modules/ampcombi2_parsetables
A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.
Description
A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.
Input
The path to the directory containing the results for the AMP tools for each processed sample or a list of files corresponding to each file generated by AMP tools.
[*amptool.tsv, *amptool.tsv] 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 Output
The output directory that contains the summary output and related alignment files for one sample.
/* The output subdirectory that contains the gbk files containing the AMP hits for each sample.
/*/contig_gbks An alignment file containing the results from the DIAMOND alignment step done on all AMP hits.
/*/*_diamond_matches.txt A file containing the summary report of all predicted AMP hits from all AMP tools given as input, the corresponding taxonomic and functional classification from the alignment step and the estimated physiochemical properties.
/*/*_ampcombi.tsv A log file that captures the standard output per sample in a log file. Can be activated by --log.
/*/*.log A log file that captures the standard output for the entire process in a log file. Can be activated by --log.
Ampcombi_parse_tables.log If the AMP reference database is not provided by the user using the flag `—amp_database’, by default the DRAMP database will be downloaded, filtered and stored in this folder.
/amp_ref_database AMP reference database converted to DIAMOND database format.
/amp_ref_database/*.dmnd AMP reference database fasta file, cleaned of diamond-uncompatible characters.
/amp_ref_database/*.clean.fasta AMP reference database in tsv-format with two columns containing header and sequence.
/amp_ref_database/*.tsv maintainer
