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lib/gamtools/matrix.py

Summary

Maintainability
C
1 day
Test Coverage

File matrix.py has 451 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
=================
The matrix module
=================
Severity: Minor
Found in lib/gamtools/matrix.py - About 6 hrs to fix

    Cyclomatic complexity is too high in function convert_from_args. (8)
    Open

    def convert_from_args(args):
    """Wrapper function to call convert from argparse"""

    if args.input_format is None:
        args.input_format = detect_file_type(args.input_file)
    Severity: Minor
    Found in lib/gamtools/matrix.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

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

    def check_windows(proximity_matrix, windows):
    """Check that a list of axis windows matches the dimensions of a proximity matrix.

    :param proximity_matrix: Input proximity matrix.
    :type proximity_matrix: :class:`numpy array <numpy.ndarray>`
    Severity: Minor
    Found in lib/gamtools/matrix.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 convert_from_args has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    Open

    def convert_from_args(args):
    """Wrapper function to call convert from argparse"""

    if args.input_format is None:
        args.input_format = detect_file_type(args.input_file)
    Severity: Minor
    Found in lib/gamtools/matrix.py - About 1 hr to fix

    Cognitive Complexity

    Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

    A method's cognitive complexity is based on a few simple rules:

    • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
    • Code is considered more complex for each "break in the linear flow of the code"
    • Code is considered more complex when "flow breaking structures are nested"

    Further reading

    Function convert has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def convert(input_file, input_format, #pylint: disable=too-many-arguments
    Severity: Major
    Found in lib/gamtools/matrix.py - About 50 mins to fix

      TODO found
      Open

          # TODO: Convert from interactions csv back into a matrix
      Severity: Minor
      Found in lib/gamtools/matrix.py by fixme

      Line too long (81 > 79 characters)
      Open

          """Retrieve a sub-region of an interaction matrix based on a location string.
      Severity: Minor
      Found in lib/gamtools/matrix.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 (91 > 79 characters)
      Open

              windows1, columns=['chrom', 'start', 'stop']).set_index(['chrom', 'start', 'stop'])
      Severity: Minor
      Found in lib/gamtools/matrix.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

          return region_from_locations(matrix_tuple, location_string1, location_string2)
      Severity: Minor
      Found in lib/gamtools/matrix.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 (90 > 79 characters)
      Open

                  'Could not determine file format, file {} has no extension'.format(file_name))
      Severity: Minor
      Found in lib/gamtools/matrix.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 location_string2: UCSC format :ref:`location string <location_string>`, \
      Severity: Minor
      Found in lib/gamtools/matrix.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.

      Inline comment should start with '# '
      Open

      def convert(input_file, input_format, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/matrix.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

      Line too long (82 > 79 characters)
      Open

      where the columns and rows are the columns and rows of the matrix, plus one header
      Severity: Minor
      Found in lib/gamtools/matrix.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.

      At least two spaces before inline comment
      Open

          proximity_matrix[upper_i] = proximity_matrix.T[upper_i] # pylint: disable=E1136
      Severity: Minor
      Found in lib/gamtools/matrix.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

      Block comment should start with '# '
      Open

          #'csv': '',
      Severity: Minor
      Found in lib/gamtools/matrix.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

      At least two spaces before inline comment
      Open

      def write_png(windows, proximity_matrix, output_file): #pylint: disable=unused-argument
      Severity: Minor
      Found in lib/gamtools/matrix.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

      Inline comment should start with '# '
      Open

      def write_png(windows, proximity_matrix, output_file): #pylint: disable=unused-argument
      Severity: Minor
      Found in lib/gamtools/matrix.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

      Line too long (85 > 79 characters)
      Open

          :param str location_string1: UCSC format :ref:`location string <location_string>`
      Severity: Minor
      Found in lib/gamtools/matrix.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

          :param matrix_tuple: Tuple of the form (x_windows_list, y_windows_list), matrix
      Severity: Minor
      Found in lib/gamtools/matrix.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

          """Format a list of tuples representing genomic windows (chrom, start, stop)
      Severity: Minor
      Found in lib/gamtools/matrix.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 (91 > 79 characters)
      Open

