modules/ampcombi
A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.
Description
A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.
Input
The path to the directory containing the results for the AMP tools for each sample processed 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 Output
The output directory that contains the summary output and related alignment files for one sample.
/* 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 and the corresponding taxonomic and functional classification from the alignment step.
/*/*_ampcombi.csv A file that concatenates all samples ampcombi summaries. This is activated with --complete_summary true.
AMPcombi_summary.csv A file that concatenates all samples ampcombi summaries. This is activated with --complete_summary true.
AMPcombi_summary.html A log file that captures the standard output ina log file. Can be activated by --log.
*.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 
