Skip to main content

Python programs for processing gene annotation files

Project 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
```

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
annot_utils-0.2.1.tar.gz (31.5 MB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page