tail-tools 0.18

UNKNOWN

This is a Python 2 based suite of tools for analysing SOLiD or Illumina sequencing reads with poly(A) tails.

Use of PyPy is recommened for speed.

License:

This software is distributed under the terms of the GPL, version 2 or later, excepting that:

• The third party javascript libraries included for convenience in directory tail_tools/web/third_party are covered by the terms of their respective licenses (also in that directory).

• The remaining files in the directory tail_tools/web are placed in the public domain.

Requirements:

• “nesoni”, available from http://vicbioinformatics.com/nesoni.shtml or using

  pip install nesoni

  You don’t need to install all of nesoni’s dependencies, just Python 2.7 or later or PyPy.

• The “convert” tool from ImageMagick.

Installation:

Easy way:

pip install tail-tools

From source:

python setup.py install

For PyPy it seems to be currently easiest to set up in a virtualenv:

virtualenv -p pypy myenv myenv/bin/pip install tail-tools

Usage:

This package contains a number of tools, which can be listed by typing:

tail-tools

The package can be used directly from the source directory with:

python -m tail_tools

These tools may also be used as part of a nesoni-style workflow python script.

Tail-tools is free software, released under the GPL (version 2).

Peak calling and statistics:

tail-tools call-peaks: peaks $SAMPLES_POLYA –types gene –shift-start 0 –shift-end 1000

tail-tools analyse-tail-lengths: myanalysis $SAMPLES_ALL –annotations peaks/relation-child.gff –types peak –saturation 0 –make-do all

tail-tools compare-peaks: mycomparison $REFERENCE peaks/relation-parent.gff peaks/relation-child.gff myanalysis-counts.csv

tail-tools geneview-webapp: geneviewer