Skip to main content

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.

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

tail-tools-0.19.tar.gz (114.8 kB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page