the error. If a localized user-facing # error message is needed, put the localized message in the error details or # localize it in the client. The optional error details may contain arbitrary # information about the error. There is a predefined set of error detail types # in the package `google.rpc` that can be used for common error conditions. # # # Language mapping # # The `Status` message is the logical representation of the error model, but it # is not necessarily the actual wire format. When the `Status` message is # exposed in different client libraries and different wire protocols, it can be # mapped differently. For example, it will likely be mapped to some exceptions # in Java, but more likely mapped to some error codes in C. # # # Other uses # # The error model and the `Status` message can be used in a variety of # environments, either with or without APIs, to provide a # consistent developer experience across different environments. # # Example uses of this error model include: # # - Partial errors. If a service needs to return partial errors to the client, # it may embed the `Status` in the normal response to indicate the partial # errors. # # - Workflow errors. A typical workflow has multiple steps. Each step may # have a `Status` message for error reporting. # # - Batch operations. If a client uses batch request and batch response, the # `Status` message should be used directly inside batch response, one for # each error sub-response. # # - Asynchronous operations. If an API call embeds asynchronous operation # results in its response, the status of those operations should be # represented directly using the `Status` message. # # - Logging. If some API errors are stored in logs, the message `Status` could # be used directly after any stripping needed for security/privacy reasons. "message": "A String", # A developer-facing error message, which should be in English. Any # user-facing error message should be localized and sent in the # google.rpc.Status.details field, or localized by the client. "code": 42, # The status code, which should be an enum value of google.rpc.Code. "details": [ # A list of messages that carry the error details. There will be a # common set of message types for APIs to use. { "a_key": "", # Properties of the object. Contains field @type with type URL. }, ], }, "done": True or False, # If the value is `false`, it means the operation is still in progress. # If true, the operation is completed, and either `error` or `response` is # available. "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned. "a_key": "", # Properties of the object. Contains field @type with type URL. }, "name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw` }
patch(readGroupSetId, body, updateMask=None, x__xgafv=None)
Updates a read group set. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This method supports patch semantics. Args: readGroupSetId: string, The ID of the read group set to be updated. The caller must have WRITE permissions to the dataset associated with this read group set. (required) body: object, The request body. (required) The object takes the form of: { # 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. # # For more genomics resource definitions, see [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) "info": { # A map of additional read group set information. "a_key": [ "", ], }, "name": "A String", # The read group set name. By default this will be initialized to the sample # name of the sequenced data contained in this set. "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read # group set. { # A read group is all the data that's processed the same way by the sequencer. "info": { # A map of additional read group information. This must be of the form # map(string key mapping to a list of string values). "a_key": [ "", ], }, "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length # the sequenced DNA fragment from end-to-end, not including the adapters. "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. "programs": [ # The programs used to generate this read group. Programs are always # identical for all read groups within a read group set. For this reason, # only the first read group in a returned set will have this field # populated. { "prevProgramId": "A String", # The ID of the program run before this one. "commandLine": "A String", # The command line used to run this program. "version": "A String", # The version of the program run. "id": "A String", # The user specified locally unique ID of the program. Used along with # `prevProgramId` to define an ordering between programs. "name": "A String", # The display name of the program. This is typically the colloquial name of # the tool used, for example 'bwa' or 'picard'. }, ], "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. "experiment": { # The experiment used to generate this read group. "sequencingCenter": "A String", # The sequencing center used as part of this experiment. "libraryId": "A String", # 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. "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to # sequencing technology in the SAM spec. "platformUnit": "A String", # 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. }, "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. "id": "A String", # The server-generated read group ID, unique for all read groups. # Note: This is different than the @RG ID field in the SAM spec. For that # value, see name. "datasetId": "A String", # The dataset to which this read group belongs. "description": "A String", # A free-form text description of this read group. }, ], "filename": "A String", # The filename of the original source file for this read group set, if any. "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. "id": "A String", # The server-generated read group set ID, unique for all read group sets. "datasetId": "A String", # The dataset to which this read group set belongs. } updateMask: string, An optional mask specifying which fields to update. Supported fields: * name. * referenceSetId. Leaving `updateMask` unset is equivalent to specifying all mutable fields. x__xgafv: string, V1 error format. Allowed values 1 - v1 error format 2 - v2 error format Returns: An object of the form: { # 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. # # For more genomics resource definitions, see [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) "info": { # A map of additional read group set information. "a_key": [ "", ], }, "name": "A String", # The read group set name. By default this will be initialized to the sample # name of the sequenced data contained in this set. "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read # group set. { # A read group is all the data that's processed the same way by