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Darcy220606 · Oct 6, 2022 · 9eab25b · 9eab25b
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@@ -3,10 +3,142 @@ Name: AMPcombi
 Version: 0.1.0
 Summary: A parsing tool for AMP tools.
 Home-page: http://pypi.python.org/pypi/AMPcombi/
-Author: Anan Ibrahim and Louisa Perelo
-Author-email: ananhamido@hotmail.com and louisa.perelo@gmail.com
+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
@@ -20,162 +152,6 @@ 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-InformaticsTopic :: Scientific/Engineering :: Information Analysis
-License-File: LICENSE.txt
-
-# 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
-``` 
-
- and the latest release can be installed directly from pip, conda, docker, this repository, or from the galaxy toolshed:
-
-pip install hAMRonization
-PyPI version PyPI downloads
-
-Or
-
-conda create --name hamronization --channel conda-forge --channel bioconda --channel defaults hamronization
-version-on-conda conda-download last-update-on-conda
-
-Or to install using docker:
-
-docker pull finlaymaguire/hamronization:latest
-Or to install the latest development version:
-
-git clone https://github.com/pha4ge/hAMRonization
-pip install hAMRonization
-### For pip installation
-
-
-
-
-
-### Create conda environment
-
-
-======================
-## 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
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Description-Content-Type: text/markdown
diff --git a/AMPcombi.egg-info/SOURCES.txt b/AMPcombi.egg-info/SOURCES.txt
@@ -1,4 +1,3 @@
-LICENSE.txt
 README.md
 setup.py
 AMPcombi.egg-info/PKG-INFO

diff --git a/AMPcombi.egg-info/entry_points.txt b/AMPcombi.egg-info/entry_points.txt
@@ -1,2 +1,3 @@
 [console_scripts]
 ampcombi = ampcombi:main
+
diff --git a/MANIFEST.txt b/MANIFEST.txt
diff --git a/ampcombi_results/amp_ref_database/amp_ref.dmnd b/ampcombi_results/amp_ref_database/amp_ref.dmnd