Description
A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.
Input
The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa
*.faa
The path to the file corresponding to the respective annotated files with either '.gbk' or '.gbff' extensions. File names must contain the corresponding sample name, i.e. sample_1.faa where "sample_1" is the sample name.
*.gbk
The name of the database to download and set up. This can either be 'DRAMP', 'APD' or 'UniRef100'.
DRAMP|APD|UniRef100
The path to the folder containing the fasta and tsv database files.
path/to/amp_*_database
Tools
ampcombi2/parsetables Documentation
A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.