pyim 0.2.0

Tool for identifying transposon insertions from targeted DNA-sequencing data.

PyIM

PyIM (Python Insertional Mutagenesis) is a python package for analyzing insertional mutagenesis data from targeted sequencing of transposon insertion sites. The package provides several command line tools for identifying insertions, calling common insertion sites (CISs) and annotating insertions/CISs directly from the command line. It also aims to provides the basic building blocks for implementing new pipelines, CIS callers, etc.

Documentation

PyIM’s documentation is available at jrderuiter.github.io/pyim.

Requirements

PyIM is written for Python 3 and requires Python 3.3 or newer to be installed. Depending on the used functionality, PyIM also has the following external dependencies:

• cutadapt/bowtie2 (Needed for identifying insertions from sequencing data)

• cimpl (R package, needed for calling CIS sites using CIMPL)

Installation

Using conda

The recommended way to install PyIM is using conda, as with conda you can install PyIM together with its external dependencies (cutadapt and bowtie2) into an isolated environment using a single command:

conda create -n pyim -c jrderuiter -c bioconda -c r pyim

Alternatively, PyIM can be installed in an existing environent using:

conda install -c jrderuiter -c bioconda -c r pyim

Conda packages are available for both OSX and Linux (64-bit).

Using pip

PyIM can be installed from Github using pip as follows:

pip install git+git://github.com/jrderuiter/pyim.git#egg=pyim

Note that in this case, external dependencies must be installed manually.

Unfortunately, PyIM is not yet available on PyPI, though this may change when the package is further developed.

License

This software is released under the MIT license.

History

0.2.0 (2017-05-10)

• Refactored pipeline structure.

• Added ShearSplink and Nextera pipelines.

0.1.0 (2016-09-01)

• Initial release.