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Python programs for processing gene annotation files

Project description

annot_utils

Build Status License: GPL v3 PyPI

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 packages

pkg_resources

Software

hstlib

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/v0.3.0.tar.gz
tar xzvf v0.3.0.tar.gz 
cd annot_utils-0.3.0
python setup.py build install --user

This package has been tested on Python 2.7, 3.5, 3.6.

Update databse

Currently, annot_utils already store annotation files from UCSC genome browser 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

Project details


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