Search¶
Command to orchestrate a whole proteome search using blast or diamond, against local or remote protein sequence databases. It retains the options for taxonomic filtering, provided by the alignment tools.
usage: coast search [-h] [-o OUT] [-e {blast,diamond}] [-k KEYWORDS]
[--taxidlist TAXIDLIST | --taxonlist TAXONLIST]
[--task {blastp,blastp-fast,blastp-short} | --sens {mid-sensitive,sensitive,more-sensitive,very-sensitive,ultra-sensitive}]
[--matrix {BLOSUM45,BLOSUM50,BLOSUM62,BLOSUM80,BLOSUM90,PAM250,PAM70,PAM30}]
[--evalue EVALUE] [--gapopen GAPOPEN]
[--gapextend GAPEXTEND] [--threads THREADS]
[-cont {docker,podman}] [-img IMAGE] [-w WEB]
[--email EMAIL] [--quiet] [--verbose]
[--generate_workspace] [--inplace_workspace]
database query
Positional Arguments¶
- database
Directory for the database against which the query will be run.
- query
Produce the similarity matrices from a GenBank or FASTA file.
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, diamond
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”
- --taxidlist
File with NCBI taxonomic IDs to filter the database by.
- --taxonlist
Comma-separated list of NCBI taxonomic IDs to filter the database by.
- --task
Possible choices: blastp, blastp-fast, blastp-short
Setting for the blast task. Read the BLAST documentation for more information.
- --sens
Possible choices: mid-sensitive, sensitive, more-sensitive, very-sensitive, ultra-sensitive
Setting for the diamond align tool sensibility.
- --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.
Default: “docker”
- -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
- -w, --web
Merlin server address.
Default: “http://rosalind.di.uminho.pt:6082/”
Email for the Merlin server run.
- --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