Command line reference for CUGO

Table of contents

• cugo
• context
• cugo_plot
• cugo_select

cugo

usage: aastk cugo [-h] (-f FASTA | -i ID_LIST) -d DB_PATH -r CUGO_RANGE -l FLANK_LOWER -u FLANK_UPPER [--annotation ANNOTATION] [--force] [--top_n TOP_N] [-b BIN_WIDTH] [-y Y_RANGE] [-t TMH_Y_RANGE] [-o OUTPUT] [-n THREADS] [--svg]

Options:

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

Mutually exclusive required arguments:

-f, --fasta FASTA
        Path to FASTA file
-i, --id_list ID_LIST
        Path to list of GlobDB protein IDs

Required arguments:

-d, --db_path DB_PATH
        Path to SQLite database
-r, --cugo_range CUGO_RANGE
        CUGO range of interest for genomic context analysis
-l, --flank_lower FLANK_LOWER
        Start of flanking window (inclusive)
-u, --flank_upper FLANK_UPPER
        End of flanking window (inclusive)

Optional:

--annotation ANNOTATION
        Select annotation from: COG_ID, KEGG_ID, Pfam_ID (default: COG_ID)
--force
        Set flag to overwrite existing files in specified path
--top_n TOP_N
        Number of top COGs to plot per position (default: 3)
-b, --bin_width BIN_WIDTH
        Bin width for amino acid sequence size plotting (default: 50)
-y, --y_range Y_RANGE
        Upper limit for sequence length plot y-axis (default: maximum length)
-t, --tmh_y_range TMH_Y_RANGE
        Upper limit for TMH plot y-axis (default: maximum length)
-o, --output OUTPUT
        Desired output directory (default: current working directory)
-n, --threads THREADS
        Number of threads to be used (default: 1)
--svg
        Generate plot in SVG format

 

context

usage: aastk context [-h] (-f FASTA | -i ID_LIST) -d DB_PATH -r CUGO_RANGE [--annotation ANNOTATION] [-o OUTPUT] [-n THREADS] [--force]

Options:

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

Mutually exclusive required arguments:

-f, --fasta FASTA
        Path to FASTA file
-i, --id_list ID_LIST
        Path to list of GlobDB protein IDs

Required arguments:

-d, --db_path DB_PATH
        Path to SQLite database
-r, --cugo_range CUGO_RANGE
        CUGO range of interest for genomic context analysis

Optional:

--annotation ANNOTATION
        Select annotation from: COG_ID, KEGG_ID, Pfam_ID (default: COG_ID)
-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

 

cugo_plot

usage: aastk cugo_plot [-h] -c CONTEXT_PATH -l FLANK_LOWER -u FLANK_UPPER [--annotation ANNOTATION] [--top_n TOP_N] [--cugo] [--size] [--all_plots] [-b BIN_WIDTH] [-y Y_RANGE] [-t TMH_Y_RANGE] [-o OUTPUT] [--force] [--svg]

Options:

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

Required arguments:

-c, --context_path CONTEXT_PATH
        Path to CUGO context file
-l, --flank_lower FLANK_LOWER
        Start of flanking window (inclusive)
-u, --flank_upper FLANK_UPPER
        End of flanking window (inclusive)

Optional:

--annotation ANNOTATION
        Select annotation from: COG_ID, KEGG_ID, Pfam_ID (default: COG_ID)
--top_n TOP_N
        Number of top COGs to plot per position (default: 3)
--cugo
        Generate CUGO plot
--size
        Generate AA sequence length plot
--all_plots
        Generate a combined plot for CUGO, AA sequence length and TMHMM
-b, --bin_width BIN_WIDTH
        Bin width for amino acid sequence size plotting (default: 50)
-y, --y_range Y_RANGE
        Upper limit for sequence length plot y-axis (default: maximum length)
-t, --tmh_y_range TMH_Y_RANGE
        Upper limit for TMH plot y-axis (default: maximum length)
-o, --output OUTPUT
        Desired output directory (default: current working directory)
--force
        Set flag to overwrite existing files in specified path
--svg
        Generate plot in SVG format

 

cugo_select

usage: aastk cugo_select [-h] -c CONTEXT_PATH -p POSITION -d DB_PATH [-o OUTPUT] [-n THREADS] [--filter_seqs] [--force]

Options:

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

Required arguments:

-c, --context_path CONTEXT_PATH
        Path to CUGO context file
-p, --position POSITION
        CUGO position to retrieve protein IDs for
-d, --db_path DB_PATH
        Path to SQLite database

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-n, --threads THREADS
        Number of threads to be used (default: 1)
--filter_seqs
        Filter datasets in FASTA format for improved homogeneity
--force
        Set flag to overwrite existing files in specified path