# -*- coding: utf-8 -*-

# Built-in modules #
import sys, os, time, shutil, re, random, math
import getpass, hashlib, datetime, collections

# Third party modules #
import sh, numpy, dateutil

# One liners #
flatter = lambda x: [item for sublist in x for item in sublist]

################################################################################
def pad_with_whitespace(string, pad=None):
    if pad is None: pad = max(map(len, string.split('\n'))) + 1
    return '\n'.join(('{0: <%i}' % pad).format(line) for line in string.split('\n'))

def mirror_lines(string):
    return '\n'.join(line[::-1] for line in string.split('\n'))

def concatenate_by_line(first, second):
    return '\n'.join(x+y for x,y in zip(first.split('\n'), second.split('\n')))

################################################################################
def sort_string_by_pairs(strings):
    """Group a list of strings by pairs, by matching those with only
    one character difference between each other together."""
    assert len(strings) % 2 == 0
    pairs = []
    strings = list(strings) # This shallow copies the list
    while strings:
        template = strings.pop()
        for i, candidate in enumerate(strings):
            if count_string_diff(template, candidate) == 1:
                pair = [template, strings.pop(i)]
                pair.sort()
                pairs.append(pair)
                break
    return pairs

################################################################################
def count_string_diff(a,b):
    """Return the number of characters in a string that don't exactly match"""
    shortest = min(len(a), len(b))
    return sum(a[i] != b[i] for i in range(shortest))

################################################################################
def iflatten(L):
    for sublist in L:
        if hasattr(sublist, '__iter__'):
            for item in iflatten(sublist): yield item
        else: yield sublist

################################################################################
class GenWithLength(object):
    """A generator with a length attribute"""
    def __init__(self, gen, length): self.gen, self.length = gen, length
    def __iter__(self): return self.gen
    def __len__(self): return self.length

###############################################################################
class Password(object):
    """A password object that will only prompt the user once per session"""
    def __str__(self): return self.value
    def __init__(self, prompt=None):
        self._value = None
        self.prompt = prompt

    @property
    def value(self):
        if self._value == None: self._value = getpass.getpass(self.prompt)
        return self._value

################################################################################
def md5sum(file_path, blocksize=65536):
    """Compute the md5 of a file. Pretty fast"""
    md5 = hashlib.md5()
    with open(file_path, "r+b") as f:
        for block in iter(lambda: f.read(blocksize), ""):
            md5.update(block)
    return md5.hexdigest()

################################################################################
def average(iterator):
    """Iterative mean"""
    count = 0
    total = 0
    for num in iterator:
        count += 1
        total += num
    return float(total)/count

###############################################################################
def moving_average(interval, windowsize, borders=None):
    """This is essentially a convolving operation. Several option exist for dealing with the border cases.

        * None: Here the returned signal will be smaller than the inputted interval.

        * zero_padding: Here the returned signal will be larger than the inputted interval and we will add zeros to the original interval before operating the convolution.

        * zero_padding_and_cut: Same as above only the result is truncated to be the same size as the original input.

        * copy_padding: Here the returned signal will be larger than the inputted interval and we will use the right and leftmost values for padding before operating the convolution.

        * copy_padding_and_cut: Same as above only the result is truncated to be the same size as the original input.

        * zero_stretching: Here we will compute the convolution only in the valid domain, then add zeros to the result so that the output is the same size as the input.

