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lib/gamtools/enrichment.py

Summary

Maintainability
D
2 days
Test Coverage

File enrichment.py has 359 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
=====================
The enrichment module
=====================
Severity: Minor
Found in lib/gamtools/enrichment.py - About 4 hrs to fix

    Cyclomatic complexity is too high in function do_enrichment. (6)
    Open

    def do_enrichment(
        pairwise_interactions,
        window_classes,
        num_permutations,
        output_prefix,
    Severity: Minor
    Found in lib/gamtools/enrichment.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    Function do_enrichment has 5 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def do_enrichment(
    Severity: Minor
    Found in lib/gamtools/enrichment.py - About 35 mins to fix

      TODO found
      Open

          # TODO: Handle split interactions where one half is permuted past the
      Severity: Minor
      Found in lib/gamtools/enrichment.py by fixme

      TODO found
      Open

          # TODO: Check that this file doesn't exist
      Severity: Minor
      Found in lib/gamtools/enrichment.py by fixme

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

              doublets_df.ix[
            (doublets_df.chrom == chrom) & (
                doublets_df.Pos_A >= chrom_lengths[chrom]),
            ['Pos_A']] = np.array(
                doublets_df.ix[
      Severity: Major
      Found in lib/gamtools/enrichment.py and 1 other location - About 6 hrs to fix
      lib/gamtools/enrichment.py on lines 171..178

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 105.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Similar blocks of code found in 2 locations. Consider refactoring.
      Open

              doublets_df.ix[
            (doublets_df.chrom == chrom) & (
                doublets_df.Pos_B >= chrom_lengths[chrom]),
            ['Pos_B']] = np.array(
                doublets_df.ix[
      Severity: Major
      Found in lib/gamtools/enrichment.py and 1 other location - About 6 hrs to fix
      lib/gamtools/enrichment.py on lines 161..168

      Duplicated Code

      Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

      Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

      When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

      Tuning

      This issue has a mass of 105.

      We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

      The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

      If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

      See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

      Refactorings

      Further Reading

      Line too long (80 > 79 characters)
      Open

          ...                                      columns=['chrom', 'Pos_A', 'Pos_B',
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (88 > 79 characters)
      Open

          ...                                      columns=['chrom', 'i', 'Enhancer', 'Gene'])
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (80 > 79 characters)
      Open

          ...                                      columns=['chrom', 'Pos_A', 'Pos_B',
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (82 > 79 characters)
      Open

          :param features_df1: Table of windows allowed on one side of the interaction \
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (88 > 79 characters)
      Open

          ...                                      columns=['chrom', 'i', 'Enhancer', 'Gene'])
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (80 > 79 characters)
      Open

          >>> enrichment.randomize_doublets(pairwise_interactions, chromosome_lengths)
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (94 > 79 characters)
      Open

          """Calculate the number of pairwise pairwise_interactions connecting each class of windows
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (83 > 79 characters)
      Open

                                    overlap21[['chrom', 'Pos_A', 'Pos_B', 'interaction']]
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (88 > 79 characters)
      Open

          ...                                      columns=['chrom', 'i', 'Enhancer', 'Gene'])
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (85 > 79 characters)
      Open

          from the first classification interact with those from the second classification.
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (84 > 79 characters)
      Open

          >>> enrichment.feature_pair_values(pairwise_interactions, window_classification,
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (80 > 79 characters)
      Open

          ...                                      columns=['chrom', 'Pos_A', 'Pos_B',
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (88 > 79 characters)
      Open

          """Subset a table of interactions given two tables of possible interacting elements.
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (88 > 79 characters)
      Open

          :param str feat1: Classification of windows allowed on one side of the interaction \
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (84 > 79 characters)
      Open

          >>> enrichment.get_feature_summary(pairwise_interactions, window_classification)
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Closing bracket does not match visual indentation
      Open

                                   ]).drop_duplicates()
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
using Python's implicit line joining inside parentheses, brackets
and braces, or using a hanging indent.

When using a hanging indent these considerations should be applied:
- there should be no arguments on the first line, and
- further indentation should be used to clearly distinguish itself
  as a continuation line.

Okay: a = (\n)
E123: a = (\n    )

Okay: a = (\n    42)
E121: a = (\n   42)
E122: a = (\n42)
E123: a = (\n    42\n    )
E124: a = (24,\n     42\n)
E125: if (\n    b):\n    pass
E126: a = (\n        42)
E127: a = (24,\n      42)
E128: a = (24,\n    42)
E129: if (a or\n    b):\n    pass
E131: a = (\n    42\n 24)

      Line too long (80 > 79 characters)
      Open

          ...                                      columns=['chrom', 'Pos_A', 'Pos_B',
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (93 > 79 characters)
      Open

          :param str feat2: Classification of windows allowed on the other side of the interaction.
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Test for membership should be 'not in'
      Open

                             if not col in ['chrom', 'start', 'stop', 'i']]
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Negative comparison should be done using "not in" and "is not".

      Okay: if x not in y:\n    pass
Okay: assert (X in Y or X is Z)
Okay: if not (X in Y):\n    pass
Okay: zz = x is not y
E713: Z = not X in Y
E713: if not X.B in Y:\n    pass
E714: if not X is Y:\n    pass
E714: Z = not X.B is Y

      Line too long (84 > 79 characters)
      Open

          both_overlap = pd.concat([overlap12[['chrom', 'Pos_A', 'Pos_B', 'interaction']],
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (80 > 79 characters)
      Open

          ...                                      columns=['chrom', 'Pos_A', 'Pos_B',
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (87 > 79 characters)
      Open

          :returns: Output path in the format <prefix>_<num_permutations>.<random_string>.csv
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (83 > 79 characters)
      Open

          >>> enrichment.randomized_summary(pairwise_interactions, window_classification,
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      Line too long (87 > 79 characters)
      Open

          :param features_df2: Table of windows allowed on the other side of the interaction.
      Severity: Minor
      Found in lib/gamtools/enrichment.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

      There are no issues that match your filters.

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