Useful Library

Some useful modules used in my routine work and analysis

Installation

git clone http://github.com/kepbod/usefullib.git /path/to/usefullib

'/path/to/usefullib' is a random pathway you like.

Usage

For Perl Modules

Add use lib "/path/to/usefullib/perl/"; and use ModuleName qw(Functions...); to your perl scripts.
'ModuleName' and 'Functions' are set according to your needs.

For Python Modules

Add import sys, sys.path.insert(0,'/path/to/usefullib/python/') and from ModuleName import Class/Function or import ModuleName to your python scripts.
'ModuleName' and 'Class/Function' are set according to your needs.

File Structure

• perl - perl modules
• python - python modules. All the modules have been moved to interval
• test - some script examples using these modules

Modules

• Overlap.pm: Deal with genomic intervals (like exons, introns...)
  Functions: OverlapMax, OverlapMap, OverlapMerge
• RefFileParse.pm: Parse reference files
  Functions: ExtractInfo
• SAMParse.pm: Parse SAM files (mainly convert reads/junctions to bases)
  Functions: ReadSplit
• interval.py: Deal with genomic intervals (like exons, introns...)
  Class: Interval
• map.py: Deal with mapping issues
  Functions: mapto, overlapwith

License

Copyright (c) 2013-2014 Xiao-Ou Zhang. See the LICENSE file for license rights and limitations (MIT).