        * copy_stretching: Here we will compute the convolution only in the valid domain, then copy the right and leftmost values so that the output is the same size as the input.
        """
    # The window size in half #
    half = int(math.floor(windowsize/2.0))
    # The normalized rectangular signal #
    window = numpy.ones(int(windowsize))/float(windowsize)
    # How do we deal with borders #
    if borders == None:
        return numpy.convolve(interval, window, 'valid')
    if borders == 'zero_padding':
        return numpy.convolve(interval, window, 'full')
    if borders == 'zero_padding_and_cut':
        return numpy.convolve(interval, window, 'same')
    if borders == 'copy_padding':
        new_interval = [interval[0]]*(windowsize-1) + interval + [interval[-1]]*(windowsize-1)
        return numpy.convolve(new_interval, window, 'valid')
    if borders == 'copy_padding_and_cut':
        new_interval = [interval[0]]*(windowsize-1) + interval + [interval[-1]]*(windowsize-1)
        return numpy.convolve(new_interval, window, 'valid')[half:-half]
    if borders == 'zero_stretching':
        result = numpy.convolve(interval, window, 'valid')
        pad = numpy.zeros(half)
        return numpy.concatenate((pad, result, pad))
    if borders == 'copy_stretching':
        result = numpy.convolve(interval, window, 'valid')
        left = numpy.ones(half)*result[0]
        right = numpy.ones(half)*result[-1]
        return numpy.concatenate((left, result, right))

################################################################################
def wait(predicate, interval=1, message=lambda: "Waiting..."):
    ball, next_ball = u"|/-\\", "|"
    sys.stdout.write("    \033[K")
    sys.stdout.flush()
    while not predicate():
        time.sleep(1)
        next_ball = ball[(ball.index(next_ball) + 1) % len(ball)]
        sys.stdout.write("\r " + str(message()) + " " + next_ball + " \033[K")
        sys.stdout.flush()
    print "\r Done. \033[K"
    sys.stdout.flush()

################################################################################
def isubsample(full_sample, k, full_sample_len=None):
    """Downsample an enumerable list of things"""
    # Determine length #
    if not full_sample_len: full_sample_len = len(full_sample)
    # Check size coherence #
    if not 0 <= k <= full_sample_len:
        raise ValueError('Required that 0 <= k <= full_sample_length')
    # Do it #
    picked = 0
    for i, element in enumerate(full_sample):
        prob = (k-picked) / (full_sample_len-i)
        if random.random() < prob:
            yield element
            picked += 1
    # Did we pick the right amount #
    assert picked == k

################################################################################
def imean(numbers):
    """Iterative mean"""
    count = 0
    total = 0
    for num in numbers:
        count += 1
        total += num
    return float(total)/count

################################################################################
def get_git_tag(directory):
    if os.path.exists(directory + '/.git'):
        return sh.git("--git-dir=" + directory + '/.git', "describe", "--tags", "--dirty", "--always").strip('\n')
    else:
        return None

###############################################################################
def reversed_lines(path):
    """Generate the lines of file in reverse order."""
    with open(path, 'r') as handle:
        part = ''
        for block in reversed_blocks(handle):
            for c in reversed(block):
                if c == '\n' and part:
                    yield part[::-1]
                    part = ''
                part += c
        if part: yield part[::-1]

def reversed_blocks(handle, blocksize=4096):
    """Generate blocks of file's contents in reverse order."""
    handle.seek(0, os.SEEK_END)
    here = handle.tell()
    while 0 < here:
        delta = min(blocksize, here)
        here -= delta
        handle.seek(here, os.SEEK_SET)
        yield handle.read(delta)

###############################################################################
def find_file_by_name(name, root=os.curdir):
    for dirpath, dirnames, filenames in os.walk(os.path.abspath(root)):
        if name in filenames: return os.path.join(dirpath, name)
    raise Exception("Could not find file '%s' in '%s'" % (name, root))

###############################################################################
def natural_sort(item):
    """
    Sort strings that contain numbers correctly.

