Metadata-Version: 1.1
Name: edittag
Version: 1.0
Summary: Design and check sets of edit metric sequence tags.
Home-page: http://baddna.github.com/edittag/
Author: Brant Faircloth
Author-email: brant.faircloth+edittag@gmail.com 
License: BSD
Description: edittag
        =======
        
        Copyright (c) 2009–2011 Brant C. Faircloth. All rights reserved.
        
        -  See ``LICENSE.md`` for standard, 2-clause BSD license covering
           computer code.
        -  Sequence tags available from
           `https://github.com/BadDNA/edittag/downloads`_ are licensed under
           `Creative Commons Attribution 3.0 United States License`_.
        
        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:
        
        -  text_ - this file is in an appropriate format for
           ``check_levenshtien_distance.py``
        -  csv_
        -  `sqlite database`_
        
        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
        ------------
        
        -  `Python 2.7.x`_ (should work on 2.6.x)
        -  `numpy`_ (tested with 1.5.1)
        -  `py-levenshtein`_ [optional but strongly recommended]
        -  `mod-primer3`_ [optional]
        -  `nose`_ [optional - for unittests]
        
        Availability
        ------------
        
        -  tar.gz
        -  repository
        -  Amazon Machine Instance # (coming soon)
        
        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/baddna/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
            make install
        
        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()
        
        
        Alternatives sources
        --------------------
        
        Amazon Machine Instance (not yet implemented)
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        1. Create an account on Amazon EC2.
        2. Start AMI # xxxxx
        
        ::
            
            # activate the edittag virtualenv
            % workon 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
            
        
        .. _`https://github.com/BadDNA/edittag/downloads`: https://github.com/BadDNA/edittag/downloads
        .. _`http://precedings.nature.com/documents/5672/version/1`: http://precedings.nature.com/documents/5672/version/1
        .. _Creative Commons Attribution 3.0 United States License: http://creativecommons.org/licenses/by/3.0/us/
        .. _text: https://github.com/downloads/BadDNA/edittag/edit_metric_tags.txt
        .. _csv: https://github.com/downloads/BadDNA/edittag/edit_metric_tags.csv
        .. _sqlite database: https://github.com/downloads/BadDNA/edittag/edit_metric_tags.sqlite.zip
        .. _Python 2.7.x: http://www.python.org/
        .. _numpy: http://numpy.scipy.org
        .. _py-levenshtein: http://pylevenshtein.googlecode.com
        .. _mod-primer3: https://github.com/BadDNA/mod-primer3
        .. _nose: http://somethingaboutorange.com/mrl/projects/nose/1.0.0/
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires: NumPy (>=1.3)
