miRBaseMiner

Version: 0.1 python version: 2.7

Any feedback and contributions are appreciated.

The workflow of miRBaseMiner

Usage

Install

Users can install miRBaseMiner by pip install miRBaseMiner. Currently, miRBaseMiner is programmed in python 2.7

miRBaseMinerInterface.py is a user interface to run miRBaseMiner

Users can set up parameters in the "SET UP" section of miRBaseMinerInterface.py After set up, user can run miRBaseMiner via python /YOUR_PATH_TO_SCRIPT/miRBaseMinerInterface.py.

Users can also have a demo run by

import miRBaseMiner as miner
miner.DMOminning()

in command line or python script. This demo run will download three versions of miRBase (v20, v21, v22), and investigate annotation from Homo sapiens.

Results

In user specified result folder (by default, the result folder will be in the current work directory), there will be two sub folders: (1) resultsTables and (2) miRBase. miRBase contains all available data within each version of miRBase under respectively folder named with version number. resultsTables contaains all output files and generated figures from each selected analysis sections. In addition, two folders will be generated in resultsTables : (1) curatedSet: curated set of annotation based on original miRBase entries; (2) Rscripts: R scripts that generated and used for data visulization.

All result files are systemically named, joined "miRBase", version information, species information and key word indicating file content with underline.

Dependency

Before run miRBaseMiner, make sure that you have all required python libraries and R packages.

python: (1)SeqIO and Seq from biopython; (2) editdistance; (3) ftplib.

R: (1) ggplot2; (2) tm; (3) wordcloud; (4) scales; (5) ggseqlogo; (6) igraph.