first commit - quite empty project

.gitignore

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+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+*.tar.gz
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+__pycache__
+
+# Sublime
+.sublime-project
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Temp files
+
+*~
+
+# Pipy codes
+
+.pypirc

LICENCE.txt

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+
+The MIT License (MIT)
+[OSI Approved License]
+
+The MIT License (MIT)
+
+Copyright (c) 2014 Zulko
+
+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.
+

Readme.md

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+# DNA Chisel
+
+In DNA Chisel you define constraints on a DNA sequence, such as:
+- DNA coding sequences that must be preserved (only synonymous mutations are authorized)
+- Restriction sites that must be preserved
+-
+- Remove patterns from a sequence, e.g. restriction sites
+- Make patterns appear in a DNA sequence, e.g. a restriction site.
+- Codon-optimize a sequence for some organism.
+
+
+
+## Examples
+
+canvas = DNACanvas(
+    sequence = "ATGCGTGTGCGTATGCGTGTGTGCGTGATG",
+    constraints = [
+        Pattern(start, end, pattern, number=1),
+        NoPattern(start, end, pattern, number=0),
+
+        PreserveCDS(start, end),
+        PreserveCDS(start, end),
+        PreserveCDS(start, end),
+
+        LocalGCContent()
+        GlobalGCContent()
+
+
+    ]
+    optimizations = [
+        codon_optimization(start=, end=, organism=)
+    ]
+
+)
+max_local_gc_content(percentage=20, window=60)
+optimization= []
+
+# Codon optimization
+
+
+## Installation

dnachisel/patterns.py

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+
+def homopolymer(letter, number):
+    return number * letter
+
+def enzyme_pattern(enzyme_site=None, enzyme_name=None):
+    if enzyme_site is None:

