Metadata-Version: 2.1
Name: apclusterv
Version: 1.0.0
Home-page: https://github.com/hbyaoherbert/Apclusterv.git
Author: haobinherbert
Author-email: haobinherbert@163.com
License: Apache
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# Apclusterv: Clustering viral genomes with Affinity Propagation
This software works in Python3.<br>
## Dependencies:<br>
   python>=3.7<br>
   pandas<br>
   numpy<br>
   networkx >= 2.8.4 <br>
   scipy >=1.8.1<br>
   scikit-learn >= 1.1.2<br>
   MCL <br>
   diamond >= 0.9.34 <br>
   prodigal >= 2.6.3<br>
   R>=3.6.1<br>
   
## Installation: <br>
   Suppose you are in a conda environment, you need to install MCL, prodigal (for ORF prediction),diamond (for alignment) and R(if not already installed, we just need stats library in r-base)
   ```bash
   conda install diamond -c bioconda 
   conda install mcl -c bioconda
   conda install prodigal -c bioconda
   conda install r-base 
   
   pip install apclusterv 
   ```
## Getting Started:<br>

   step1. preduct ORFs from the DNA file with the following command:  <br>
   ```bash
   prepare contig_dna_fasta 
   ```
   (contig_dna_fasta is the path to the dna sequences for clustering)
   
   step2. execute clustering with the following command:
   ```bash
   apclusterv contig_dna_fasta 
   ```
## Results <br>
   The program will create tmp/ directory. The clustering result is tmp/cluster_result.I.A.csv
   (cluster_result.3.10.csv by default)

