Command line reference for database utilities

Table of contents

• database
• database_check
• export_fasta

database

usage: aastk database [--help] --cog_gff COG_GFF -k KEGG_GFF -p PFAM_GFF -a ALL_PROTEINS --taxonomy_path TAXONOMY_PATH -c CULTURE_COLLECTION_PATH -h HIGH_LEVEL_ENVIRONMENT_PATH -l LOW_LEVEL_ENVIRONMENT_PATH -g GLOBDB_VERSION [-o OUTPUT] [-t TMHMM_DIR]

Options:

--help
        Show this help message and exit

Required arguments:

--cog_gff COG_GFF
        Path to (.tar.gz) GFF directory containing COG annotations
-k, --kegg_gff KEGG_GFF
        Path to (.tar.gz) GFF directory containing KEGG annotations
-p, --pfam_gff PFAM_GFF
        Path to (.tar.gz) GFF directory containing Pfam annotations
-a, --all_proteins ALL_PROTEINS
        Path to FASTA file containing all GlobDB protein sequences
--taxonomy_path TAXONOMY_PATH
        Path to gzipped taxonomy TSV file
-c, --culture_collection_path CULTURE_COLLECTION_PATH
        Path to culture collection data TSV file
-h, --high_level_environment_path HIGH_LEVEL_ENVIRONMENT_PATH
        Path to high level environment data TSV file
-l, --low_level_environment_path LOW_LEVEL_ENVIRONMENT_PATH
        Path to high level environment data TSV file
-g, --globdb_version GLOBDB_VERSION
        GlobDB version (example: r226)

Optional:

-o, --output OUTPUT
        Desired output directory (default: current working directory)
-t, --tmhmm_dir TMHMM_DIR
        Directory containing tmhmm files

 

database_check

usage: aastk database_check [-h] -d DB_PATH [-o OUTPUT] [--force]

Options:

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

Required arguments:

-d, --db_path DB_PATH
        Path to SQLite database

Optional:

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

 

export_fasta

usage: aastk export_fasta [-h] -d DB_PATH [-o OUTPUT] [-n THREADS] [--force]

Options:

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

Required arguments:

-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)
--force
        Set flag to overwrite existing files in specified path