Python utils.open_profile函数代码示例

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本文整理汇总了Python中utils.open_profile函数的典型用法代码示例。如果您正苦于以下问题：Python open_profile函数的具体用法？Python open_profile怎么用？Python open_profile使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。

在下文中一共展示了open_profile函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Python代码示例。

示例1: test_scale

    def test_scale(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        filename_left = self.empty()
        filename_right = self.empty()

        with utils.open_profile(self.profile(counts_left, 8)) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8)) as handle_right:
                with utils.open_profile(filename_left, 'w') as out_left:
                    with utils.open_profile(filename_right, 'w') as out_right:
                        kmer.scale(handle_left, handle_right, out_left, out_right)

        if sum(counts_left.values()) < sum(counts_right.values()):
            scale_left = sum(counts_right.values()) / sum(counts_left.values())
            scale_right = 1.0
        else:
            scale_left = 1.0
            scale_right = sum(counts_left.values()) / sum(counts_right.values())

        for s in counts_left:
            counts_left[s] *= scale_left
        for s in counts_right:
            counts_right[s] *= scale_right

        utils.test_profile_file(filename_left, counts_left, 8)
        utils.test_profile_file(filename_right, counts_right, 8)

开发者ID:Biomarino，项目名称:kPAL，代码行数:26，代码来源:test_kmer.py

示例2: test_balance

    def test_balance(self):
        counts = utils.counts(utils.SEQUENCES, 8)
        filename = self.empty()

        with utils.open_profile(self.profile(counts, 8)) as input_handle:
            with utils.open_profile(filename, 'w') as output_handle:
                kmer.balance(input_handle, output_handle)
        counts.update(dict((utils.reverse_complement(s), c) for s, c in counts.items()))
        utils.test_profile_file(filename, counts, 8)

开发者ID:Biomarino，项目名称:kPAL，代码行数:9，代码来源:test_kmer.py

示例3: test_profile_from_file_save

    def test_profile_from_file_save(self):
        counts = utils.counts(utils.SEQUENCES, 4)
        with utils.open_profile(self.profile(counts, 4), 'r') as profile_handle:
            profile = klib.Profile.from_file(profile_handle)

        filename = self.empty()
        with utils.open_profile(filename, 'w') as profile_handle:
            profile.save(profile_handle)

        utils.test_profile_file(filename, counts, 4)

开发者ID:LUMC，项目名称:kPAL，代码行数:10，代码来源:test_klib.py

示例4: test_distance

    def test_distance(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
                kmer.distance(handle_left, handle_right, out)

        assert out.getvalue() == 'left right %.10f\n' % 0.4626209323

开发者ID:Biomarino，项目名称:kPAL，代码行数:10，代码来源:test_kmer.py

示例5: test_distance_smooth

    def test_distance_smooth(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
                kmer.distance(handle_left, handle_right, out, do_smooth=True, precision=3)

        assert out.getvalue() == 'left right 0.077\n'

开发者ID:Biomarino，项目名称:kPAL，代码行数:10，代码来源:test_kmer.py

示例6: test_merge

    def test_merge(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        filename = self.empty()

        with utils.open_profile(self.profile(counts_left, 8)) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8)) as handle_right:
                with utils.open_profile(filename, 'w') as profile_handle:
                    kmer.merge(handle_left, handle_right, profile_handle)
        utils.test_profile_file(filename, counts_left + counts_right, 8)

开发者ID:Biomarino，项目名称:kPAL，代码行数:10，代码来源:test_kmer.py

示例7: test_distance_smooth_expr

    def test_distance_smooth_expr(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
                kmer.distance(handle_left, handle_right, out, do_smooth=True,
                              precision=3, custom_summary='np.max(values)')

        assert out.getvalue() == 'left right 0.474\n'

开发者ID:Biomarino，项目名称:kPAL，代码行数:11，代码来源:test_kmer.py

示例8: test_distance_pairwise_expr

    def test_distance_pairwise_expr(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
                kmer.distance(handle_left, handle_right, out, precision=3,
                              custom_pairwise='abs(left - right) / (left + right + 1000)')

        assert out.getvalue() == 'left right 0.001\n'

