Compare

Command to run reciprocal blast alignments between the user provided proteomes.

usage: coast compare [-h] [-o OUT] [-e {blast}] [-k KEYWORDS]
                     [--task {blastp,blastp-fast,blastp-short}]
                     [--matrix {BLOSUM45,BLOSUM50,BLOSUM62,BLOSUM80,BLOSUM90,PAM250,PAM70,PAM30}]
                     [--evalue EVALUE] [--gapopen GAPOPEN]
                     [--gapextend GAPEXTEND] [--threads THREADS]
                     [-cont {docker,podman}] [-img IMAGE] [--quiet]
                     [--verbose] [--generate_workspace] [--inplace_workspace]
                     queries [queries ...]

Positional Arguments

queries

Produce the similarity matrices from different GenBanks and FASTAs files. Each represents an organism.

Named Arguments

-o, --out

The directory where the output will be delivered.

Default: “/home/docs/checkouts/readthedocs.org/user_builds/coast-tools/checkouts/latest/docs”

-e, --engine

Possible choices: blast

Alignment Engine.

Default: “blast”

-k, --keywords

This option is only taken into account when a GenBank File is provided, in such cases, it identifies the annotation keywords used to identify proteins, default is only using CDS.

Default: “CDS”

--task

Possible choices: blastp, blastp-fast, blastp-short

Setting for the blast task. Read the BLAST documentation for more information.

--matrix

Possible choices: BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, PAM250, PAM70, PAM30

Scoring matrix

--evalue

E-Value Threshold

--gapopen

Gap open penalty.

--gapextend

Gap extension penalty.

--threads

Number of threads available for the engine to run. Read the respective engine’s documentation for further details.

-cont, --containerization

Possible choices: docker, podman

Containerization system, if not provided will run with local software. It must be OCI complaint. Be sure that your user has docker execution priviliges, so you dont need to provide sudo authorization.

-img, --image

Image for the container to run the selected engine. Be sure that the container contains the actual software installed. If you dont provide a -cont argument, it will be run with docker as default. If your system lacks docker it will error out

--quiet

Deactivate verbose terminal output along the created files.This is already the default behaviour.

Default: False

--verbose

Activate verbose terminal output along the created files.

Default: False

--generate_workspace

Create the workspace inside a named and dated directory.

Default: True

--inplace_workspace

Generate all files straight to the current working directory or the specified directory.

Default: True