Metadata-Version: 2.1
Name: MHC-Annotation
Version: 0.0.8
Summary: UNKNOWN
Home-page: https://github.com/DiltheyLab/MHC-annotation
Author: Torsten Houwaart
Author-email: houwaart@hhu.de
License: MIT
Description: # MHC-annotation
        Tools to annotate haplotypes of MHC with gene and transcript information 
        
        ## Dependencies
        There is only a few dependencies which you have to take care of yourself. 
        
        ### conda environment
        The easiest way to take of these dependencies is to utilize the environment.yml in this repository to create a conda environment.
        `conda create --name mhca -f environment_mhca.yml`
        
        ### manually
        The script assumes that you have **minimap2** installed and that it is callable with `minimap2` on the command line.
        There are several ways to install this dependency depending on your environment. Giving two examples:
        - `sudo apt-get install minimap2`
        - `conda install -c bioconda minimap2`
        
        You will also need the python packages *biopython* and *bcbio-gff*. You can install them in a conda environment with:
        
        - `conda install -c bioconda bcbio-gff`
        - `conda install -c bioconda biopython`
        
        ## Install
        Install this package with pip.
        
        `pip install MHC-annotation`
        
        ## Usage
        
        This tools assumes that you are trying to annotate a sequence that stems from the human MHC region (also known as: HLA-region). If you supply any other sequence, you will most likely receive no meaningful result.
        You can annotate a fasta file with the following command:
        
        `mhca annotate <your_sequence.fa> <output_folder>`
        
        You can check whether the transcript in the resulting gff file would produce meaningful products.
        
        `mhca check_CDS <your_sequence.fa> <output_folder/your_sequence.gff>`
        
Platform: UNKNOWN
Requires-Python: >=3.7
Description-Content-Type: text/markdown
