Metadata-Version: 2.1
Name: AMPcombi
Version: 0.1.2
Summary: A parsing tool for AMP tools.
Home-page: http://pypi.python.org/pypi/AMPcombi/
Author: Anan Ibrahim, Louisa Perelo
Author-email: ananhamido@hotmail.com, louperelo@gmail.com
License: LICENSE.txt
Description: # AMPcombi : Antimicorbial peptides parsing and functional classification tool
        
        # ![Logo](docs/amp-combi-logo.png)
        
        This tool parses the results of amp prediction tools into a single table and aligns the hits against a reference database of antimicrobial peptides for functional classifications.
        
        For parsing: AMpcombi is developed to parse the output of these **amp prediction tools**:
         
        | Tool | Version | Link |
        | ------------- | ------------- | ------------- |
        | Ampir  | 1.1.0  | https://github.com/Legana/ampir |
        | AMPlify  | 1.0.3  | https://github.com/bcgsc/AMPlify |
        | Macrel  | 1.1.0  | https://github.com/BigDataBiology/macrel |
        | HMMsearch  | 3.3.2  | https://github.com/EddyRivasLab/hmmer |
        | EnsembleAMPpred  | - | https://pubmed.ncbi.nlm.nih.gov/33494403/ |
        | NeuBI  | -  | https://github.com/nafizh/NeuBI |
        
        For classification: AMPcombi is developed to offer functional annotation of the detcted AMPs by alignemnt to **AMP reference databases**, for e.g.,:
        
        | Tool | Version | Link |
        | ------------- | ------------- | ------------- |
        | DRAMP  | 3.0 | https://github.com/CPU-DRAMP/DRAMP-3.0 |
        
        Alignment to the reference database is done using [diamond blastp v.2.0.15](https://www.nature.com/articles/s41592-021-01101-x)
        
        ======================
        ## Installation
        ======================
        
        To install AMPcombi:
        
        Add dependencies of the tool; python > 3.0, biopython, pandas and diamond.
        Installation can be done using:
        
         - pip installation
        ```
        pip install AMPcombi
        ```
         - git repository
         ```
         git clone https://github.com/Darcy220606/AMPcombi.git
         ```
         - conda
        ```
        conda env create -f ampcombi/environment.yml
        ```
        or
        ```
         conda install AMPcombi
        ```
        
        ======================
        ## Usage:
        ======================
        
        There are two basic commands to run AMPcombi:
        
        1. Using `--amp_results`
        ```console
        ampcombi --amp_results path/to/my/result_folder/
        ```
        
        Here the head folder containing output files has to be given. AMPcombi finds and summarizes the output files from different tools, if the folder is structured  and named as: `/result_folder/toolsubdir/samplesubdir/sample.tool.filetype`.
         - Note that the filetype ending might vary and can be specified with `--tooldict`, if it is different from the default.
        
        
        ```console
        amp_results/
        ├── tool_1/
        |   ├── sample_1/
        |   |   └── sample_1.tool_1.tsv
        |   └── sample_2/
        |   |   └── sample_2.tool_1.tsv
        ├── tool_2/
        |   ├── sample_1/
        |   |   └── sample_1.tool_2.txt
        |   └── sample_2/
        |   |   └── sample_2.tool_2.txt
        ├── tool_3/
            ├── sample_1/
            |   └── sample_1.tool_3.predict
            └── sample_2/
                └── sample_2.tool_3.predict
        ```
        
        2. Using `--path_list` and `--sample_list`
        
        ```console
        ampcombi --path_list [[list of paths to sample_1-outputs][list of paths to sample_2-outputs]] --sample_list [sample_1, sample_2] 
        ```
        
        Here the paths to the output-files to be summarized can be given as a list for each sample. Together with this option a list of sample-names has to be supplied.
        
        
        ### Input options:
        | command | definition | default | example |
        | ------------- | ------------- | ------------- | ------------- |
        | --amp_results | path to the folder containing different tool's output files | ./test_files/ | ../amp_results |
        | --sample_list  | list of samples' names | [] | [sample_1, sample_2] |
        | --path_list  | list of paths to output files | [] | [[paths to sample_1 output], [paths to sample_2 outputs]] |
        | --outdir  | name of the output directory | ./ampcombi_results/ | ./ampcombi_results/ |
        | --cutoff  | probability cutoff to filter AMPs | 0 | 0.5 |
        | --faa_folder  | path to the folder containing the samples` .faa files, Filenames have to contain the corresponding sample-name, i.e. sample_1.faa | ./test_faa/ | ./faa_files/|
        | --tooldict | dictionary of AMP-tools and their respective output file endings | {'ampir':'ampir.tsv', 'amplify':'amplify.tsv', 'macrel':'macrel.tsv', 'hmmer_hmmsearch':'hmmsearch.txt', 'ensembleamppred':'ensembleamppred.txt'} | - |
        | --amp_database | path to the folder containing the reference database files: (1) a fasta file with <.fasta> file extension and (2) the corresponding table with with functional and taxonomic classifications in <.tsv> file extension | [DRAMP 'general amps'](http://dramp.cpu-bioinfor.org/downloads/) database | ./amp_ref_database/ |
        
         - Note: The fasta file corresponding to the AMP database should not contain any characters other than ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W',',Y']
          - Note: The refernce database table should be tab delimited.
        
        
        ======================
        ## Contribution:
        ======================
        
        AMPcombi is a tool developed for parsing results from published AMP prediction tools. We therfore welcome fellow contributers who would like to add new AMP prediction tools results for parsing and alignment.
        
        ### Adding a new tool to AMPcombi
        In `ampcombi/reformat_tables.py` 
        - add a new tool function to read the output to a pandas dataframe
        - add the new function to the `read_path` function
        
        
        In `ampcombi/main.py`
        - add your default `tool:tool.fileending`to the default of `--tooldict`
        
        
        ======================
        
        
        **Authors**: @louperelo and @darcy220606
        
Keywords: Proteomics,Antimicrobial peptides,DiamondStandardization,Formatting,Functional annotation
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Description-Content-Type: text/markdown
