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Remove excessive blank lines (PEP8 E303).

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1 parent bfa8b25 commit 9c76921b919bc19e063168b295ad355b26e8357b @cbrueffer cbrueffer committed with peterjc Dec 5, 2012
Showing with 0 additions and 320 deletions.
  1. +0 −3 Bio/Align/AlignInfo.py
  2. +0 −1 Bio/Align/Generic.py
  3. +0 −2 Bio/AlignIO/EmbossIO.py
  4. +0 −1 Bio/AlignIO/FastaIO.py
  5. +0 −2 Bio/AlignIO/StockholmIO.py
  6. +0 −2 Bio/Alphabet/__init__.py
  7. +0 −1 Bio/Blast/Applications.py
  8. +0 −1 Bio/Blast/NCBIStandalone.py
  9. +0 −1 Bio/Compass/__init__.py
  10. +0 −1 Bio/Crystal/__init__.py
  11. +0 −2 Bio/Data/CodonTable.py
  12. +0 −2 Bio/FSSP/__init__.py
  13. +0 −1 Bio/GenBank/__init__.py
  14. +0 −1 Bio/Graphics/BasicChromosome.py
  15. +0 −5 Bio/Graphics/GenomeDiagram/_AbstractDrawer.py
  16. +0 −14 Bio/Graphics/GenomeDiagram/_CircularDrawer.py
  17. +0 −5 Bio/Graphics/GenomeDiagram/_Colors.py
  18. +0 −5 Bio/Graphics/GenomeDiagram/_Diagram.py
  19. +0 −2 Bio/Graphics/GenomeDiagram/_Feature.py
  20. +0 −9 Bio/Graphics/GenomeDiagram/_FeatureSet.py
  21. +0 −8 Bio/Graphics/GenomeDiagram/_Graph.py
  22. +0 −10 Bio/Graphics/GenomeDiagram/_GraphSet.py
  23. +0 −7 Bio/Graphics/GenomeDiagram/_LinearDrawer.py
  24. +0 −7 Bio/Graphics/GenomeDiagram/_Track.py
  25. +0 −2 Bio/HMM/MarkovModel.py
  26. +0 −1 Bio/HotRand.py
  27. +0 −1 Bio/KDTree/KDTree.py
  28. +0 −3 Bio/MarkovModel.py
  29. +0 −2 Bio/Motif/MEME.py
  30. +0 −2 Bio/Motif/Parsers/MEME.py
  31. +0 −1 Bio/Motif/_Motif.py
  32. +0 −1 Bio/NMR/xpktools.py
  33. +0 −1 Bio/NeuralNetwork/Gene/Schema.py
  34. +0 −2 Bio/Nexus/Nexus.py
  35. +0 −2 Bio/Nexus/Trees.py
  36. +0 −2 Bio/PDB/Atom.py
  37. +0 −1 Bio/PDB/Chain.py
  38. +0 −1 Bio/PDB/Dice.py
  39. +0 −1 Bio/PDB/FragmentMapper.py
  40. +0 −1 Bio/PDB/HSExposure.py
  41. +0 −3 Bio/PDB/PDBList.py
  42. +0 −1 Bio/PDB/ResidueDepth.py
  43. +0 −1 Bio/Phylo/PhyloXML.py
  44. +0 −1 Bio/Phylo/PhyloXMLIO.py
  45. +0 −2 Bio/PopGen/FDist/Controller.py
  46. +0 −3 Bio/PopGen/FDist/__init__.py
  47. +0 −4 Bio/PopGen/GenePop/Controller.py
  48. +0 −3 Bio/PopGen/GenePop/EasyController.py
  49. +0 −1 Bio/PopGen/GenePop/FileParser.py
  50. +0 −1 Bio/PopGen/GenePop/__init__.py
  51. +0 −1 Bio/PopGen/SimCoal/Cache.py
  52. +0 −1 Bio/Restriction/Restriction.py
  53. +0 −2 Bio/SCOP/Cla.py
  54. +0 −1 Bio/SCOP/Des.py
  55. +0 −1 Bio/SCOP/Dom.py
  56. +0 −2 Bio/SCOP/Hie.py
  57. +0 −2 Bio/SCOP/Raf.py
  58. +0 −2 Bio/SCOP/Residues.py
  59. +0 −10 Bio/SCOP/__init__.py
  60. +0 −1 Bio/Search.py
  61. +0 −1 Bio/Seq.py
  62. +0 −1 Bio/SeqFeature.py
  63. +0 −1 Bio/SeqIO/UniprotIO.py
  64. +0 −1 Bio/SeqRecord.py
  65. +0 −2 Bio/SeqUtils/CodonUsage.py
  66. +0 −1 Bio/SeqUtils/ProtParam.py