    >>> l = ['v1.3.12', 'v1.3.3', 'v1.2.5', 'v1.2.15', 'v1.2.3', 'v1.2.1']
    >>> l.sort(key=natural_sort)
    >>> l.__repr__()
    "['v1.2.1', 'v1.2.3', 'v1.2.5', 'v1.2.15', 'v1.3.3', 'v1.3.12']"
    """
    if item is None: return 0
    def try_int(s):
        try: return int(s)
        except ValueError: return s
    return map(try_int, re.findall(r'(\d+|\D+)', item))

###############################################################################
def which(cmd, safe=False):
    """https://github.com/jc0n/python-which"""
    def is_executable(path):
        return os.path.exists(path) and os.access(path, os.X_OK) and not os.path.isdir(path)
    path, name = os.path.split(cmd)
    if path:
        if is_executable(cmd): return cmd
    else:
        for path in os.environ['PATH'].split(os.pathsep):
            candidate = os.path.join(path, cmd)
            if is_executable(candidate): return candidate
    if not safe: raise Exception('which failed to locate a proper command path "%s"' % cmd)

################################################################################
def tail(path, window=20):
    with open(path, 'r') as f:
        BUFSIZ = 1024
        f.seek(0, 2)
        num_bytes = f.tell()
        size = window + 1
        block = -1
        data = []
        while size > 0 and num_bytes > 0:
            if num_bytes - BUFSIZ > 0:
                # Seek back one whole BUFSIZ
                f.seek(block * BUFSIZ, 2)
                # Read BUFFER
                data.insert(0, f.read(BUFSIZ))
            else:
                # File too small, start from beginning
                f.seek(0,0)
                # Only read what was not read
                data.insert(0, f.read(num_bytes))
            linesFound = data[0].count('\n')
            size -= linesFound
            num_bytes -= BUFSIZ
            block -= 1
        return '\n'.join(''.join(data).splitlines()[-window:])

################################################################################
def head(path, window=20):
    with open(path, 'r') as handle:
        return ''.join(handle.next() for line in xrange(window))

###############################################################################
def split_thousands(s, tSep='\'', dSep='.'):
    """
    Splits a number on thousands.
    http://code.activestate.com/recipes/498181-add-thousands-separator-commas-to-formatted-number/

    >>> split_thousands(1000012)
    "1'000'012"
    """
    # Check input #
    if s is None: return 0
    # Check for int #
    if round(s, 13) == s: s = int(s)
    # Make string #
    if not isinstance(s, str): s = str(s)
    # Unreadable code #
    cnt = 0
    numChars = dSep + '0123456789'
    ls = len(s)
    while cnt < ls and s[cnt] not in numChars: cnt += 1
    lhs = s[0:cnt]
    s = s[cnt:]
    if dSep == '': cnt = -1
    else: cnt = s.rfind(dSep)
    if cnt > 0:
        rhs = dSep + s[cnt+1:]
        s = s[:cnt]
    else:
        rhs = ''
    splt=''
    while s != '':
        splt= s[-3:] + tSep + splt
        s = s[:-3]
    return lhs + splt[:-1] + rhs

################################################################################
def gps_deg_to_float(data):
    m = re.search(u"(\d+?)°(\d+?)\'(\d+?)\'\'", data.strip())
    degs, mins, secs = [0.0 if m.group(i) is None else int(m.group(i)) for i in range(1, 4)]
    comp_dir = -1 if data[-1] in ('N', 'E') else 1
    return (degs + (mins / 60) + (secs / 3600)) * comp_dir

################################################################################
def is_integer(string):
    try: int(string)
    except ValueError: return False
    return True

################################################################################
def reverse_compl_with_name(old_seq):
    """Reverse a SeqIO sequence, but keep its name intact"""
    new_seq = old_seq.reverse_complement()
    new_seq.id = old_seq.id
    new_seq.description = old_seq.description
    return new_seq

################################################################################
def prepend_to_file(path, data, bufsize=1<<15):
    # Backup the file #
    backupname = path + os.extsep + 'bak'
    # Remove previous backup if it exists #
    try: os.unlink(backupname)
    except OSError: pass
    os.rename(path, backupname)
    # Open input/output files,  note: outputfile's permissions lost #
    with open(backupname) as inputfile:
        with open(path, 'w') as outputfile:
            outputfile.write(data)
            buf = inputfile.read(bufsize)
            while buf:
                outputfile.write(buf)
                buf = inputfile.read(bufsize)
    # Remove backup on success #
    os.remove(backupname)

def append_to_file(path, data):
    with open(path, "a") as handle:
        handle.write(data)

################################################################################
def pretty_now():
    """Prints some thing like '2014-07-24 11:12:45 CEST+0200'"""
    now = datetime.datetime.now(dateutil.tz.tzlocal())
    return now.strftime("%Y-%m-%d %H:%M:%S %Z%z")

################################################################################
def andify(list_of_strings):
    """
    Given a list of strings will join them with commas
    and a final "and" word.

