Diamond BLASTp

Diamond BLASTp is Diamond's mode for protein sequence searches. For more information, see the tool's GitHub repo and wiki.

Function Call

toolchest.diamond_blastp(
    inputs,
    output_path=None,
    tool_args="",
    is_async=False,
)
toolchest$diamond_blastp(
    inputs,
    output_path = NULL,
    tool_args = "",
    is_async = FALSE
)

Function Arguments

See the Notes section below for more details.

Argument

Use in place of:

Description

inputs

-q, --query

Path to a file that will be passed in as input. This can be a local filepath or an AWS S3 URI.
FASTA or FASTQ formats are supported, as well as gzip-compressed FASTA/FASTQ files.

output_path

-o, --out

(optional) File path where the output will be downloaded.
If omitted, skips download. The outputs can be downloaded manually.

tool_args

all other arguments

(optional) Additional arguments to be passed to Diamond BLASTp. 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.

Diamond BLASTp runs are aligned against the SeqScreen database by default. See the Databases section for more details.

Output Files

A log file from the Diamond run will be outputted in the output_path directory alongside the Diamond BLASTp outputs.

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.

Async runs

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

Tool Versions

Toolchest currently supports version 2.0.14 of Diamond. Every request to run Diamond BLASTp with Toolchest will default to this version.

Databases

Toolchest currently supports the following databases for Diamond BLASTp:

database_name

database_version

Description

diamond_blastp_standard

1

SeqScreen Diamond BLASTx Database. See the SeqScreen wiki for more details.

Supported Additional Arguments

  • -f
  • --fast
  • -l
  • --mid-sensitive
  • --min-orf
  • --more-sensitive
  • --no-self-hits
  • --outfmt
  • --sallseqid
  • --salltitles
  • --sensitive
  • --strand
  • --ultra-sensitive
  • --unal
  • --very-sensitive

Additional arguments can be specified under the tool_args argument.


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