Bam2x

bam2x is a python bioinformatics library.


 * 1) BAM2X is zhuxp's adventure of unix philosophy on bioinformatics playground.
 * 2) The philosophy of Design: Keep it simple, but leave good interface.
 * 3) The goal of  BAM2X is providing a uniform IO and DBI python functions for all kinds of Biological Data.

download git clone https://github.com/nimezhu/bam2x bam2x

install

Step 1. install dependent library (Prerequisites)
 * https://code.google.com/p/pysam/ [REQUIRED]
 * https://pypi.python.org/pypi/twobitreader [REQUIRED for genome sequence query]
 * https://bitbucket.org/james_taylor/bx-python/wiki/Home [REQUIRED for bigwig query]
 * http://ghmm.org/  [OPTIONAL, REQUIRED for xbam2trans.py ]

Step 2. download bam2x git clone git://github.com/nimezhu/bam2x.git bam2x

Step 3. add bam2x lib to your python library path add these three lines into your ~/.profile or your ~/.bash_profile BAM2X="$HOME/bam2x"   # change to where you put bam2x export PYTHONPATH="$BAM2X/lib:$PYTHONPATH" export PATH="$PATH:$BAM2X/bin:$BAM2X/scripts/"

or cd bam2x ./setup.py build ./setup.py install --prefix=install_path