Metadata-Version: 1.1
Name: annot_utils
Version: 0.3.0b1
Summary: Python programs for processing gene annotation files
Home-page: https://github.com/friend1ws/annot_utils
Author: Yuichi Shiraishi
Author-email: friend1ws@gamil.com
License: GPLv3
Description: # annot_utils
        
        [![Build Status](https://travis-ci.org/friend1ws/annot_utils.svg?branch=master)](https://travis-ci.org/friend1ws/annot_utils)
        [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
        [![PyPI](https://img.shields.io/pypi/v/annot-utils.svg?)](https://pypi.python.org/pypi/annot-utils)
        
        ## Introduction
        `annot_utils` is a software for generating tabix-indexed annotation files, which can be shared by other softwares by Y.S.
        Currently, this software support only annotatioin files for hg19 (GRCh37), hg38 (GRCh38) and mm10 (GRCm38).
        
        ## Dependency
        
        ### Python
        
        Python (>= 2.7), `pkg_resources` packages
        
        ## Software
        
        [hstlib](http://www.htslib.org)
        
        ## Install
        
        ``annot_utils`` is available through pypi. 
        To install, type:
        ```
        pip install annot_utils 
        ```
        When you are not the root user, you may want to type:
        ```
        pip install annot_utils --user
        ```
        
        Alternatively, install from the source code:
        ```
        wget https://github.com/friend1ws/annot_utils/archive/v0.2.0.tar.gz
        tar xzvf v0.2.0.tar.gz 
        cd annot_utils-0.2.0
        python setup.py build install --user
        ```
        
        ## Update databse
        Currently, `annot_utils` already store annotation files from [UCSC genome browser](https://genome.ucsc.edu) and several other sources upon installation.
        If you want to update the annotation files:
        ```
        cd annot_utils/resource
        bash prep_data.sh
        ```
        Then, install the software from the source code.
        
        ## Commands
        
        ### gene
        
        Generate gene annotation bed flies indexed by tabix.
        
        ```
        annot_utils gene [-h] 
                         [--gene_model {refseq,gencode}] [--grc]
                         [--genome_id {hg19,hg38,mm10}] [--add_ref_id]
                         gene.bed.gz
        ```
        
        
        ### exon
        
        Generate exon annotation bed flies indexed by tabix.
        
        
        ```
        annot_utils exon [-h] 
                         [--gene_model {refseq,gencode}] [--grc]
                         [--genome_id {hg19,hg38,mm10}] [--add_ref_id]
                         exon.bed.gz
        ```
        
        
        ### coding
        
        Generate regional (coding, intronic, 5'UTR, 3'UTR and so on) annotation bed flies indexed by tabix.
        
        ```
        annot_utils coding [-h] 
                           [--gene_model {refseq,gencode}] [--grc]
                           [--genome_id {hg19,hg38,mm10}] [--add_ref_id]
                           coding.bed.gz
        ```
        
        ### junction
        
        Generate annotated splicing junction bed files indexed by tabix.
        
        ```
        annot_utils junction
        usage: annot_utils junction [-h] 
                                    [--gene_model {refseq,gencode}] [--grc]
                                    [--genome_id {hg19,hg38,mm10}] [--add_ref_id]
                                    junction.bed.gz
        ```
        
        ### boundary
        
        
        Generate exon intron boundary annotation files index by tabix.
        
        ```
        annot_utils boundary [-h] 
                             [--genome_id {hg19,hg38,mm10}] [--grc]
                             [--donor_size donor_size]
                             [--acceptor_size acceptor_size]
                             boudary.bed.gz
        ```
        
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
