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[ aws . omics ]

list-read-sets¶

Description¶

Retrieves a list of read sets.

Synopsis¶

  list-read-sets
--sequence-store-id <value>
[--filter <value>]
[--cli-input-json <value>]
[--starting-token <value>]
[--page-size <value>]
[--max-items <value>]
[--generate-cli-skeleton <value>]
[--debug]
[--endpoint-url <value>]
[--no-verify-ssl]
[--no-paginate]
[--output <value>]
[--query <value>]
[--profile <value>]
[--region <value>]
[--version <value>]
[--color <value>]
[--no-sign-request]
[--ca-bundle <value>]
[--cli-read-timeout <value>]
[--cli-connect-timeout <value>]

Options¶

--sequence-store-id (string)

The jobs' sequence store ID.

--filter (structure)

A filter to apply to the list.

name -> (string)

A name to filter on.

status -> (string)

A status to filter on.

referenceArn -> (string)

A genome reference ARN to filter on.

createdAfter -> (timestamp)

The filter's start date.

createdBefore -> (timestamp)

The filter's end date.

sampleId -> (string)

The read set source's sample ID.

subjectId -> (string)

The read set source's subject ID.

generatedFrom -> (string)

Where the source originated.

creationType -> (string)

The creation type of the read set.

Shorthand Syntax:

name=string,status=string,referenceArn=string,createdAfter=timestamp,createdBefore=timestamp,sampleId=string,subjectId=string,generatedFrom=string,creationType=string

JSON Syntax:

{
  "name": "string",
  "status": "ARCHIVED"|"ACTIVATING"|"ACTIVE"|"DELETING"|"DELETED"|"PROCESSING_UPLOAD"|"UPLOAD_FAILED",
  "referenceArn": "string",
  "createdAfter": timestamp,
  "createdBefore": timestamp,
  "sampleId": "string",
  "subjectId": "string",
  "generatedFrom": "string",
  "creationType": "IMPORT"|"UPLOAD"
}

--cli-input-json (string) Performs service operation based on the JSON string provided. The JSON string follows the format provided by --generate-cli-skeleton. If other arguments are provided on the command line, the CLI values will override the JSON-provided values. It is not possible to pass arbitrary binary values using a JSON-provided value as the string will be taken literally.

--starting-token (string)

A token to specify where to start paginating. This is the NextToken from a previously truncated response.

For usage examples, see Pagination in the AWS Command Line Interface User Guide .

--page-size (integer)

The size of each page to get in the AWS service call. This does not affect the number of items returned in the command's output. Setting a smaller page size results in more calls to the AWS service, retrieving fewer items in each call. This can help prevent the AWS service calls from timing out.

For usage examples, see Pagination in the AWS Command Line Interface User Guide .

--max-items (integer)

The total number of items to return in the command's output. If the total number of items available is more than the value specified, a NextToken is provided in the command's output. To resume pagination, provide the NextToken value in the starting-token argument of a subsequent command. Do not use the NextToken response element directly outside of the AWS CLI.

For usage examples, see Pagination in the AWS Command Line Interface User Guide .

--generate-cli-skeleton (string) Prints a JSON skeleton to standard output without sending an API request. If provided with no value or the value input, prints a sample input JSON that can be used as an argument for --cli-input-json. If provided with the value output, it validates the command inputs and returns a sample output JSON for that command.

Global Options¶

--debug (boolean)

Turn on debug logging.

--endpoint-url (string)

Override command's default URL with the given URL.

--no-verify-ssl (boolean)

By default, the AWS CLI uses SSL when communicating with AWS services. For each SSL connection, the AWS CLI will verify SSL certificates. This option overrides the default behavior of verifying SSL certificates.

--no-paginate (boolean)

Disable automatic pagination.

--output (string)

The formatting style for command output.

json
text
table

--query (string)

A JMESPath query to use in filtering the response data.

--profile (string)

Use a specific profile from your credential file.

--region (string)

The region to use. Overrides config/env settings.

--version (string)

Display the version of this tool.

--color (string)

Turn on/off color output.

on
off
auto

--no-sign-request (boolean)

Do not sign requests. Credentials will not be loaded if this argument is provided.

--ca-bundle (string)

The CA certificate bundle to use when verifying SSL certificates. Overrides config/env settings.

--cli-read-timeout (int)

The maximum socket read time in seconds. If the value is set to 0, the socket read will be blocking and not timeout. The default value is 60 seconds.

--cli-connect-timeout (int)

The maximum socket connect time in seconds. If the value is set to 0, the socket connect will be blocking and not timeout. The default value is 60 seconds.

Examples¶

Note

To use the following examples, you must have the AWS CLI installed and configured. See the Getting started guide in the AWS CLI User Guide for more information.

Unless otherwise stated, all examples have unix-like quotation rules. These examples will need to be adapted to your terminal's quoting rules. See Using quotation marks with strings in the AWS CLI User Guide .

To get a list of read sets

The following list-read-sets example gets a list of read sets for a sequence store with id 1234567890.

aws omics list-read-sets \
    --sequence-store-id 1234567890

Output:

{
    "readSets": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890/readSet/1234567890",
            "creationTime": "2022-11-23T21:55:00.515Z",
            "fileType": "FASTQ",
            "id": "1234567890",
            "name": "HG00146",
            "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "sampleId": "fastq-sample",
            "sequenceStoreId": "1234567890",
            "status": "ACTIVE",
            "subjectId": "fastq-subject"
        }
    ]
}

For more information, see Omics Storage in the Amazon Omics Developer Guide.

Output¶

nextToken -> (string)

A pagination token that's included if more results are available.

readSets -> (list)

A list of read sets.

(structure)

A read set.

id -> (string)

The read set's ID.

arn -> (string)

The read set's ARN.

sequenceStoreId -> (string)

The read set's sequence store ID.

subjectId -> (string)

The read set's subject ID.

sampleId -> (string)

The read set's sample ID.

status -> (string)

The read set's status.

name -> (string)

The read set's name.

description -> (string)

The read set's description.

referenceArn -> (string)

The read set's genome reference ARN.

fileType -> (string)

The read set's file type.

sequenceInformation -> (structure)

Details about a sequence.

totalReadCount -> (long)

The sequence's total read count.

totalBaseCount -> (long)

The sequence's total base count.

generatedFrom -> (string)

Where the sequence originated.

alignment -> (string)

The sequence's alignment setting.

creationTime -> (timestamp)

When the read set was created.

statusMessage -> (string)

The status for a read set. It provides more detail as to why the read set has a status.

creationType -> (string)

The creation type of the read set.

etag -> (structure)

The entity tag (ETag) is a hash of the object representing its semantic content.

algorithm -> (string)

The algorithm used to calculate the read set’s ETag(s).

source1 -> (string)

The ETag hash calculated on Source1 of the read set.

source2 -> (string)

The ETag hash calculated on Source2 of the read set.

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