Metadata-Version: 2.0
Name: aimhii
Version: 0.5.3
Summary: A pipeline for mapping insertion mutants from whole genome shotgun data
Home-page: http://granek.bitbucket.org/projects/aimhii
Author: Josh Granek
Author-email: joshua.granek@duke.edu
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Requires-Dist: numpy (>=1.8.1)
Requires-Dist: biopython (>=1.64)
Requires-Dist: matplotlib (>=1.3.1)
Requires-Dist: pysam (>=0.7.7)
Requires-Dist: HTSeq (>=0.6.1)

AIMHII
=======================

This package provides software for identifying the genome insertion points random mutants generated by insertional mutagenesis, which have been sequenced as a pool.

The package will install two executables: aimhii and extract_chimeras.

aimhii will run a full analysis starting from sequence data (a FASTQ file), genome sequence, and insert sequence.  extract_chimeras just runs the last step of this analysis, assuming you already have a BAM file and a concatenated genome-insert sequence.

For details see the project website http://granek.bitbucket.org/projects/aimhii/

Changes since v0.5.2: Shifted debugging prints to logging and added scripts for generating synthetic sequences
Changes since v0.5.1: Lowered pysam version requirement to allow installation using apt-get in Debian v8.
Changes since v0.5.0: Fixed problem with missing DESCRIPTION.rst.