    >>> andify(['Apples', 'Oranges', 'Mangos'])
    'Apples, Oranges and Mangos'
    """
    result = ', '.join(list_of_strings)
    comma_index = result.rfind(',')
    if comma_index > -1: result = result[:comma_index] + ' and' + result[comma_index+1:]
    return result

################################################################################
class OrderedSet(collections.OrderedDict, collections.MutableSet):
    """A recipe for an ordered set.
    http://stackoverflow.com/a/1653978/287297"""

    def update(self, *args, **kwargs):
        if kwargs:
            raise TypeError("update() takes no keyword arguments")

        for s in args:
            for e in s:
                self.add(e)

    def add(self, elem):
        self[elem] = None

    def discard(self, elem):
        self.pop(elem, None)

    def __le__(self, other):
        return all(e in other for e in self)

    def __lt__(self, other):
        return self <= other and self != other

    def __ge__(self, other):
        return all(e in self for e in other)

    def __gt__(self, other):
        return self >= other and self != other

    def __repr__(self):
        return 'OrderedSet([%s])' % (', '.join(map(repr, self.keys())))

    def __str__(self):
        return '{%s}' % (', '.join(map(repr, self.keys())))

    difference = property(lambda self: self.__sub__)
    difference_update = property(lambda self: self.__isub__)
    intersection = property(lambda self: self.__and__)
    intersection_update = property(lambda self: self.__iand__)
    issubset = property(lambda self: self.__le__)
    issuperset = property(lambda self: self.__ge__)
    symmetric_difference = property(lambda self: self.__xor__)
    symmetric_difference_update = property(lambda self: self.__ixor__)
    union = property(lambda self: self.__or__)

################################################################################
def get_next_item(iterable):
    """Gets the next item of an iterable.
    If the iterable is exhausted, returns None."""
    try: x = iterable.next()
    except StopIteration: x = None
    except AttributeError: x = None
    return x

# -*- coding: utf-8 -*-

# Built-in modules #
import sys, os, time, shutil, re, random, math
import getpass, hashlib, datetime, collections

# Third party modules #
import sh, numpy, dateutil

# One liners #
flatter = lambda x: [item for sublist in x for item in sublist]

################################################################################
def pad_with_whitespace(string, pad=None):
    if pad is None: pad = max(map(len, string.split('\n'))) + 1
    return '\n'.join(('{0: <%i}' % pad).format(line) for line in string.split('\n'))

def mirror_lines(string):
    return '\n'.join(line[::-1] for line in string.split('\n'))

def concatenate_by_line(first, second):
    return '\n'.join(x+y for x,y in zip(first.split('\n'), second.split('\n')))

################################################################################
def sort_string_by_pairs(strings):
    """Group a list of strings by pairs, by matching those with only
    one character difference between each other together."""
    assert len(strings) % 2 == 0
    pairs = []
    strings = list(strings) # This shallow copies the list
    while strings:
        template = strings.pop()
        for i, candidate in enumerate(strings):
            if count_string_diff(template, candidate) == 1:
                pair = [template, strings.pop(i)]
                pair.sort()
                pairs.append(pair)
                break
    return pairs

################################################################################
def count_string_diff(a,b):
    """Return the number of characters in a string that don't exactly match"""
    shortest = min(len(a), len(b))
    return sum(a[i] != b[i] for i in range(shortest))

################################################################################
def iflatten(L):
    for sublist in L:
        if hasattr(sublist, '__iter__'):
            for item in iflatten(sublist): yield item
        else: yield sublist

