Skip to content

Latest commit

 

History

History
73 lines (49 loc) · 2.14 KB

README.md

File metadata and controls

73 lines (49 loc) · 2.14 KB

An R-interface for the IRIDA API

This is an R package that wraps the IRIDA API.

Currently, it supports querying an IRIDA project for its samples, and can retrieve sequence information for a given sample.

Configuration

To access the IRIDA api, you will need an API client ID and API secret, as well as your username and password. Ask your IRIDA system administrator for these. In addition, you will need to supply the irida API link. These read into the package via a configuration file, by default config.yml in the root directory:

default:
  irida-api-url:
  irida-user: 
  irida-api-client: 
  irida-api-secret:

You can supply the path to your own configuration file from R:

options(RiRida.config_path = "/path/to/config.yml")

Usage

To retrieve all samples and basic metadata from a project that you have permission to access, supply the IRIDA project ID (the numerical ID, e.g., 123)

project_samples(project_id = 123)

To retrieve the sequences associated with a sample, supply a sample ID (or vector of sample IDs). Note that this function queries an IRIDA API in parallel to speed up retrieval if you have a lot of samples to investigate. To limit (or speed up) retrieval, set the n_con parameter to an appropriate number of simultaneous connections.

get_all_sequence_info(samples = c(1,2,3,4,5), n_con = 10)

This function formats the response from the API into a dataframe. In case you want more fine control over e.g., the formatting of the response, you can use some helper functions along with httr2 functions. For example, for sequence retrieval of a single IRIDA sample:

req_irida_sequences(sample_id = 12, type = "all") |> # Helper function
    httr2::req_perform() |> 
    httr2::resp_body_json() # httr2 functions for API interaction

Here, the details of accessing the IRIDA api are wrapped into req_irida_sequences(). Using type = "all" requests a list of all sequences associated with the sample, while type = "pairs" requests only paired end sequences. The rest of the API call and retrieval can be handled by the user using httr2 functions.