annot-utils 0.3.0b2

Python programs for processing gene annotation files

# annot_utils

[](https://travis-ci.org/friend1ws/annot_utils)
[](https://www.gnu.org/licenses/gpl-3.0)
[](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
```