This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
Project Description

Copyright (c) 2009-2012 Brant C. Faircloth. All rights reserved.

Description

edittag is a software collection for designing sets of edit metric sequence tags, checking sequence tags for conformation to the edit metric, and integrating sequence tags to platform-specific sequencing adapters and PCR primers. edittag differs from other approaches:

  • edittag generates arbitrary lengths of edit-metric sequence tags in reasonable time frames using multiprocessing
  • edittag produces edit metric sequence tag sets conform to the edit distance selected
  • edittag used primer3 to integrate sequence tags to PCR primers

We provide several large sets of edit metric sequence tags designed using edittag in the following formats:

Documentation

You can find documentation here:

http://faircloth-lab.github.com/edittag/

Citation

Faircloth BC, Glenn TC. Large sets of edit-metric sequence identification tags to facilitate large-scale multiplexing of reads from massively parallel sequencing. http://precedings.nature.com/documents/5672/version/1

Dependencies

Availability

  • tar.gz
  • repository

Installation

easy_install

easy_install edittag

tar.gz

wget package.tar.gz
tar -xzf package.tar.gz
python setup.py install

repository

git clone git://github.com/faircloth-lab/edittag.git edittag

optional package (py-levenshtein)

wget http://pylevenshtein.googlecode.com/files/python-Levenshtein-0.10.1.tar.bz2
tar -xzvf python-Levenshtein-0.10.1.tar.bz2
python setup.py install

optional package (primer3)

If you wish to design primers incorporating edit metric sequence tags, you need to first install a modified version of primer3::

git clone git://github.com/baddna/mod-primer3.git
cd mod-primer3/src
make

Ensure that you move the binaries from mod-primer3 to a location in your path (move at least primer3-long and primer3_config into identical directories in your path).

Testing

# Testing requires numpy and nose
import edittag
edittag.test()

Using edittag

# generate some tags
% design_edit_metric_tags.py --tag-length=6 --edit-distance=3 \
    --no-polybase --gc --comp --min-and-greater --output tmp/tags.txt

# validate the 6 nucleotide, edit distance 3 tag set
% validate_edit_metric_tags.py
    --input=tmp/tags.txt
    --section='6nt ed3'
    --verbose

# add those tags to a primer set
% add_tags_to_primers.py --left-primer=GTTATGCATGAACGTAATGCTC
    --right-primer=CGCGCATGGTGGATTCACAATCC \
    --input tmp/tags.txt --section='6nt ed3'
    --sort=pair_hairpin_either,pair_penalty,cycles \
    --remove-common --keep-database \
    --output tmp/trnH_tagged_with_10_nt_ed_5_tags.csv
Release History

Release History

1.1

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

1.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
edittag-1.1.tar.gz (108.1 kB) Copy SHA256 Checksum SHA256 Source Jul 13, 2012

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS HPE HPE Development Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting