tail-tools 0.20

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.





Peak calling and statistics:
============================

tail-tools call-peaks: peaks $SAMPLES_POLYA \
--types gene --shift-start 0 --shift-end 1000
#
# --shift-end should be chosen appropriate to the genome
#

tail-tools analyse-tail-lengths: myanalysis $SAMPLES_ALL \
--annotations peaks/relation-child.gff --types peak \
--saturation 0 --make-do all
#
# --saturation 1 to de-duplicate alignments
#


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

tail-tools geneview-webapp: geneviewer