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 |
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/activateDownload source code.
cd /path/to/your/download/
git clone https://github.com/bioShaun/omsTools.gitInstall 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 .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- Two import modules in this project gtf and transcript are from AssemblyLine by mkiyer