Metadata-Version: 1.1
Name: mirtop
Version: 0.3.6a0
Summary: Small RNA-seq annotation
Home-page: http://github.com/mirtop/mirtop
Author: Lorena Pantano
Author-email: lorena.pantano@gmail.com
License: MIT
Description: mirtop
        ---------
        
        [![](https://travis-ci.org/miRTop/mirtop.svg?branch=master)](https://travis-ci.org/miRTop/mirtop#)
        [![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
        
        Command line tool to annotate with a standard naming miRNAs e isomiRs.
        
        This tool adapt the miRNA GFF3 format agreed on here: https://github.com/miRTop/incubator/blob/master/format/definition.md
        
        Chat
        ----
        
        [Ask question, ideas](https://gitter.im/mirtop/Lobby#)
        [Contributors to code](https://gitter.im/mirtop/devel)
        
        Cite
        ---------
        
        http://mirtop.github.io
        
        About
        -----
        
        Join the team: https://orgmanager.miguelpiedrafita.com/join/15463928
        
        Read more: http://mirtop.github.io
        
        Installation
        ------------
        
        ### Bioconda
        
        `conda install mirtop -c bioconda`
        
        ### PIP
        
        `pip install mirtop`
        
        ### develop version
        
        Thes best solution is to install conda to get an independent enviroment.
        
        ```
        wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
        
        bash Miniconda-latest-Linux-x86_64.sh -b -p ~/mirtop_env
        
        export PATH=$PATH:~/mirtop_env
        
        conda install -c bioconda pysam pybedtools pandas biopython samtools
        
        git clone http://github.com/miRTop/mirtop
        
        cd mirtop
        
        python setup.py develop
        ```
        
        Quick start
        -----------
        
        Read complete commands at: https://mirtop.readthedocs.org
        
        ```
        git clone mirtop
        cd mirtop/data/example/annotate
        mirtop gff --sps hsa --hairpin hairpin.fa --gtf hsa.gff3 -o test_out sim_isomir.bam
        ```
        
        Output
        ------
        
        The `mirtop gff` generates the GFF3 adapter format to capture miRNA variations. The output is explained [here](https://github.com/miRTop/incubator/blob/master/format/definition.md).
        
        Contributors
        ------------
        
        * [Lorena Pantano](https://github.com/lpantano) (Bioinformatic Core, Harvard Chan School, Boston, USA)
        * [Shruthi Bhat Bandyadka](https://github.com/sbb25) (Partners Personalized Medicine, Cambridge MA, USA)
        
Keywords: RNA-seq miRNA isomiRs annotation
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
