Summer 2014 Source Code

Contents

This is the git repo that contains all code written during the summer of 2014 for the P20 internship.

Creating VCF Files

• chromoprocessor/chromoprocessor.py: processes multiple bam files in parallel
• tovcf/tovcf.py: converts an Excel file to a VCF file
• parallel/chromosplit.py: processes a single bam file in parallel

Processing VCF Files

• vcfparse/vcfparse.py: extracts the specified regions from a VCF file
• vcfrename/vcfrename.py: renames the sample columns in a VCF file

Graphing

• graph/: this directory contains R scripts written for specific data, they aren't meant to be general

Et Cetera

• install.py: installs the Python modules needed for the programs in this repo

Installation

Most of the Python programs depend on external libraries and modules. Each dependency is listed in the README for that particular program. However, if you plan on using all the programs at some point in time, you can run install.py and it will install all the Python modules that chromoprocessor, vcfparse, and tovcf need for the user.

Note: install.py also installs pip

For additional information see each program's respective README