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Line too long (81 > 79 characters)
Open

            of all possible combinations of windows within the different regions.
Severity: Minor
Found in lib/gamtools/cosegregation.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

            of all possible combinations of windows within the different regions.
Severity: Minor
Found in lib/gamtools/cosegregation.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

    :param str matrix_type: Type of :ref:`proximity matrix <proximity_matrices>`\
Severity: Minor
Found in lib/gamtools/cosegregation.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 (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 (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 (87 > 79 characters)
Open

    bottom_percentile, top_percentile = (int(pct) for pct in percentile_str.split(','))
Severity: Minor
Found in lib/gamtools/call_windows.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.

Indentation contains mixed spaces and tabs
Open

                 min_reads=None):
Severity: Minor
Found in lib/gamtools/call_windows.py by pep8

Never mix tabs and spaces.

The most popular way of indenting Python is with spaces only.  The
second-most popular way is with tabs only.  Code indented with a
mixture of tabs and spaces should be converted to using spaces
exclusively.  When invoking the Python command line interpreter with
the -t option, it issues warnings about code that illegally mixes
tabs and spaces.  When using -tt these warnings become errors.
These options are highly recommended!

Okay: if a == 0:\n    a = 1\n    b = 1
E101: if a == 0:\n        a = 1\n\tb = 1

Line too long (80 > 79 characters)
Open

    if len(fastqc_module) == 1 and module_name == '>>Overrepresented sequences':
Severity: Minor
Found in lib/gamtools/qc/fastqc.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

    :returns: left reference, right reference (at least one must be a column of \
Severity: Minor
Found in lib/gamtools/qc/pass_qc.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 right: Either a series of QC values or a value to compare QC values to.
Severity: Minor
Found in lib/gamtools/qc/pass_qc.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, found 1
Open

def get_df_stats(segregation_df):
Severity: Minor
Found in lib/gamtools/qc/segregation.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 (89 > 79 characters)
Open

    """Take a table of n columns and return the n-dimensional co-segregation frequencies.
Severity: Minor
Found in lib/gamtools/cosegregation.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

    :returns: An n-dimensional contingency table giving the cosegregation frequencies of all \
Severity: Minor
Found in lib/gamtools/cosegregation.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

    """Calculate the normalized pointwise mutual information (npmi) matrix for a given
Severity: Minor
Found in lib/gamtools/cosegregation.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 ':' in loc_string:
Severity: Minor
Found in lib/gamtools/cosegregation.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 (83 > 79 characters)
Open

    plot_coverage_histogram(sample_name, sample_coverage_data, sample_fitting_data)
Severity: Minor
Found in lib/gamtools/call_windows.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: segregation_table (a :ref:`segregation table <segregation_table>`) and \
Severity: Minor
Found in lib/gamtools/call_windows.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

              'the genomic window size for this dataset.'.format(window_coverage))
Severity: Minor
Found in lib/gamtools/resolution.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.
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