omsTools

A Tool Box for NGS analysis

omsTools is a collection of scripts for NGS (mainly for RNAseq) analysis.

Currently it includes following scripts:

Name	Function
oms_lncRNA_classify	Classify lncRNA according to its relative location to mRNA
oms_gtf_split	Split gtf file according to its field or attribute
oms_transcript_feature	Extract basic information of gene/transcript/exon/intron from gtf file
oms_gtf2bed	Convert gtf to bed12 and bed6(including tss, exon and intron feature)
oms_kill	Kill job by job name in linux

Installation

A number of scripts will be added to omsTools not long. My suggestion is to install omsTools in a virtual environment, so that you could keep up with the updating.

Create a venv folder and activate the environment.

cd /path/to/your/environment/
mkdir om004_venv
virtualenv om004_venv
. om004_venv/bin/activate

Download source code.

cd /path/to/your/download/
git clone https://github.com/bioShaun/omsTools.git

Install omsTools.

cd /path/to/your/download/omsTools
pip install -e .

Update omsTools.

# remember to activate your virtual environment first.
cd /path/to/your/download/omsTools
git pull origin master
pip install -e .

Usage

After installation, run omstools to find out all the available tools and their description. Input following command will output the usage of the specific script you need.

name_of_script -h

Acknowledgement

Two import modules in this project gtf and transcript are from AssemblyLine by mkiyer