UNKNOWN
Project description
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
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