the sequencer. "info": { # A map of additional read group information. This must be of the form # map (string key mapping to a list of string values). "a_key": [ "", ], }, "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length # the sequenced DNA fragment from end-to-end, not including the adapters. "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. "programs": [ # The programs used to generate this read group. Programs are always # identical for all read groups within a read group set. For this reason, # only the first read group in a returned set will have this field # populated. { "prevProgramId": "A String", # The ID of the program run before this one. "commandLine": "A String", # The command line used to run this program. "version": "A String", # The version of the program run. "id": "A String", # The user specified locally unique ID of the program. Used along with # `prevProgramId` to define an ordering between programs. "name": "A String", # The display name of the program. This is typically the colloquial name of # the tool used, for example 'bwa' or 'picard'. }, ], "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. "experiment": { # The experiment used to generate this read group. "sequencingCenter": "A String", # The sequencing center used as part of this experiment. "libraryId": "A String", # 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. "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to # sequencing technology in the SAM spec. "platformUnit": "A String", # 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. }, "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. "id": "A String", # The server-generated read group ID, unique for all read groups. # Note: This is different than the @RG ID field in the SAM spec. For that # value, see name. "datasetId": "A String", # The dataset to which this read group belongs. "description": "A String", # A free-form text description of this read group. }, ], "filename": "A String", # The filename of the original source file for this read group set, if any. "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. "id": "A String", # The server-generated read group set ID, unique for all read group sets. "datasetId": "A String", # The dataset to which this read group set belongs. }
search(body, x__xgafv=None)
Searches for read group sets matching the criteria. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). Args: body: object, The request body. (required) The object takes the form of: { # The read group set search request. "pageToken": "A String", # The continuation token, which is used to page through large result sets. # To get the next page of results, set this parameter to the value of # `nextPageToken` from the previous response. "datasetIds": [ # Restricts this query to read group sets within the given datasets. At least # one ID must be provided. "A String", ], "name": "A String", # Only return read group sets for which a substring of the name matches this # string. "pageSize": 42, # The maximum number of results to return in a single page. If unspecified, # defaults to 256. The maximum value is 1024. } x__xgafv: string, V1 error format. Allowed values 1 - v1 error format 2 - v2 error format Returns: An object of the form: { # The read group set search response. "nextPageToken": "A String", # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of # results. This field will be empty if there aren't any additional results. "readGroupSets": [ # The list of matching read group sets. { # 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. # # For more genomics resource definitions, see [Fundamentals of Google # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) "info": { # A map of additional read group set information. "a_key": [ "", ], }, "name": "A String", # The read group set name. By default this will be initialized to the sample # name of the sequenced data contained in this set. "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read # group set. { # A read group is all the data that's processed the same way by the sequencer. "info": { # A map of additional read group information. This must be of the form # map(string key mapping to a list of string values). "a_key": [ "", ], }, "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length # the sequenced DNA fragment from end-to-end, not including the adapters. "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec. "programs": [ # The programs used to generate this read group. Programs are always # identical for all read groups within a read group set. For this reason, # only the first read group in a returned set will have this field # populated. { "prevProgramId": "A String", # The ID of the program run before this one. "commandLine": "A String", # The command line used to run this program. "version": "A String", # The version of the program run. "id": "A String", # The user specified locally unique ID of the program. Used along with # `prevProgramId` to define an ordering between programs. "name": "A String", # The display name of the program. This is typically the colloquial name of # the tool used, for example 'bwa' or 'picard'. }, ], "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group. "experiment": { # The experiment used to generate this read group. "sequencingCenter": "A String", # The sequencing center used as part of this experiment. "libraryId": "A String", # 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. "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to # sequencing technology in the SAM spec. "platformUnit": "A String", # 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. }, "referenceSetId": "A String", # The reference set the reads in this read group are aligned to. "id": "A String", # The server-generated read group ID, unique for all read groups. # Note: This is different than the @RG ID field in the SAM spec. For that # value, see name. "datasetId": "A String", # The dataset to which this read group belongs. "description": "A String", # A free-form text description of this read group. }, ], "filename": "A String", # The filename of the original source file for this read group set, if any. "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned. "id": "A String", # The server-generated read group set ID, unique for all read group sets. "datasetId": "A String", # The dataset to which this read group set belongs. }, ], }
search_next(previous_request, previous_response)
Retrieves the next page of results. Args: previous_request: The request for the previous page. (required) previous_response: The response from the request for the previous page. (required) Returns: A request object that you can call 'execute()' on to request the next page. Returns None if there are no more items in the collection.