################################################################################
class GenWithLength(object):
    """A generator with a length attribute"""
    def __init__(self, gen, length): self.gen, self.length = gen, length
    def __iter__(self): return self.gen
    def __len__(self): return self.length

###############################################################################
class Password(object):
    """A password object that will only prompt the user once per session"""
    def __str__(self): return self.value
    def __init__(self, prompt=None):
        self._value = None
        self.prompt = prompt

    @property
    def value(self):
        if self._value == None: self._value = getpass.getpass(self.prompt)
        return self._value

################################################################################
def md5sum(file_path, blocksize=65536):
    """Compute the md5 of a file. Pretty fast"""
    md5 = hashlib.md5()
    with open(file_path, "r+b") as f:
        for block in iter(lambda: f.read(blocksize), ""):
            md5.update(block)
    return md5.hexdigest()

################################################################################
def average(iterator):
    """Iterative mean"""
    count = 0
    total = 0
    for num in iterator:
        count += 1
        total += num
    return float(total)/count

###############################################################################
def moving_average(interval, windowsize, borders=None):
    """This is essentially a convolving operation. Several option exist for dealing with the border cases.

        * None: Here the returned signal will be smaller than the inputted interval.

        * zero_padding: Here the returned signal will be larger than the inputted interval and we will add zeros to the original interval before operating the convolution.

        * zero_padding_and_cut: Same as above only the result is truncated to be the same size as the original input.

        * copy_padding: Here the returned signal will be larger than the inputted interval and we will use the right and leftmost values for padding before operating the convolution.

        * copy_padding_and_cut: Same as above only the result is truncated to be the same size as the original input.

        * zero_stretching: Here we will compute the convolution only in the valid domain, then add zeros to the result so that the output is the same size as the input.

        * copy_stretching: Here we will compute the convolution only in the valid domain, then copy the right and leftmost values so that the output is the same size as the input.
        """
    # The window size in half #
    half = int(math.floor(windowsize/2.0))
    # The normalized rectangular signal #
    window = numpy.ones(int(windowsize))/float(windowsize)
    # How do we deal with borders #
    if borders == None:
        return numpy.convolve(interval, window, 'valid')
    if borders == 'zero_padding':
        return numpy.convolve(interval, window, 'full')
    if borders == 'zero_padding_and_cut':
        return numpy.convolve(interval, window, 'same')
    if borders == 'copy_padding':
        new_interval = [interval[0]]*(windowsize-1) + interval + [interval[-1]]*(windowsize-1)
        return numpy.convolve(new_interval, window, 'valid')
    if borders == 'copy_padding_and_cut':
        new_interval = [interval[0]]*(windowsize-1) + interval + [interval[-1]]*(windowsize-1)
        return numpy.convolve(new_interval, window, 'valid')[half:-half]
    if borders == 'zero_stretching':
        result = numpy.convolve(interval, window, 'valid')
        pad = numpy.zeros(half)
        return numpy.concatenate((pad, result, pad))
    if borders == 'copy_stretching':
        result = numpy.convolve(interval, window, 'valid')
        left = numpy.ones(half)*result[0]
        right = numpy.ones(half)*result[-1]
        return numpy.concatenate((left, result, right))

################################################################################
def wait(predicate, interval=1, message=lambda: "Waiting..."):
    ball, next_ball = u"|/-\\", "|"
    sys.stdout.write("    \033[K")
    sys.stdout.flush()
    while not predicate():
        time.sleep(1)
        next_ball = ball[(ball.index(next_ball) + 1) % len(ball)]
        sys.stdout.write("\r " + str(message()) + " " + next_ball + " \033[K")
        sys.stdout.flush()
    print "\r Done. \033[K"
    sys.stdout.flush()

