CHANGES.txt

v<0.1.0>, <date> -- Initial release.
v<0.1.1>, <date> -- minor changes.
v<0.1.2>, <date> -- minor changes.
v<0.1.3>, <10.10.2022> -- PyPi package and conda-recipe / biocontainer release.
v<0.1.4>, <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
v<0.1.5>, <27.10.2022> -- Initial release.
    -- adapt reading of hmmer_hmmsearch output to deal with varying header lines
    -- fix syntax in "if" statements in "check_input.py"
    -- include "check_faa_path" function, to find .faa files also in subdirectories
v<0.1.6>, <02.11.2022>
    -- Included the HTML output for the complete summary
    -- add option --threads for diamond (make database and alignment)
    -- included check if database was downloaded once to not download again
v<0.1.7>, <03.11.2022>
    -- Included the possibility of only submitting one .faa file instead of the faa-folder path (in case of summarizing only one single sample)
v<0.1.8>, <14.02.2023>
    -- Linked to Zenodo archive
v<0.2.0>, <09.02.2024>
    -- Change the output extension from `.csv` to `.tsv`
    -- Added a new feature to estimate the isoelectric point, mwt, structure fraction and hydrophobicity
    -- The DRAMP db `.tsv` was filtered to retain only necessary columns
    -- Added the tool AMPtransformer
    -- Added the tool AMPgram
    -- Fixed hmmsearch to now parse both single and multi models
    -- Fixed the dependencies in the environment.yml file
    -- Added a log file for each sample, besides the main log for the complete summary. Beneficial when used in pipelines like nf-core/funcscan
    -- Added the parameter '--sample_metadata' an optional flag to add a file with sample metadata
    -- Added the parameter '--contig_metadata' an optional flag to add a file with contig metadata
    -- Removed tooldictionary parameter '--tooldict' and added a parameter for each tool instead '--<tool>_file' to assign the extension of the files per tool
    -- Added the parameter `--hmm_evalue` to filter the hmm results in the table based on E-value
    -- Added the parameter `--aminoacid_length` to retain hits with a specific length
    -- Added the parameter `--db_evalue` to filter out classification hits below specific diamond E-values
    -- Renamed the parameter `--cutoff` to `--amp_cutoff`
    -- Added the parameter '--gbk' to add gbk files as input for parsing to include contig ids and other important values
    -- Added the parameter '--window_size_stop_codon' that adjusts the window size to look for stop codons
    -- Added the parameter '--remove_stop_codons' that removes hits with no stop codons found in the vicinity
    -- Added the parameter '--window_size_transporter' that adjusts the window size to look for 'transporter' proteins
    -- Added a new output directory per sample that holds the gbk files for the contigs with hits
    -- Added the submodule to cluster the AMP hits with the parameters to modify the clustering using [MMSeqs2](https://github.com/soedinglab/MMseqs2) for e.g., '--cluster_cov_mode' '--cluster_mode' '--cluster_coverage' '--cluster_seq_id' '--cluster_sensitivity' '--cluster_remove_singletons' '--cluster_retain_label' '--cluster_min_member'
    -- Added the submodule to predict signaling peptide using [SignalP-6.0h](https://services.healthtech.dtu.dk/services/SignalP-6.0/)
    -- Removed the HTML output for the complete summary and replaced it with  shiny for python app that can be viewed using the commandline
    -- Updated AMPcombi to use subcommands for ease of use with standardized and portable pipelines
v<0.2.1>, <14.03.2024>
    -- Fixed the package versions in setup
    -- Adjusted readme for installation setup
    -- Fixed the `./temp` dir removal step at the end of the process
    -- Changed the default matrix in diamond blastp to PAM250
v<0.2.2>, <21.03.2024>
    -- Added a check if ./temp dir is found before removal. This caused problems with pipeline setups
v<2.0.0>, <XX.11.2024>
    -- Added the function to use the output from [InterProScan](https://github.com/ebi-pf-team/interproscan) if supplied with `--use_interproscan` and `--interproscan_output` to remove any AMPs classified as ribosomal proteins
    -- Fix DRAMP download script to remove any non aminoacid characters  
    -- Added APD and UniRef100 databases to identify the AMP classes
    -- Removed DIAMOND alignment and replaced it by MMseqs2 search
    -- Fixed error 'Nonetype' when no AMP hits are retrieved by teh set thresholds or no AMP hits aligned to the database chosen
    -- Created Read the Docs for AMPcombi documentation