Description

A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.

Input

Name
Description
Pattern

0 ()

1 ()

faa_input (file)

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

gbk_input (file)

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

opt_amp_db (string)

The name of the database to download and set up. This can either be 'DRAMP', 'APD' or 'UniRef100'.

DRAMP|APD|UniRef100

opt_amp_db_dir (directory)

The path to the folder containing the fasta and tsv database files.

path/to/amp_*_database

opt_interproscan (directory)

A path to a file corresponding to the respective tsv files containing protein classifications of the annotated CDSs. The file must be the raw output from InterProScan.

*.tsv

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

ampcombi2/parsetables Documentation

A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.

https://github.com/Darcy220606/AMPcombi/tree/devLicense: MIT
Authors