################################################################################
def isubsample(full_sample, k, full_sample_len=None):
    """Downsample an enumerable list of things"""
    # Determine length #
    if not full_sample_len: full_sample_len = len(full_sample)
    # Check size coherence #
    if not 0 <= k <= full_sample_len:
        raise ValueError('Required that 0 <= k <= full_sample_length')
    # Do it #
    picked = 0
    for i, element in enumerate(full_sample):
        prob = (k-picked) / (full_sample_len-i)
        if random.random() < prob:
            yield element
            picked += 1
    # Did we pick the right amount #
    assert picked == k

################################################################################
def imean(numbers):
    """Iterative mean"""
    count = 0
    total = 0
    for num in numbers:
        count += 1
        total += num
    return float(total)/count

################################################################################
def get_git_tag(directory):
    if os.path.exists(directory + '/.git'):
        return sh.git("--git-dir=" + directory + '/.git', "describe", "--tags", "--dirty", "--always").strip('\n')
    else:
        return None

###############################################################################
def reversed_lines(path):
    """Generate the lines of file in reverse order."""
    with open(path, 'r') as handle:
        part = ''
        for block in reversed_blocks(handle):
            for c in reversed(block):
                if c == '\n' and part:
                    yield part[::-1]
                    part = ''
                part += c
        if part: yield part[::-1]

def reversed_blocks(handle, blocksize=4096):
    """Generate blocks of file's contents in reverse order."""
    handle.seek(0, os.SEEK_END)
    here = handle.tell()
    while 0 < here:
        delta = min(blocksize, here)
        here -= delta
        handle.seek(here, os.SEEK_SET)
        yield handle.read(delta)

###############################################################################
def find_file_by_name(name, root=os.curdir):
    for dirpath, dirnames, filenames in os.walk(os.path.abspath(root)):
        if name in filenames: return os.path.join(dirpath, name)
    raise Exception("Could not find file '%s' in '%s'" % (name, root))

###############################################################################
def natural_sort(item):
    """
    Sort strings that contain numbers correctly.

    >>> l = ['v1.3.12', 'v1.3.3', 'v1.2.5', 'v1.2.15', 'v1.2.3', 'v1.2.1']
    >>> l.sort(key=natural_sort)
    >>> l.__repr__()
    "['v1.2.1', 'v1.2.3', 'v1.2.5', 'v1.2.15', 'v1.3.3', 'v1.3.12']"
    """
    if item is None: return 0
    def try_int(s):
        try: return int(s)
        except ValueError: return s
    return map(try_int, re.findall(r'(\d+|\D+)', item))

###############################################################################
def which(cmd, safe=False):
    """https://github.com/jc0n/python-which"""
    def is_executable(path):
        return os.path.exists(path) and os.access(path, os.X_OK) and not os.path.isdir(path)
    path, name = os.path.split(cmd)
    if path:
        if is_executable(cmd): return cmd
    else:
        for path in os.environ['PATH'].split(os.pathsep):
            candidate = os.path.join(path, cmd)
            if is_executable(candidate): return candidate
    if not safe: raise Exception('which failed to locate a proper command path "%s"' % cmd)

################################################################################
def tail(path, window=20):
    with open(path, 'r') as f:
        BUFSIZ = 1024
        f.seek(0, 2)
        num_bytes = f.tell()
        size = window + 1
        block = -1
        data = []
        while size > 0 and num_bytes > 0:
            if num_bytes - BUFSIZ > 0:
                # Seek back one whole BUFSIZ
                f.seek(block * BUFSIZ, 2)
                # Read BUFFER
                data.insert(0, f.read(BUFSIZ))
            else:
                # File too small, start from beginning
                f.seek(0,0)
                # Only read what was not read
                data.insert(0, f.read(num_bytes))
            linesFound = data[0].count('\n')
            size -= linesFound
            num_bytes -= BUFSIZ
            block -= 1
        return '\n'.join(''.join(data).splitlines()[-window:])

################################################################################
def head(path, window=20):
    with open(path, 'r') as handle:
        return ''.join(handle.next() for line in xrange(window))

###############################################################################
def split_thousands(s, tSep='\'', dSep='.'):
    """
    Splits a number on thousands.
    http://code.activestate.com/recipes/498181-add-thousands-separator-commas-to-formatted-number/