          :param list windows: List of tuples in the format (chromosome, start_coord, stop_coord)
      Severity: Minor
      Found in lib/gamtools/matrix.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

          proximity_matrix[upper_i] = proximity_matrix.T[upper_i] # pylint: disable=E1136
      Severity: Minor
      Found in lib/gamtools/matrix.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 (86 > 79 characters)
      Open

          """Check that a list of axis windows matches the dimensions of a proximity matrix.
      Severity: Minor
      Found in lib/gamtools/matrix.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

          i1_start, i1_stop = segregation.index_from_location_string(windows1_df, location_string1)
      Severity: Minor
      Found in lib/gamtools/matrix.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

          i2_start, i2_stop = segregation.index_from_location_string(windows2_df, location_string2)
      Severity: Minor
      Found in lib/gamtools/matrix.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 (91 > 79 characters)
      Open

                  if None, location_string2 is set equal to location_string1 (i.e. the function \
      Severity: Minor
      Found in lib/gamtools/matrix.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 (91 > 79 characters)
      Open

                  if None, location_string2 is set equal to location_string1 (i.e. the function \
      Severity: Minor
      Found in lib/gamtools/matrix.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

          :param str location_string1: UCSC format :ref:`location string <location_string>`
      Severity: Minor
      Found in lib/gamtools/matrix.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.

      At least two spaces before inline comment
      Open

      def convert(input_file, input_format, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/matrix.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

      Line too long (80 > 79 characters)
      Open

      row and one column of row names. Text files are human readable but take up a lot
      Severity: Minor
      Found in lib/gamtools/matrix.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

      def write_png(windows, proximity_matrix, output_file): #pylint: disable=unused-argument
      Severity: Minor
      Found in lib/gamtools/matrix.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 (95 > 79 characters)
      Open

          :raises ValueError: If the number of windows doesn't match the proximity matrix dimensions.
      Severity: Minor
      Found in lib/gamtools/matrix.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 (91 > 79 characters)
      Open

              windows2, columns=['chrom', 'start', 'stop']).set_index(['chrom', 'start', 'stop'])
      Severity: Minor
      Found in lib/gamtools/matrix.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 (86 > 79 characters)
      Open

          :returns: List of lists giving genomic locations for each bin on each axis, and a\
      Severity: Minor
      Found in lib/gamtools/matrix.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

      SUPPORTED_FORMATS = list(set(list(INPUT_FORMATS.keys()) + list(OUTPUT_FORMATS.keys())))
      Severity: Minor
      Found in lib/gamtools/matrix.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 (81 > 79 characters)
      Open

      def region_from_locations(matrix_tuple, location_string1, location_string2=None):
      Severity: Minor
      Found in lib/gamtools/matrix.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

          """Open an interaction matrix and retrieve a sub-region based on a location string.
      Severity: Minor
      Found in lib/gamtools/matrix.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

                             delim_whitespace=True, comment='#').set_index('distance')
      Severity: Minor
      Found in lib/gamtools/matrix.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.

      Expected 2 blank lines after class or function definition, found 1
      Open

      OUTPUT_FORMATS = {
      Severity: Minor
      Found in lib/gamtools/matrix.py by pep8

      Separate top-level function and class definitions with two blank lines.

      Method definitions inside a class are separated by a single blank
line.

Extra blank lines may be used (sparingly) to separate groups of
related functions.  Blank lines may be omitted between a bunch of
related one-liners (e.g. a set of dummy implementations).

Use blank lines in functions, sparingly, to indicate logical
sections.

Okay: def a():\n    pass\n\n\ndef b():\n    pass
Okay: def a():\n    pass\n\n\nasync def b():\n    pass
Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
Okay: default = 1\nfoo = 1
Okay: classify = 1\nfoo = 1

E301: class Foo:\n    b = 0\n    def bar():\n        pass
E302: def a():\n    pass\n\ndef b(n):\n    pass
E302: def a():\n    pass\n\nasync def b(n):\n    pass
E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
E303: def a():\n\n\n\n    pass
E304: @decorator\n\ndef a():\n    pass
E305: def a():\n    pass\na()
E306: def a():\n    def b():\n        pass\n    def c():\n        pass

      Line too long (88 > 79 characters)
      Open

          :param str location_string2: UCSC format :ref:`location string <location_string>`, \
      Severity: Minor
      Found in lib/gamtools/matrix.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.

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