  67. +0 −1 Bio/SubsMat/MatrixInfo.py
  68. +0 −9 Bio/UniGene/UniGene.py
  69. +0 −1 Bio/_py3k/__init__.py
  70. +0 −4 BioSQL/Loader.py
  71. +0 −2 Doc/examples/getgene.py
  72. +0 −26 Doc/examples/nmr/simplepredict.py
  73. +0 −2 Scripts/scop_pdb.py
  74. +0 −1 Scripts/xbbtools/nextorf.py
  75. +0 −1 Scripts/xbbtools/xbb_blast.py
  76. +0 −2 Scripts/xbbtools/xbb_sequence.py
  77. +0 −3 Scripts/xbbtools/xbb_widget.py
  78. +0 −1 Tests/test_AlignIO_FastaIO.py
  79. +0 −3 Tests/test_CAPS.py
  80. +0 −1 Tests/test_Cluster.py
  81. +0 −12 Tests/test_Crystal.py
  82. +0 −1 Tests/test_EmbossPrimer.py
  83. +0 −3 Tests/test_Entrez.py
  84. +0 −4 Tests/test_File.py
  85. +0 −1 Tests/test_GACrossover.py
  86. +0 −1 Tests/test_GARepair.py
  87. +0 −3 Tests/test_GenomeDiagram.py
  88. +0 −1 Tests/test_GraphicsChromosome.py
  89. +0 −2 Tests/test_HMMGeneral.py
  90. +0 −2 Tests/test_Motif.py
  91. +0 −4 Tests/test_NCBITextParser.py
  92. +0 −1 Tests/test_Nexus.py
  93. +0 −3 Tests/test_ParserSupport.py
  94. +0 −1 Tests/test_Phylo.py
  95. +0 −1 Tests/test_PopGen_GenePop.py
  96. +0 −1 Tests/test_PopGen_GenePop_nodepend.py
  97. +0 −1 Tests/test_ProtParam.py
  98. +0 −2 Tests/test_SCOP_Astral.py
  99. +0 −3 Tests/test_SCOP_Cla.py
  100. +0 −2 Tests/test_SCOP_Des.py
  101. +0 −4 Tests/test_SCOP_Dom.py
  102. +0 −2 Tests/test_SCOP_Hie.py
  103. +0 −5 Tests/test_SCOP_Raf.py
  104. +0 −6 Tests/test_SCOP_Residues.py
  105. +0 −5 Tests/test_SCOP_Scop.py
  106. +0 −1 Tests/test_SearchIO_blast_tab.py
  107. +0 −1 Tests/test_SeqIO.py
  108. +0 −1 Tests/test_SeqIO_QualityIO.py
  109. +0 −2 Tests/test_Seq_objs.py
  110. +0 −12 Tests/test_SwissProt.py
  111. +0 −1 Tests/test_bgzf.py
  112. +0 −1 Tests/test_pairwise2.py
  113. +0 −2 Tests/test_prodoc.py
  114. +0 −2 Tests/test_prosite1.py
  115. +0 −1 Tests/test_prosite2.py
  116. +0 −1 Tests/test_psw.py
View
@@ -300,7 +300,6 @@ def _pair_replacement(self, seq1, seq2, weight1, weight2,
return start_dict
-
def _get_all_letters(self):
"""Returns a string containing the expected letters in the alignment."""
all_letters = self.alignment._alphabet.letters
@@ -352,7 +351,6 @@ def _get_base_replacements(self, skip_items = []):
return base_dictionary, skip_items
-
def pos_specific_score_matrix(self, axis_seq = None,
chars_to_ignore = []):
"""Create a position specific score matrix object for the alignment.
@@ -417,7 +415,6 @@ def pos_specific_score_matrix(self, axis_seq = None,
pssm_info.append((left_seq[residue_num],
score_dict))
-
return PSSM(pssm_info)
def _get_base_letters(self, letters):
View
@@ -161,7 +161,6 @@ def format(self, format):
#See also the SeqRecord class and its format() method using Bio.SeqIO
return self.__format__(format)
-
def __format__(self, format_spec):
"""Returns the alignment as a string in the specified file format.