    >>> split_thousands(1000012)
    "1'000'012"
    """
    # Check input #
    if s is None: return 0
    # Check for int #
    if round(s, 13) == s: s = int(s)
    # Make string #
    if not isinstance(s, str): s = str(s)
    # Unreadable code #
    cnt = 0
    numChars = dSep + '0123456789'
    ls = len(s)
    while cnt < ls and s[cnt] not in numChars: cnt += 1
    lhs = s[0:cnt]
    s = s[cnt:]
    if dSep == '': cnt = -1
    else: cnt = s.rfind(dSep)
    if cnt > 0:
        rhs = dSep + s[cnt+1:]
        s = s[:cnt]
    else:
        rhs = ''
    splt=''
    while s != '':
        splt= s[-3:] + tSep + splt
        s = s[:-3]
    return lhs + splt[:-1] + rhs

################################################################################
def gps_deg_to_float(data):
    m = re.search(u"(\d+?)°(\d+?)\'(\d+?)\'\'", data.strip())
    degs, mins, secs = [0.0 if m.group(i) is None else int(m.group(i)) for i in range(1, 4)]
    comp_dir = -1 if data[-1] in ('N', 'E') else 1
    return (degs + (mins / 60) + (secs / 3600)) * comp_dir

################################################################################
def is_integer(string):
    try: int(string)
    except ValueError: return False
    return True

################################################################################
def reverse_compl_with_name(old_seq):
    """Reverse a SeqIO sequence, but keep its name intact"""
    new_seq = old_seq.reverse_complement()
    new_seq.id = old_seq.id
    new_seq.description = old_seq.description
    return new_seq

################################################################################
def prepend_to_file(path, data, bufsize=1<<15):
    # Backup the file #
    backupname = path + os.extsep + 'bak'
    # Remove previous backup if it exists #
    try: os.unlink(backupname)
    except OSError: pass
    os.rename(path, backupname)
    # Open input/output files,  note: outputfile's permissions lost #
    with open(backupname) as inputfile:
        with open(path, 'w') as outputfile:
            outputfile.write(data)
            buf = inputfile.read(bufsize)
            while buf:
                outputfile.write(buf)
                buf = inputfile.read(bufsize)
    # Remove backup on success #
    os.remove(backupname)

def append_to_file(path, data):
    with open(path, "a") as handle:
        handle.write(data)

################################################################################
def pretty_now():
    """Prints some thing like '2014-07-24 11:12:45 CEST+0200'"""
    now = datetime.datetime.now(dateutil.tz.tzlocal())
    return now.strftime("%Y-%m-%d %H:%M:%S %Z%z")

################################################################################
def andify(list_of_strings):
    """
    Given a list of strings will join them with commas
    and a final "and" word.

    >>> andify(['Apples', 'Oranges', 'Mangos'])
    'Apples, Oranges and Mangos'
    """
    result = ', '.join(list_of_strings)
    comma_index = result.rfind(',')
    if comma_index > -1: result = result[:comma_index] + ' and' + result[comma_index+1:]
    return result

################################################################################
class OrderedSet(collections.OrderedDict, collections.MutableSet):
    """A recipe for an ordered set.
    http://stackoverflow.com/a/1653978/287297"""

    def update(self, *args, **kwargs):
        if kwargs:
            raise TypeError("update() takes no keyword arguments")

        for s in args:
            for e in s:
                self.add(e)

    def add(self, elem):
        self[elem] = None

    def discard(self, elem):
        self.pop(elem, None)

    def __le__(self, other):
        return all(e in other for e in self)

    def __lt__(self, other):
        return self <= other and self != other

    def __ge__(self, other):
        return all(e in self for e in other)

    def __gt__(self, other):
        return self >= other and self != other

    def __repr__(self):
        return 'OrderedSet([%s])' % (', '.join(map(repr, self.keys())))

    def __str__(self):
        return '{%s}' % (', '.join(map(repr, self.keys())))

    difference = property(lambda self: self.__sub__)
    difference_update = property(lambda self: self.__isub__)
    intersection = property(lambda self: self.__and__)
    intersection_update = property(lambda self: self.__iand__)
    issubset = property(lambda self: self.__le__)
    issuperset = property(lambda self: self.__ge__)
    symmetric_difference = property(lambda self: self.__xor__)
    symmetric_difference_update = property(lambda self: self.__ixor__)
    union = property(lambda self: self.__or__)