开发者ID:Biomarino，项目名称:kPAL，代码行数:11，代码来源:test_kmer.py

示例9: test_distance_pairwise_name

    def test_distance_pairwise_name(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        out = StringIO()

        with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
                kmer.distance(handle_left, handle_right, out, precision=3,
                              custom_pairwise='numpy.multiply')

        assert out.getvalue() == 'left right 0.084\n'

开发者ID:Biomarino，项目名称:kPAL，代码行数:11，代码来源:test_kmer.py

示例10: test_cat_prefixes

    def test_cat_prefixes(self):
        counts_a = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_b = utils.counts(utils.SEQUENCES_RIGHT, 8)
        filename = self.empty()

        with utils.open_profile(self.profile(counts_a, 8, name='X')) as handle_a:
            with utils.open_profile(self.profile(counts_b, 8, name='X')) as handle_b:
                with utils.open_profile(filename, 'w') as profile_handle:
                    kmer.cat([handle_a, handle_b], profile_handle, prefixes=['a_', 'b_'])
        utils.test_profile_file(filename, counts_a, 8, name='a_X')
        utils.test_profile_file(filename, counts_b, 8, name='b_X')

开发者ID:Biomarino，项目名称:kPAL，代码行数:11，代码来源:test_kmer.py

示例11: test_shrink

    def test_shrink(self):
        counts = utils.counts(utils.SEQUENCES, 8)
        filename = self.empty()

        with utils.open_profile(self.profile(counts, 8)) as input_handle:
            with utils.open_profile(filename, 'w') as output_handle:
                kmer.shrink(input_handle, output_handle, 1)

        counts = Counter(dict((t, sum(counts[u] for u in counts
                                            if u.startswith(t)))
                                    for t in set(s[:-1] for s in counts)))
        utils.test_profile_file(filename, counts, 7)

开发者ID:Biomarino，项目名称:kPAL，代码行数:12，代码来源:test_kmer.py

示例12: test_smooth_custom_name

    def test_smooth_custom_name(self):
        # See test_kdistlib.test_ProfileDistance_dynamic_smooth
        counts_left = Counter(['AC', 'AG', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA', 'TG', 'TT'])
        counts_right = Counter(['AC', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA', 'TC', 'TG', 'TT'])
        filename_left = self.empty()
        filename_right = self.empty()

        with utils.open_profile(self.profile(counts_left, 2)) as handle_left:
            with utils.open_profile(self.profile(counts_right, 2)) as handle_right:
                with utils.open_profile(filename_left, 'w') as out_left:
                    with utils.open_profile(filename_right, 'w') as out_right:
                        kmer.smooth(handle_left, handle_right, out_left, out_right, custom_summary='numpy.max')

开发者ID:Biomarino，项目名称:kPAL，代码行数:12，代码来源:test_kmer.py

示例13: test_shuffle

    def test_shuffle(self):
        # See test_klib.profile_shuffle
        counts = utils.counts(utils.SEQUENCES, 2)
        filename = self.empty()

        with utils.open_profile(self.profile(counts, 2)) as input_handle:
            with utils.open_profile(filename, 'w') as output_handle:
                np.random.seed(100)
                kmer.shuffle(input_handle, output_handle)

        counts = dict(zip([''.join(s) for s in itertools.product('ACGT', repeat=2)],
                          [13,  7,  6, 18, 12,  1, 13, 17, 16, 12, 23, 27, 24, 17, 18, 12]))
        utils.test_profile_file(filename, counts, 2)

开发者ID:Biomarino，项目名称:kPAL，代码行数:13，代码来源:test_kmer.py

示例14: test_merge_custom_name

    def test_merge_custom_name(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        filename = self.empty()

        with utils.open_profile(self.profile(counts_left, 8)) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8)) as handle_right:
                with utils.open_profile(filename, 'w') as profile_handle:
                    kmer.merge(handle_left, handle_right, profile_handle, custom_merger='numpy.multiply')

        counts_mult = Counter(dict((s, counts_left[s] * counts_right[s])
                                   for s in set(counts_left) & set(counts_right)))

        utils.test_profile_file(filename, counts_mult, 8)

