Changelog

v0.1.0

Initial release.

v0.1.1

  • Minor changes.

v0.1.2

  • Minor changes.

v0.1.3, 10.10.2022

  • PyPi package and conda-recipe / biocontainer release.

v0.1.4, 18.10.2022

  • Included a new optional argument “–complete_summary” to concatenate the results from multiple samples in one table.

  • Added a universal log file to append to an existing log file rather than creating multiple new ones every time a sample is run.

  • The “–path_list” can be called multiple times to include a list of files from individual samples in multiple lists.

v0.1.5, 27.10.2022

  • Adapted reading of HMMER hmmsearch output to deal with varying header lines.

  • Fixed syntax in “if” statements in “check_input.py”.

  • Included “check_faa_path” function to find .faa files also in subdirectories.

v0.1.6, 02.11.2022

  • Included the HTML output for the complete summary.

  • Added option –threads for DIAMOND (make database and alignment).

  • Included check if database was downloaded once to prevent repeated downloads.

v0.1.7, 03.11.2022

  • Added the option to submit a single .faa file instead of the faa-folder path (useful for summarizing a single sample).

v0.1.8, 14.02.2023

  • Linked to Zenodo archive.

v0.2.0, 09.02.2024

  • Changed the output extension from .csv to .tsv.

  • Added a new feature to estimate the isoelectric point, molecular weight, structure fraction, and hydrophobicity.

  • Filtered the DRAMP db .tsv to retain only necessary columns.

  • Added the AMPtransformer and AMPgram tools.

  • Enhanced hmmsearch to parse both single and multi models.

  • Fixed dependencies in the environment.yml file.

  • Created a log file for each sample, in addition to the main log for the complete summary (useful for pipelines like nf-core/funcscan).

  • Added optional –sample_metadata and –contig_metadata flags.

  • Removed –tooldict parameter; added individual parameters for each tool.

  • Added parameters –hmm_evalue, –aminoacid_length, and –db_evalue to filter results based on specific criteria.

  • Renamed –cutoff to –amp_cutoff.

  • Included new parameters for input gbk files, window size for stop codons, transporter searches, and output handling.

  • Added submodules for AMP clustering (using MMSeqs2) and signaling peptide prediction (using SignalP-6.0).

  • Replaced HTML output with a Shiny for Python app accessible via the command line.

  • Updated to subcommands for standardized use.

v0.2.1, 14.03.2024

  • Fixed package versions in setup.

  • Updated readme for installation setup.

  • Fixed ./temp dir removal at the end of the process.

  • Changed the default matrix in DIAMOND blastp to PAM250.

v0.2.2, 21.03.2024

  • Added a check for ./temp dir before attempting removal to prevent issues with pipelines.

v2.0.0, 15.11.2024

  • Added support for using InterProScan output (–use_interproscan and –interproscan_output) to remove AMPs classified as ribosomal proteins.

  • Updated README and added documentation on Read the Docs.

  • Improved DRAMP download script to remove non-amino acid characters.

  • Added APD and UniRef100 databases to enhance AMP classification.

  • Replaced DIAMOND alignment with MMseqs2 search.

  • Fixed “NoneType” error when no AMP hits are retrieved or alignments fail to meet thresholds.

  • Created Read the Docs for AMPcombi documentation.

v2.0.1, 18.11.2024

  • Fixed the python dependencies.

  • Updated version numbers.

v3.0.0, <17.04.2026>

Breaking change (to comply with semantic versioning):

  • Updated behaviour of boolean CLI flags.

  • Replaced --cluster_remove_singletons with --cluster_keep_singletons.

Other changes:

  • Added parameter --write_gbk to make saving of contig sequences optional.

  • Improved behaviour of saving contig sequences: If --write_gbk is activated, contig sequences are saved in one concatenated file instead of multiple individual files.

  • Updated documentation, added column descriptions of AMPcombi summary files.