################################################################################
def get_next_item(iterable):
    """Gets the next item of an iterable.
    If the iterable is exhausted, returns None."""
    try: x = iterable.next()
    except StopIteration: x = None
    except AttributeError: x = None
    return x

# -*- coding: utf-8 -*- # Built-in modules # # Third party modules # # One liners # ################################################################################ ################################################################################ Group a list of strings by pairs, by matching those with only     one character difference between each other together. # This shallow copies the list ################################################################################ Return the number of characters in a string that don't exactly match ################################################################################ ################################################################################ A generator with a length attribute ############################################################################### A password object that will only prompt the user once per session ################################################################################ Compute the md5 of a file. Pretty fast ################################################################################ Iterative mean ############################################################################### This is essentially a convolving operation. Several option exist for dealing with the border cases.          * None: Here the returned signal will be smaller than the inputted interval.          * zero_padding: Here the returned signal will be larger than the inputted interval and we will add zeros to the original interval before operating the convolution.          * zero_padding_and_cut: Same as above only the result is truncated to be the same size as the original input.          * copy_padding: Here the returned signal will be larger than the inputted interval and we will use the right and leftmost values for padding before operating the convolution.          * copy_padding_and_cut: Same as above only the result is truncated to be the same size as the original input.          * zero_stretching: Here we will compute the convolution only in the valid domain, then add zeros to the result so that the output is the same size as the input.          * copy_stretching: Here we will compute the convolution only in the valid domain, then copy the right and leftmost values so that the output is the same size as the input. # The window size in half # # The normalized rectangular signal # # How do we deal with borders # ################################################################################ ################################################################################ Downsample an enumerable list of things # Determine length # # Check size coherence # # Do it # # Did we pick the right amount # ################################################################################ Iterative mean ################################################################################ ############################################################################### Generate the lines of file in reverse order. Generate blocks of file's contents in reverse order. ############################################################################### ############################################################################### Sort strings that contain numbers correctly.      >>> l = ['v1.3.12', 'v1.3.3', 'v1.2.5', 'v1.2.15', 'v1.2.3', 'v1.2.1']     >>> l.sort(key=natural_sort)     >>> l.__repr__()     "['v1.2.1', 'v1.2.3', 'v1.2.5', 'v1.2.15', 'v1.3.3', 'v1.3.12']" ############################################################################### https://github.com/jc0n/python-which ################################################################################ # Seek back one whole BUFSIZ # Read BUFFER # File too small, start from beginning # Only read what was not read ################################################################################ ############################################################################### Splits a number on thousands.     http://code.activestate.com/recipes/498181-add-thousands-separator-commas-to-formatted-number/      >>> split_thousands(1000012)     "1'000'012" # Check input # # Check for int # # Make string # # Unreadable code # ################################################################################ ################################################################################ ################################################################################ Reverse a SeqIO sequence, but keep its name intact ################################################################################ # Backup the file # # Remove previous backup if it exists # # Open input/output files,  note: outputfile's permissions lost # # Remove backup on success # ################################################################################ Prints some thing like '2014-07-24 11:12:45 CEST+0200' ################################################################################ Given a list of strings will join them with commas     and a final "and" word.      >>> andify(['Apples', 'Oranges', 'Mangos'])     'Apples, Oranges and Mangos' ################################################################################ A recipe for an ordered set.     http://stackoverflow.com/a/1653978/287297 ################################################################################ Gets the next item of an iterable.     If the iterable is exhausted, returns None.