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Indentation contains tabs
Open

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

On new projects, spaces-only are strongly recommended over tabs.

Okay: if True:\n    return
W191: if True:\n\treturn

At least two spaces before inline comment
Open

class DelayedImportError(): #pylint: disable=too-few-public-methods
Severity: Minor
Found in lib/gamtools/utils.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 (87 > 79 characters)
Open

    :param str location_strings: One or more :ref:`location strings <location_string>`.
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

          never detected across the dataset in calculation. This is the default \
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 (85 > 79 characters)
Open

              'least {:.0f} times. This value should be at least 20, try increasing '
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 (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.

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 (83 > 79 characters)
Open

    help='Get the radial position of each genomic window from a segmentation file')
Severity: Minor
Found in lib/gamtools/main.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 test_function(args): #pylint: disable=unused-argument
Severity: Minor
Found in lib/gamtools/main.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

from distutils.version import LooseVersion #pylint: disable=no-name-in-module,import-error
Severity: Minor
Found in lib/gamtools/pipeline.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

                            'create_empty_bedgraph %(genome_file)s %(targets)s; fi'],
Severity: Minor
Found in lib/gamtools/pipeline.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.

Too many blank lines (2)
Open

    def task_merge_bp_coverage(self):
Severity: Minor
Found in lib/gamtools/pipeline.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 (81 > 79 characters)
Open

                    self.args.output_dir, self.args.fitting_folder, '{0}'.format(
Severity: Minor
Found in lib/gamtools/pipeline.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.

Block comment should start with '# '
Open

    #pylint: disable=too-many-locals
Severity: Minor
Found in lib/gamtools/bias.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

Missing whitespace after ':'
Open

    bin_comb_means = {labels:np.nanmean(np.concatenate(values, axis=None))
Severity: Minor
Found in lib/gamtools/bias.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Line too long (97 > 79 characters)
Open

        '#Base  Mean    Median  Lower Quartile  Upper Quartile  10th Percentile 90th Percentile',
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.

Expected 2 blank lines, found 1
Open

def is_fq_screen_header_row(fields):
Severity: Minor
Found in lib/gamtools/qc/screen.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

Expected 2 blank lines, found 1
Open

def write_contamination_stats(input_files, output_file):
Severity: Minor
Found in lib/gamtools/qc/screen.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

Expected 2 blank lines, found 1
Open

def proportion_with_neighbours(block_list):
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 (86 > 79 characters)
Open

    :returns: :ref:`proximity matrix <proximity_matrices>` giving the co-segregation \
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.
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