Command line reference for Meta
Table of contents
meta
usage: aastk meta [-h] -d DB_PATH -f FASTA [-o OUTPUT] [-n THREADS] [--include_annotation] [--include_culture_collection] [--include_high_level_environment] [--include_low_level_environment] [--include_taxonomy] [--all_metadata] [--force]
Options:
-h, --help
Show this help message and exit
Required arguments:
-d, --db_path DB_PATH
Path to SQLite database-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)--include_annotation
Include annotation metadata in output--include_culture_collection
Include culture collection metadata in output--include_high_level_environment
Include high level environment metadata in output--include_low_level_environment
Include low level environment metadata in output--include_taxonomy
Include taxonomy metadata in output--all_metadata
Include all metadata in output file--force
Set flag to overwrite existing files in specified path
list_metadata
Protein metadata
Sequence information
- parent_ID
- aa_length
- strand
Annotations
- COG_ID
- KEGG_ID
- Pfam_ID
- Predicted transmembrane helixes
Genome metadata
Taxonomy
- genome_ID
- domain
- phylum
- class
- order_tax
- family
- genus
- species
Culture information
- culture_collection
High-level environment data
- animal_associated
- aquatic
- built
- other
- sediment
- soil
- unassigned_high_level
Low-level environment data
- human
- invertebrate
- other_vertebrate
- unspecified_animal
- aquatic_other
- aquatic_unspecified
- freshwater
- groundwater
- marine
- built_other
- drinking_water
- wastewater
- air
- bacteria
- eukaryote_other
- food
- geothermal
- hypersaline
- other_unspecified
- plant_associated
- subsurface
- synthetic
- viral
- freshwater_sediment
- marine_sediment
- sediment_unspecified
- desert
- forest
- rhizosphere
- soil_agricultural
- soil_other
- soil_unspecified
- tundra_wetland
- unassigned_low_level