Command line reference for CASM

Table of contents

• casm
• matrix
• cluster
• casm_plot
• casm_select

casm

usage: aastk casm [-h] (--subset SUBSET | --subset_size SUBSET_SIZE) --fasta FASTA [-n THREADS] [-o OUTPUT] [-d DB_PATH] [-p PERPLEXITY] [-i ITERATIONS] [--exaggeration EXAGGERATION] [--metadata_protein METADATA_PROTEIN] [--force] [-e EARLY_CLUST] [-f FULL_CLUST] [-m MATRIX_PATH] [--metadata_matrix METADATA_MATRIX] [--keep] [-s] [--svg]

Options:

-h, --help
        Show this help message and exit

Mutually exclusive required arguments:

--subset SUBSET
        Path to subset fasta to use as DIAMOND alignment reference set
--subset_size SUBSET_SIZE
        Number of sequences to randomly subset from input FASTA file

Required arguments:

--fasta FASTA
        Path to FASTA file

Optional:

-n, --threads THREADS
        Number of threads to be used (default: 1)
-o, --output OUTPUT
        Desired output directory (default: current working directory)
-d, --db_path DB_PATH
        Path to SQLite database
-p, --perplexity PERPLEXITY
        Perplexity value for tSNE clustering
-i, --iterations ITERATIONS
        Number of clustering iterations
--exaggeration EXAGGERATION
        Exaggeration value for tSNE clustering
--metadata_protein METADATA_PROTEIN
        Select metadata for plotting; run "aastk metadata_categories" to view available categories
--force
        Set flag to overwrite existing files in specified path
-e, --early_clust EARLY_CLUST
        Path to early clustering TSV file
-f, --full_clust FULL_CLUST
        Path to full clustering TSV file
-m, --matrix_path MATRIX_PATH
        Path to .npy file containing alignment matrix
--metadata_matrix METADATA_MATRIX
        Path to matrix metadata file
--keep
        Keep intermediate files in specified paths
-s, --show
        Show cluster number at cluster centers in output plots
--svg
        Generate plot in SVG format

 

matrix

usage: aastk matrix [-h] (-s SUBSET | --subset_size SUBSET_SIZE) -f FASTA [-o OUTPUT] [-n THREADS] [--force]

Options:

-h, --help
        Show this help message and exit

Mutually exclusive required arguments:

-s, --subset SUBSET
        Path to subset fasta to use as DIAMOND alignment reference set
--subset_size SUBSET_SIZE
        Number of sequences to randomly subset from input FASTA file

Required arguments:

-f, --fasta FASTA
        Path to FASTA file

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-n, --threads THREADS
        Number of threads to be used (default: 1)
--force
        Set flag to overwrite existing files in specified path

 

cluster

usage: aastk cluster [-h] -m MATRIX_PATH --metadata_matrix METADATA_MATRIX [-o OUTPUT] [-p PERPLEXITY] [-i ITERATIONS] [-e EXAGGERATION] [-n THREADS] [--force]

Options:

-h, --help
        Show this help message and exit

Required arguments:

-m, --matrix_path MATRIX_PATH
        Path to .npy file containing alignment matrix
--metadata_matrix METADATA_MATRIX
        Path to matrix metadata file

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-p, --perplexity PERPLEXITY
        Perplexity value for tSNE clustering
-i, --iterations ITERATIONS
        Number of clustering iterations
-e, --exaggeration EXAGGERATION
        Exaggeration value for tSNE clustering
-n, --threads THREADS
        Number of threads to be used (default: 1)
--force
        Set flag to overwrite existing files in specified path

 

casm_plot

usage: aastk casm_plot [-h] -e EARLY_CLUST -f FULL_CLUST [-o OUTPUT] [-d DB_PATH] [--metadata_protein METADATA_PROTEIN] [-s] [--svg] [--force]

Options:

-h, --help
        Show this help message and exit

Required arguments:

-e, --early_clust EARLY_CLUST
        Path to early clustering TSV file
-f, --full_clust FULL_CLUST
        Path to full clustering TSV file

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-d, --db_path DB_PATH
        Path to SQLite database
--metadata_protein METADATA_PROTEIN
        Select metadata for plotting; run "aastk metadata_categories" to view available categories
-s, --show
        Show cluster number at cluster centers in output plots
--svg
        Generate plot in SVG format
--force
        Set flag to overwrite existing files in specified path

 

casm_select

usage: aastk casm_select [-h] --full_clust FULL_CLUST -f FASTA -n NO_CLUSTER [-o OUTPUT] [--force]

Options:

-h, --help
        Show this help message and exit

Required arguments:

--full_clust FULL_CLUST
        Path to full clustering TSV file
-f, --fasta FASTA
        Path to FASTA file
-n, --no_cluster NO_CLUSTER
        Number of cluster of choice in TSV file

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
--force
        Set flag to overwrite existing files in specified path