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