annot_utils2

Introduction

annot_utils2 is yet another annot_utils (software for generating tabix-indexed annotation files, which can be shared by other softwares by yuichi shiraishi)

Gencode dabase is fixed to Gencode19.
Annotation style is updated

Dependency

Python packages

pkg_resources

Software

hstlib

Install

annot_utils2 is available through pypi. To install, type:

pip install annot_utils2

When you are not the root user, you may want to type:

pip install annot_utils2 --user

Alternatively, install from the source code:

wget https://github.com/friend1ws/annot_utils2/archive/v0.3.0.tar.gz
tar xzvf v0.3.0.tar.gz 
cd annot_utils2-0.3.0
python setup.py build install --user

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

Update databse

Currently, annot_utils2 already store annotation files from UCSC genome browser and several other sources upon installation. If you want to update the annotation files:

cd annot_utils2/resource
bash prep_data.sh

Then, install the software from the source code.

Commands

gene

Generate gene annotation bed flies indexed by tabix.

annot_utils2 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_utils2 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_utils2 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_utils2 junction
usage: annot_utils2 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_utils2 boundary [-h] 
                     [--genome_id {hg19,hg38,mm10}] [--grc]
                     [--donor_size donor_size]
                     [--acceptor_size acceptor_size]
                     boudary.bed.gz

yasunorikogure/annot_utils