Showing 473 of 473 total issues
Expected 2 blank lines, found 1 Open
def get_script(script_name):
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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
help='Discard the listed samples (default: discard samples not in the list)')
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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
It allows to avoid divergence far from the main diagonal with a very few reads.
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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: :class:`pandas.DataFrame` giving the radial position of each window
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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
from . import call_windows, segregation, qc, select_samples, cosegregation, utils
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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
'samtools view -q %(minimum_mapq)s -F 4 -bS - > %(targets)s'],
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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 (89 > 79 characters) Open
'actions': ['echo "chrom start stop %(dependencies)s" > %(targets)s',
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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
'file_dep': [segregation_path(self.args.output_dir, window_size)],
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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
'targets': [swap_extension(segregation_file, '.passed_qc.table')],
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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
means_matrix[ix_1, ix_2] = bin_comb_means[get_key(col_labels[ix_1], col_labels[ix_2])]
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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)
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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
help='If specified, require at least this many reads to call a window as positive')
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- Exclude checks
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
from distutils.version import LooseVersion #pylint: disable=no-name-in-module,import-error
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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.
Invalid escape sequence '.' Open
vnum_regexp = b'^Version:\s(?P<version>(\d+\.){1,2}(\d+))'
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Invalid escape sequences are deprecated in Python 3.6.
Okay: regex = r'\.png$'
W605: regex = '\.png$'
Line too long (93 > 79 characters) Open
"actions": ['bedGraphToBigWig %(dependencies)s %(genome_file)s %(targets)s'],
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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
'actions': ['%(mapping_stats_script)s %(dependencies)s > %(targets)s'],
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- Exclude checks
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
:param segregation_table: Input :ref:`segregation table <segregation_table>`
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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 \
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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
window_coverage = get_segregation_coverage_qc(segregation_table, skip_chroms,
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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']]
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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.