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src/c/o/cogent-1.5.3/cogent/maths/stats/alpha_diversity.py   cogent(Download)
    ymtx = []
    for i in range(num_repeats):
        ymtx.append( array([observed_species(rarefaction.subsample(counts,n)) \
        for n in xvals]))
    ymtx = asarray(ymtx)

src/p/y/pycogent-HEAD/cogent/maths/stats/alpha_diversity.py   pycogent(Download)
    ymtx = []
    for i in range(num_repeats):
        ymtx.append( array([observed_species(rarefaction.subsample(counts,n)) \
        for n in xvals]))
    ymtx = asarray(ymtx)

src/q/i/qiime-1.8.0/qiime/parse.py   qiime(Download)
from cogent.util.dict2d import Dict2D
from cogent.util.misc import unzip
from cogent.maths.stats.rarefaction import subsample
from numpy import concatenate, repeat, zeros, nan, asarray
from numpy.random import permutation
    if too_big_samples.shape[0]:    #means that there were some
        for i in too_big_samples:
            otu_table[:,i] = subsample(otu_table[:,i].ravel(), \
                max_seqs_per_sample)
    return sample_ids, otu_ids, otu_table, lineages

src/q/i/qiime-1.8.0/qiime/pycogent_backports/alpha_diversity.py   qiime(Download)
    ymtx = []
    for i in range(num_repeats):
        ymtx.append( array([observed_species(rarefaction.subsample(counts,n)) \
        for n in xvals]))
    ymtx = asarray(ymtx)

src/q/i/qiime-1.8.0/qiime/rarefaction.py   qiime(Download)
import numpy
from numpy import inf
from cogent.maths.stats.rarefaction import (subsample,
                                                  subsample_freq_dist_nonzero,
                                                  subsample_random,

src/q/i/qiime-1.8.0/scripts/single_rarefaction.py   qiime(Download)
__email__ = "justinak@gmail.com"
 
from cogent.maths.stats.rarefaction import subsample, subsample_multinomial
from qiime.util import parse_command_line_parameters
from qiime.util import make_option

src/q/i/qiime-1.8.0/scripts/multiple_rarefactions.py   qiime(Download)
__email__ = "justinak@gmail.com"
 
from cogent.maths.stats.rarefaction import subsample, subsample_multinomial
from qiime.util import parse_command_line_parameters, create_dir
from qiime.util import make_option

src/c/o/cogent-1.5.3/tests/test_maths/test_stats/test_rarefaction.py   cogent(Download)
#!/usr/bin/env python
#file test_parse.py
from numpy import array
from cogent.util.unit_test import TestCase, main
from cogent.maths.stats.rarefaction import (subsample,
        actual = {}
        for i in range(1000):
            e = subsample(b,2)
            actual[tuple(e)] = None
        self.assertEqual(actual, {(1,0,1):None,(2,0,0):None})
 
        obs = subsample(b,2)

src/p/y/pycogent-HEAD/tests/test_maths/test_stats/test_rarefaction.py   pycogent(Download)
#!/usr/bin/env python
#file test_parse.py
from numpy import array
from cogent.util.unit_test import TestCase, main
from cogent.maths.stats.rarefaction import (subsample,
        actual = {}
        for i in range(1000):
            e = subsample(b,2)
            actual[tuple(e)] = None
        self.assertEqual(actual, {(1,0,1):None,(2,0,0):None})
 
        obs = subsample(b,2)