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

tc.rapsearch2(
    inputs,
    output_path=None,
    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 one or more files to use as input. The files can be a local or remote, see Using Files.
output_path	-o	(optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see Using Files.
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 Async Runs for more.

*See the Databases section for more details.

Tool Versions

Toolchest currently supports version 2.24 of RAPSearch2.

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.