RAPSearch2 is an aligner for protein similarity searches. It aligns DNA reads or protein sequences against a protein database. For more information, see the tool's homepage, GitHub repo,. and Sourceforge page.

Function Call

toolchest.rapsearch2(
    inputs,
    output_path=None,
    database_name="rapsearch2_seqscreen",
    database_version="1",
    tool_args="",
    is_async=False,
)

toolchest$rapsearch2(
    inputs,
    output_path = NULL,
    database_name = "rapsearch2_seqscreen",
    database_version = "1",
    tool_args = "",
    is_async = FALSE
)

Function Arguments

See the Notes section below for more details.

Argument	Use in place of:	Description
`inputs`	`-q`	Path to a file that will be passed in as input. This can be a local filepath or an AWS S3 URI.
`output_path`	`-o`	(optional) Base path (directory) to where the outputs will be downloaded. (Functions identically to RAPSearch2's `-o` argument). If omitted, skips download. The outputs can be downloaded manually.
`database_name`	`-d`*	(optional) Name of database to use for RAPSearch2 alignment. Defaults to `"GRCh38"` (human genome).
`database_version`	`-d`*	(optional) Version of database to use for RAPSearch2 alignment. Defaults to `"1"`.
`tool_args`	all other arguments	(optional) Additional arguments to be passed to RAPSearch2. This should be a string of arguments like the command line. See Supported Additional Arguments for more details.
`is_async`		Whether to run a job asynchronously.

*See the Databases section for more details.

Return Value

This function call returns a Toolchest output object, which contains the run ID and locations of downloaded output files. See Output Objects for more details.

Notes

Amazon AWS S3 inputs

Publicly available files stored on AWS's S3 service can be passed in as inputs, using the file's S3 URI.

For private files, Toolchest must have access to the file.

Async runs

Set the is_async parameter to true if you would like to run a RAPSearch2 job asynchronously. See Async Runs for more information.

Tool Versions

Toolchest currently supports version 2.24 of RAPSearch2. Every request to run RAPSearch2 with Toolchest will default to this version.

Databases

Toolchest currently supports the following databases for RAPSearch2:

`database_name`	`database_version`	Description
`rapsearch_seqscreen`	`1`	SeqScreen RAPSearch2 Database. See the SeqScreen wiki for more details.

Supported Additional Arguments

-a
-b
-e
-g
-i
-l
-p
-s
-t
-v
-w
-x

Additional arguments can be specified under the tool_args argument.