ez_setup.py

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+
+#!python
+"""Bootstrap setuptools installation
+
+If you want to use setuptools in your package's setup.py, just include this
+file in the same directory with it, and add this to the top of your setup.py::
+
+from ez_setup import use_setuptools
+use_setuptools()
+
+If you want to require a specific version of setuptools, set a download
+mirror, or use an alternate download directory, you can do so by supplying
+the appropriate options to ``use_setuptools()``.
+
+This file can also be run as a script to install or upgrade setuptools.
+"""
+import os
+import shutil
+import sys
+import tempfile
+import tarfile
+import optparse
+import subprocess
+
+from distutils import log
+
+try:
+    from site import USER_SITE
+except ImportError:
+    USER_SITE = None
+
+DEFAULT_VERSION = "0.9.6"
+DEFAULT_URL = "https://pypi.python.org/packages/source/s/setuptools/"
+
+def _python_cmd(*args):
+    args = (sys.executable,) + args
+    return subprocess.call(args) == 0
+
+def _install(tarball, install_args=()):
+    # extracting the tarball
+    tmpdir = tempfile.mkdtemp()
+    log.warn('Extracting in %s', tmpdir)
+    old_wd = os.getcwd()
+    try:
+        os.chdir(tmpdir)
+        tar = tarfile.open(tarball)
+        _extractall(tar)
+        tar.close()
+
+        # going in the directory
+        subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+        os.chdir(subdir)
+        log.warn('Now working in %s', subdir)
+
+        # installing
+        log.warn('Installing Setuptools')
+        if not _python_cmd('setup.py', 'install', *install_args):
+            log.warn('Something went wrong during the installation.')
+            log.warn('See the error message above.')
+            # exitcode will be 2
+            return 2
+    finally:
+        os.chdir(old_wd)
+        shutil.rmtree(tmpdir)
+
+
+def _build_egg(egg, tarball, to_dir):
+    # extracting the tarball
+    tmpdir = tempfile.mkdtemp()
+    log.warn('Extracting in %s', tmpdir)
+    old_wd = os.getcwd()
+    try:
+        os.chdir(tmpdir)
+        tar = tarfile.open(tarball)
+        _extractall(tar)
+        tar.close()
+
+        # going in the directory
+        subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
+        os.chdir(subdir)
+        log.warn('Now working in %s', subdir)
+
+        # building an egg
+        log.warn('Building a Setuptools egg in %s', to_dir)
+        _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
+
+    finally:
+        os.chdir(old_wd)
+        shutil.rmtree(tmpdir)
+    # returning the result
+    log.warn(egg)
+    if not os.path.exists(egg):
+        raise IOError('Could not build the egg.')
+
+
+def _do_download(version, download_base, to_dir, download_delay):
+    egg = os.path.join(to_dir, 'setuptools-%s-py%d.%d.egg'
+                       % (version, sys.version_info[0], sys.version_info[1]))
+    if not os.path.exists(egg):
+        tarball = download_setuptools(version, download_base,
+                                      to_dir, download_delay)
+        _build_egg(egg, tarball, to_dir)
+    sys.path.insert(0, egg)
+    import setuptools
+    setuptools.bootstrap_install_from = egg
+
+
+def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+                   to_dir=os.curdir, download_delay=15):
+    # making sure we use the absolute path
+    to_dir = os.path.abspath(to_dir)
+    was_imported = 'pkg_resources' in sys.modules or \
+        'setuptools' in sys.modules
+    try:
+        import pkg_resources
+    except ImportError:
+        return _do_download(version, download_base, to_dir, download_delay)
+    try:
+        pkg_resources.require("setuptools>=" + version)
+        return
+    except pkg_resources.VersionConflict:
+        e = sys.exc_info()[1]
+        if was_imported:
+            sys.stderr.write(
+            "The required version of setuptools (>=%s) is not available,\n"
+            "and can't be installed while this script is running. Please\n"
+            "install a more recent version first, using\n"
+            "'easy_install -U setuptools'."
+            "\n\n(Currently using %r)\n" % (version, e.args[0]))
+            sys.exit(2)
+        else:
+            del pkg_resources, sys.modules['pkg_resources'] # reload ok
+            return _do_download(version, download_base, to_dir,
+                                download_delay)
+    except pkg_resources.DistributionNotFound:
+        return _do_download(version, download_base, to_dir,
+                            download_delay)
+
+
+def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+                        to_dir=os.curdir, delay=15):
+    """Download setuptools from a specified location and return its filename
+
+`version` should be a valid setuptools version number that is available
+as an egg for download under the `download_base` URL (which should end
+with a '/'). `to_dir` is the directory where the egg will be downloaded.
+`delay` is the number of seconds to pause before an actual download
+attempt.
+"""
+    # making sure we use the absolute path
+    to_dir = os.path.abspath(to_dir)
+    try:
+        from urllib.request import urlopen
+    except ImportError:
+        from urllib2 import urlopen
+    tgz_name = "setuptools-%s.tar.gz" % version
+    url = download_base + tgz_name
+    saveto = os.path.join(to_dir, tgz_name)
+    src = dst = None
+    if not os.path.exists(saveto): # Avoid repeated downloads
+        try:
+            log.warn("Downloading %s", url)
+            src = urlopen(url)
+            # Read/write all in one block, so we don't create a corrupt file
+            # if the download is interrupted.
+            data = src.read()
+            dst = open(saveto, "wb")
+            dst.write(data)
+        finally:
+            if src:
+                src.close()
+            if dst:
+                dst.close()
+    return os.path.realpath(saveto)
+
+
+def _extractall(self, path=".", members=None):
+    """Extract all members from the archive to the current working
+directory and set owner, modification time and permissions on
+directories afterwards. `path' specifies a different directory
+to extract to. `members' is optional and must be a subset of the
+list returned by getmembers().
+"""
+    import copy
+    import operator
+    from tarfile import ExtractError
+    directories = []
+
+    if members is None:
+        members = self
+
+    for tarinfo in members:
+        if tarinfo.isdir():
+            # Extract directories with a safe mode.
+            directories.append(tarinfo)
+            tarinfo = copy.copy(tarinfo)
+            tarinfo.mode = 448 # decimal for oct 0700
+        self.extract(tarinfo, path)
+
+    # Reverse sort directories.
+    if sys.version_info < (2, 4):
+        def sorter(dir1, dir2):
+            return cmp(dir1.name, dir2.name)
+        directories.sort(sorter)
+        directories.reverse()
+    else:
+        directories.sort(key=operator.attrgetter('name'), reverse=True)
+
+    # Set correct owner, mtime and filemode on directories.
+    for tarinfo in directories:
+        dirpath = os.path.join(path, tarinfo.name)
+        try:
+            self.chown(tarinfo, dirpath)
+            self.utime(tarinfo, dirpath)
+            self.chmod(tarinfo, dirpath)
+        except ExtractError:
+            e = sys.exc_info()[1]
+            if self.errorlevel > 1:
+                raise
+            else:
+                self._dbg(1, "tarfile: %s" % e)
+
+
+def _build_install_args(options):
+    """
+Build the arguments to 'python setup.py install' on the setuptools package
+"""
+    install_args = []
+    if options.user_install:
+        if sys.version_info < (2, 6):
+            log.warn("--user requires Python 2.6 or later")
+            raise SystemExit(1)
+        install_args.append('--user')
+    return install_args
+
+def _parse_args():
+    """
+Parse the command line for options
+"""
+    parser = optparse.OptionParser()
+    parser.add_option(
+        '--user', dest='user_install', action='store_true', default=False,
+        help='install in user site package (requires Python 2.6 or later)')
+    parser.add_option(
+        '--download-base', dest='download_base', metavar="URL",
+        default=DEFAULT_URL,
+        help='alternative URL from where to download the setuptools package')
+    options, args = parser.parse_args()
+    # positional arguments are ignored
+    return options
+
+def main(version=DEFAULT_VERSION):
+    """Install or upgrade setuptools and EasyInstall"""
+    options = _parse_args()
+    tarball = download_setuptools(download_base=options.download_base)
+    return _install(tarball, _build_install_args(options))
+
+if __name__ == '__main__':
+    sys.exit(main())