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src/c/o/cogent-1.5.3/cogent/core/usage.py   cogent(Download)
from cogent.maths.stats.special import fix_rounding_error
from cogent.util.array import euclidean_distance
from cogent.util.misc import Delegator, FunctionWrapper, InverseDict
from cogent.core.genetic_code import GeneticCodes, GeneticCode as GenCodeClass
from cogent.core.info import Info as InfoClass
    SplitBlocks = ['UU', 'CA','AU','AA','AG','GA'] #UCAG order]
 
    AbbreviationsToBlocks = InverseDict(BlockAbbreviations)
    NamesToBlocks = InverseDict(BlockNames)
 

src/p/y/pycogent-HEAD/cogent/core/usage.py   pycogent(Download)
from cogent.maths.stats.special import fix_rounding_error
from cogent.util.array import euclidean_distance
from cogent.util.misc import Delegator, FunctionWrapper, InverseDict
from cogent.core.genetic_code import GeneticCodes, GeneticCode as GenCodeClass
from cogent.core.info import Info as InfoClass
    SplitBlocks = ['UU', 'CA','AU','AA','AG','GA'] #UCAG order]
 
    AbbreviationsToBlocks = InverseDict(BlockAbbreviations)
    NamesToBlocks = InverseDict(BlockNames)
 

src/c/o/cogent-1.5.3/cogent/parse/sprinzl.py   cogent(Download)
#/usr/bin/env python
"""Parsers for the Sprinzl tRNA databases.
"""
from cogent.util.misc import InverseDict
from string import strip, maketrans
        if first:   #label line
            label_fields = fields[5:]
            labels = InverseDict(enumerate(label_fields))
            first = False
        else:
            line = line.replace('.', '0')
            fields = line.split('\t')
            labels = InverseDict(enumerate(fields[num_blanks:]))
            first = False
            offset = 0

src/p/y/pycogent-HEAD/cogent/parse/sprinzl.py   pycogent(Download)
#/usr/bin/env python
"""Parsers for the Sprinzl tRNA databases.
"""
from cogent.util.misc import InverseDict
from string import strip, maketrans
        if first:   #label line
            label_fields = fields[5:]
            labels = InverseDict(enumerate(label_fields))
            first = False
        else:
            line = line.replace('.', '0')
            fields = line.split('\t')
            labels = InverseDict(enumerate(fields[num_blanks:]))
            first = False
            offset = 0

src/q/i/qiime-1.8.0/qiime/make_otu_table.py   qiime(Download)
from sys import stderr
from numpy import array, zeros
from cogent.util.misc import flatten, InverseDict
from qiime.format import format_otu_table
from qiime.parse import parse_otu_map

src/c/o/cogent-1.5.3/cogent/core/tree.py   cogent(Download)
from cogent.maths.stats.test import correlation
from operator import or_
from cogent.util.misc import InverseDict
from random import shuffle, choice
 

src/p/y/pycogent-HEAD/cogent/core/tree.py   pycogent(Download)
from cogent.maths.stats.test import correlation
from operator import or_
from cogent.util.misc import InverseDict
from random import shuffle, choice
 

src/c/o/cogent-1.5.3/tests/test_util/test_misc.py   cogent(Download)
from cogent.app.util import get_tmp_filename
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import (iterable, max_index, min_index,
    flatten, is_iterable, is_char, is_char_or_noniterable,
    is_str_or_noniterable, not_list_tuple, list_flatten,
            {'x':'a',1:'b',None:'c',('a','b'):'d'})
        self.assertRaises(TypeError, InverseDict, {'a':['a','b','c']})
        d = InverseDict({'a':3, 'b':3, 'c':3})
        self.assertEqual(len(d), 1)
        assert 3 in d

src/p/y/pycogent-HEAD/tests/test_util/test_misc.py   pycogent(Download)
from cogent.app.util import get_tmp_filename
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import (iterable, max_index, min_index,
    flatten, is_iterable, is_char, is_char_or_noniterable,
    is_str_or_noniterable, not_list_tuple, list_flatten,
            {'x':'a',1:'b',None:'c',('a','b'):'d'})
        self.assertRaises(TypeError, InverseDict, {'a':['a','b','c']})
        d = InverseDict({'a':3, 'b':3, 'c':3})
        self.assertEqual(len(d), 1)
        assert 3 in d