/usr/share/pyshared/cogent/seqsim/randomization.py is in python-cogent 1.5.3-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 | #!/usr/bin/env python
"""Provides utility methods for randomization.
"""
from random import shuffle
from cogent.util.misc import find_many
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Development"
def shuffle_range(items, start, end):
"""Randomizes region of items between start and end indices, in-place.
Shuffle affects items[start] but not items[end], as ususal for
slice operations.
Items slices must be assignable.
No return value, as per standard for in-place operations.
"""
length = len(items)
#handle negative indices
if start < 0:
start += length
if end < 0:
end += length
#skip if 0 or 1 items
if end - start > 1: #shuffle has no effect on 0 or 1 item
curr = items[start:end]
shuffle(curr)
items[start:end] = curr[:]
def shuffle_between(items, constructor=None):
"""Returns function that shuffles each part of seq between specified items.
If constructor is not passed, uses ''.join() for subclasses of strings,
and seq.__class__ for everything else.
Note that each interval between items is shuffled independently: use
shuffle_except to keep a particular item in place while shuffling
everything else.
The resulting function takes only the sequence as an argument, so can be
passed e.g. to map().
"""
c = constructor
def result(seq):
"""Returns copy of seq shuffled between specified items."""
#figure out the appropriate constructor, if not supplied
if c is None:
if isinstance(seq, str):
constructor = lambda x: seq.__class__(''.join(x))
else:
constructor = seq.__class__
else:
constructor = c
#figure out where to cut the sequence
cut_sites = find_many(seq, items)
#want to shuffle sequence before first and after last match as well
if (not cut_sites) or cut_sites[0] != 0:
cut_sites.insert(0, 0)
seq_length = len(seq)
if cut_sites[-1] != seq_length:
cut_sites.append(seq_length)
#shuffle each pair of (i, i+1) matches, excluding position of match
curr_seq = list(seq)
for start, end in zip(cut_sites, cut_sites[1:]):
shuffle_range(curr_seq, start+1, end) #remember to exclude start
#return the shuffled copy
return constructor(curr_seq)
#return the resulting function
return result
#example of shuffle_between
shuffle_peptides = shuffle_between('KR', ''.join)
def shuffle_except_indices(items, indices):
"""Shuffles all items in list in place, except at specified indices.
items must be slice-assignable.
Uses linear algorithm, so suitable for long lists.
"""
length = len(items)
if not length:
return []
orig = items[:]
sorted_indices = indices[:]
#make indices positive
for i, s in enumerate(sorted_indices):
if s < 0:
sorted_indices[i] = length + s
sorted_indices.sort()
sorted_indices.reverse()
last = None
for i in sorted_indices:
if i != last: #skip repeated indices in list
del items[i]
last = i
shuffle(items)
sorted_indices.reverse()
last = None
for i in sorted_indices:
if i != last:
items.insert(i, orig[i])
last = i
def shuffle_except(items, constructor=None):
"""Returns function that shuffles a sequence except specified items.
If constructor is not passed, uses ''.join() for subclasses of strings,
and seq.__class__ for everything else.
Note that all intervals are shuffled together; use shuffle_between
to shuffle the items in each interval separately.
The resulting function takes only the sequence as an argument, so can be
passed e.g. to map().
"""
c = constructor
def result(seq):
"""Returns copy of seq shuffled between specified items."""
#figure out the appropriate constructor, if not supplied
if c is None:
if isinstance(seq, str):
constructor = lambda x: seq.__class__(''.join(x))
else:
constructor = seq.__class__
else:
constructor = c
#figure out where to cut the sequence
cut_sites = find_many(seq, items)
new_seq = list(seq)
shuffle_except_indices(new_seq, cut_sites)
return constructor(new_seq)
#return the resulting function
return result
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