开发者ID:Biomarino，项目名称:kPAL，代码行数:14，代码来源:test_kmer.py

示例15: test_merge_custom_expr

    def test_merge_custom_expr(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        filename = self.empty()

        with utils.open_profile(self.profile(counts_left, 8)) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8)) as handle_right:
                with utils.open_profile(filename, 'w') as profile_handle:
                    kmer.merge(handle_left, handle_right, profile_handle, custom_merger='(left + right) * np.logical_xor(left, right)')

        counts_xor = counts_left + counts_right
        for s in set(counts_left) & set(counts_right):
            del counts_xor[s]

        utils.test_profile_file(filename, counts_xor, 8)

开发者ID:Biomarino，项目名称:kPAL，代码行数:15，代码来源:test_kmer.py

示例16: test_count

 def test_count(self):
     counts = utils.counts(utils.SEQUENCES, 8)
     filename = self.empty()
     with open(self.fasta(utils.SEQUENCES)) as fasta_handle:
         with utils.open_profile(filename, 'w') as profile_handle:
             kmer.count([fasta_handle], profile_handle, 8)
     utils.test_profile_file(filename, counts, 8)

开发者ID:Biomarino，项目名称:kPAL，代码行数:7，代码来源:test_kmer.py

示例17: test_convert

 def test_convert(self):
     counts = utils.counts(utils.SEQUENCES, 8)
     filename = self.empty()
     with open(self.profile_old_format(counts, 8)) as handle:
         with utils.open_profile(filename, 'w') as profile_handle:
             kmer.convert([handle], profile_handle)
     utils.test_profile_file(filename, counts, 8)

开发者ID:Biomarino，项目名称:kPAL，代码行数:7，代码来源:test_kmer.py

示例18: test_positive

    def test_positive(self):
        counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
        counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
        filename_left = self.empty()
        filename_right = self.empty()

        with utils.open_profile(self.profile(counts_left, 8)) as handle_left:
            with utils.open_profile(self.profile(counts_right, 8)) as handle_right:
                with utils.open_profile(filename_left, 'w') as out_left:
                    with utils.open_profile(filename_right, 'w') as out_right:
                        kmer.positive(handle_left, handle_right, out_left, out_right)

        utils.test_profile_file(filename_left, Counter(s for s in counts_left.elements()
                                                             if s in counts_right), 8)
        utils.test_profile_file(filename_right, Counter(s for s in counts_right.elements()
                                                              if s in counts_left), 8)

开发者ID:Biomarino，项目名称:kPAL，代码行数:16，代码来源:test_kmer.py

示例19: test_get_balance

    def test_get_balance(self):
        counts = utils.counts(utils.SEQUENCES, 8)
        out = StringIO()

        with utils.open_profile(self.profile(counts, 8)) as input_handle:
            kmer.get_balance(input_handle, out, precision=3)

        assert out.getvalue() == '1 0.669\n'

开发者ID:Biomarino，项目名称:kPAL，代码行数:8，代码来源:test_kmer.py

示例20: test_count_by_record

 def test_count_by_record(self):
     counts_by_record = [utils.counts(record, 8) for record in utils.SEQUENCES]
     names = [str(i) for i, _ in enumerate(counts_by_record)]
     filename = self.empty()
     with open(self.fasta(utils.SEQUENCES, names=names)) as fasta_handle:
         with utils.open_profile(filename, 'w') as profile_handle:
             kmer.count([fasta_handle], profile_handle, 8, by_record=True)
     for name, counts in zip(names, counts_by_record):
         utils.test_profile_file(filename, counts, 8, name=name)

开发者ID:LUMC，项目名称:kPAL，代码行数:9，代码来源:test_kmer.py

注：本文中的utils.open_profile函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。

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Python utils.open_profile函数代码示例

示例1: test_scale

示例2: test_balance

示例3: test_profile_from_file_save

示例4: test_distance

示例5: test_distance_smooth

示例6: test_merge

示例7: test_distance_smooth_expr

示例8: test_distance_pairwise_expr

示例9: test_distance_pairwise_name

示例10: test_cat_prefixes

示例11: test_shrink

示例12: test_smooth_custom_name

示例13: test_shuffle

示例14: test_merge_custom_name

示例15: test_merge_custom_expr

示例16: test_count

示例17: test_convert

示例18: test_positive

示例19: test_get_balance

示例20: test_count_by_record

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