v.0.2.2

Patch release to fix some minor bugs found that interferes with pipeline managers (ex. adding a check for the removal of './temp' dir)

v.0.2.1

-- 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.0.2.0

AMPcombi v.0.2.0:
This update was done with extensive scientific advice from Dr. Rosa Herbst.

Changes made include:

• 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 '--_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 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
• 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 piplines

v.0.1.8

Linked to Zenodo archive

v0.1.7

-- Included the possibility of only submitting one .faa file instead of the faa-folder path (in case of summarizing only one single sample)

v0.1.6

This release bumps version to 0.1.6 with these changes included:
-- 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.0.1.5

• 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

AMPcombi v0.1.4

Notable changes:

• 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 multple times to include a list of files from individual samples in multple lists

v0.1.3

latest

pypi package release