First version of a barcode design toolkit.

LICENSE

+Copyright (c) 2013 Leiden University Medical Center <humgen@lumc.nl>
+Copyright (c) 2013 Jeroen F.J. Laros <j.f.j.laros@lumc.nl>
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

barcode/__init__.py

+"""
+barcode: Design NGS barcodes.
+
+Copyright (c) 2013 Leiden University Medical Center <humgen@lumc.nl>
+Copyright (c) 2013 Jeroen F.J. Laros <j.f.j.laros@lumc.nl>
+
+Licensed under the MIT license, see the LICENSE file.
+"""
+
+# On the event of a new release, we update the __version_info__ package
+# global and set RELEASE to True.
+# Before a release, a development version is denoted by a __version_info__
+# ending with a 'dev' item and RELEASE is set to False.
+#
+# We follow a versioning scheme compatible with setuptools [1] where the
+# __version_info__ variable always contains the version of the upcomming
+# release (and not that of the previous release), post-fixed with a 'dev'
+# item. Only in a release commit, this 'dev' item is removed (and added
+# again in the next commit).
+#
+# [1] http://peak.telecommunity.com/DevCenter/setuptools#specifying-your-project-s-version
+
+RELEASE = False
+
+__version_info__ = ('0', '1', 'dev')
+
+
+__version__ = '.'.join(__version_info__)
+__author__ = 'LUMC, Jeroen F.J. Laros'
+__contact__ = 'j.f.j.laros@@lumc.nl'
+__homepage__ = 'https://git.lumc.nl/j.f.j.laros/barcode'

barcode/barcode.py

+#!/usr/bin/env python
+
+"""
+Design NGS barcodes.
+
+
+Use any of the positional arguments with the -h option for more information.
+"""
+
+import argparse
+import Levenshtein
+
+__nucleotides = ['A', 'C', 'G', 'T']
+
+def docSplit(func):
+    return func.__doc__.split("\n\n")[0]
+
+def __allWords(bucket, word, length, result):
+    """
+    Generate all possible words of a certain length over a specified alphabet.
+
+    @arg bucket: An alphabet.
+    @type bucket: list[str]
+    @arg word: A word over the alphabet {bucket}.
+    @type word: str
+    @arg length: Lenth of the barcodes.
+    @type length: int
+    @arg result: Constructed words.
+    @type result: list[str]
+    """
+    if length:
+        for i in bucket:
+            __allWords(bucket, word + i, length - 1, result)
+    else:
+        result.append(word)
+#__allWords
+
+def allBarcodes(length):
+    """
+    Generate all possible barcodes of a certain length.
+
+    @arg length: Lenth of the barcodes.
+    @type length: int
+    """
+    result = []
+
+    __allWords(__nucleotides, "", length, result)
+
+    return result
+#allBarcodes
+
+def __filterStretch(barcode, stretches):
+    """
+    Test whether {barcode} contains none of the stretches in {stretches}.
+
+    @arg barcode: A barcode.
+    @type barcode: str
+    @arg stretches:
+    @type stretches: list[str]
+    """
+    for i in stretches:
+        if i in barcode:
+            return False
+
+    return True
+#__filterStretch
+
+def filterStretches(barcodes, max_stretch):
+    """
+    Filter a list of barcodes for mononucleotide stretches.
+
+    @arg barcodes: List of barcodes.
+    @type barcodes: list[str]
+    @arg max_stretch: Maximum mononucleotide stretch length.
+    @type max_stretch: int
+    """
+    stretches = map(lambda x: max_stretch * x, __nucleotides)
+    result = []
+
+    for i in barcodes:
+        if __filterStretch(i, stretches):
+            result.append(i)
+
+    return result
+#filterStretches
+
+def __filterDistance(barcodes, candidate, min_dist):
+    """
+    Test whether {candidate} can be added to {barcodes} based on the minimum
+    distance between {candidate} and all barcodes in {barcodes}.
+
+    @arg barcodes: List of barcodes.
+    @type barcodes: list[str]
+    @arg candidate: Candidate barcode.
+    @type candidate: str
+    @arg min_dist: Minimum distance between the barcodes.
+    @type min_dist: int
+    """
+    for i in barcodes:
+        if Levenshtein.distance(i, candidate) < min_dist:
+            return False
+
+    return True
+#__filterDistance
+
+def filterDistance(barcodes, min_dist):
+    """
+    Filter a list of barcodes for distances with other barcodes.
+
+    @arg barcodes: List of barcodes.
+    @type barcodes: list[str]
+    @arg min_dist: Minimum distance between the barcodes.
+    @type min_dist: int
+    """
+    result = []
+
+    for i in barcodes:
+        if __filterDistance(result, i, min_dist):
+            result.append(i)
+
+    return result
+#filterDistance
+
+def barcode(length, max_stretch, min_dist):
+    """
+    Make a set of barcodes, filter them for mononucleotide stretches and for
+    distances with other barcodes.
+
+    @arg length: Lenth of the barcodes.
+    @type length: int
+    @arg max_stretch: Maximum mononucleotide stretch length.
+    @type max_stretch: int
+    @arg min_dist: Minimum distance between the barcodes.
+    @type min_dist: int
+    """
+    return filterDistance(filterStretches(allBarcodes(length), max_stretch),
+        min_dist)
+#barcode
+
+def main():
+    """
+    Main entry point.
+    """
+    output_parser = argparse.ArgumentParser(add_help=False)
+    output_parser.add_argument("OUTPUT", type=argparse.FileType('w'),
+        help="output file")
+
+    usage = __doc__.split("\n\n\n")
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        description=usage[0], epilog=usage[1])
+    subparsers = parser.add_subparsers(dest="subcommand")
+
+    parser_makebc = subparsers.add_parser("makebc",
+        parents=[output_parser], description=docSplit(barcode))
+    parser_makebc.add_argument("-l", dest="length", type=int, default=8,
+        help="lenght of the barcodes")
+    parser_makebc.add_argument("-s", dest="stretch", type=int, default=2,
+        help="maximum mononucleotide stretch length")
+    parser_makebc.add_argument("-d", dest="distance", type=int, default=3,
+        help="minimum distance between the barcodes")
+
+    args = parser.parse_args()
+
+    if args.subcommand == "makebc":
+        args.OUTPUT.write("\n".join(barcode(args.length, args.stretch,
+            args.distance)))
+#main
+
+if __name__ == "__main__":
+    main()

setup.py

+import sys
+from setuptools import setup
+
+if sys.version_info < (2, 6):
+    raise Exception('barcode requires Python 2.6 or higher.')
+
+# Todo: How does this play with pip freeze requirement files?
+requires = ['Levenshtein']
+
+# Python 2.6 does not include the argparse module.
+try:
+    import argparse
+except ImportError:
+    requires.append('argparse')
+
+import barcode as distmeta
+
+setup(
+    name='barcode',
+    version=distmeta.__version__,
+    description='Design NGS barcodes.',
+    long_description=distmeta.__doc__,
+    author=distmeta.__author__,
+    author_email=distmeta.__contact__,
+    url=distmeta.__homepage__,
+    license='MIT License',
+    platforms=['any'],
+    packages=['barcode'],
+    install_requires=requires,
+    entry_points = {
+        'console_scripts': [
+            'barcode = barcode.barcode:main'
+        ]
+    },
+    classifiers = [
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Science/Research',
+        'Intended Audience :: Developers',
+        'Operating System :: OS Independent',
+        'Programming Language :: Python',
+        'Topic :: Scientific/Engineering',
+    ],
+    keywords='bioinformatics'
+)