View
@@ -88,7 +88,6 @@ def next(self):
ids = []
seqs = []
-
while line[0] == "#":
#Read in the rest of this alignment header,
#try and discover the number of records expected
@@ -609,7 +608,6 @@ def next(self):
assert [r.id for r in alignments[4]] \
== ["ref_rec", "gi|94970041|receiver"]
-
alignments = list(EmbossIterator(StringIO(pair_example3)))
assert len(alignments) == 1
assert len(alignments[0]) == 2
View
@@ -591,7 +591,6 @@ def build_hsp():
"""
-
from StringIO import StringIO
alignments = list(FastaM10Iterator(StringIO(simple_example)))
@@ -406,7 +406,6 @@ def next(self):
# multiple lines
#Next line...
-
assert len(seqs) <= len(ids)
#assert len(gs) <= len(ids)
#assert len(gr) <= len(ids)
@@ -454,7 +453,6 @@ def next(self):
else:
raise StopIteration
-
def _identifier_split(self, identifier):
"""Returns (name,start,end) string tuple from an identier."""
if '/' in identifier:
View
@@ -98,8 +98,6 @@ class RNAAlphabet(NucleotideAlphabet):
generic_rna = RNAAlphabet()
-
-
########### Other per-sequence encodings
class SecondaryStructure(SingleLetterAlphabet):
@@ -691,7 +691,6 @@ def __init__(self, cmd=None, **kwargs):
self.parameters = extra_parameters
_NcbiblastCommandline.__init__(self, cmd, **kwargs)
-
def _validate(self):
incompatibles = {"subject_loc":["db", "gilist", "negative_gilist", "seqidlist", "remote"],
"culling_limit":["best_hit_overhang","best_hit_score_edge"],
@@ -700,7 +700,6 @@ def _scan_parameters(self, uhandle, consumer):
# S1: 41 (21.7 bits)
# S2: 32 (16.9 bits)
-
# Blast 2.2.4 can sometimes skip the whole parameter section.
# BLAT also skips the whole parameter section.
# Thus, check to make sure that the parameter section really
View
@@ -119,7 +119,6 @@ def __init__(self):
self.hit_aln=''
self.positives=''
-
def query_coverage(self):
"""Return the length of the query covered in the alignment."""
s = self.query_aln.replace("=", "")
View
@@ -101,7 +101,6 @@ def __str__(self):
output = wrap_line(output)
return output
-
def __eq__(self, other):
if len(self.data) != len(other.data):
return 0
View
@@ -855,8 +855,6 @@ def register_ncbi_table(name, alt_name, id,
start_codons = [ 'ATT', 'ATG', 'GTG', ]
)
-
-
#Basic sanity test,
for key, val in generic_by_name.iteritems():
assert key in ambiguous_generic_by_name[key].names
View
@@ -84,8 +84,6 @@ def __repr__(self):
__str__ = __repr__
-
-
class FSSPSumRec(object):
""" Contains info from an FSSP summary record"""
def __init__(self,in_str):
View
@@ -1054,7 +1054,6 @@ def location(self, content):
warnings.warn(BiopythonParserWarning("Couldn't parse feature location: %r" \
% (location_line)))
-
def feature_qualifier(self, key, value):
"""When we get a qualifier key and its value.
@@ -346,7 +346,6 @@ def _draw_labels(self, cur_drawing, left_labels, right_labels):
cur_drawing.add(label_string)
-
class ChromosomeSegment(_ChromosomeComponent):
"""Draw a segment of a chromosome.
@@ -244,7 +244,6 @@ def draw_arrow(point1, point2, color=colors.lightgreen, border=None,
if boxwidth < 0:
headlength *= -1 #reverse it
-
shafttop = 0.5*(boxheight+shaftheight)
shaftbase = boxheight-shafttop
headbase = boxwidth-headlength
@@ -277,7 +276,6 @@ def angle2trig(theta):
s = sin(theta * pi / 180)
return(c, s, -s, c) # Vector for rotating point around an origin
-
def intermediate_points(start, end, graph_data):
""" intermediate_points(start, end, graph_data)
@@ -473,7 +471,6 @@ def set_page_size(self, pagesize, orientation):
else:
self.pagesize = (shortside, longside)
-
def set_margins(self, x, y, xl, xr, yt, yb):
""" set_margins(self, x, y, xl, xr, yt, yb)
@@ -528,7 +525,6 @@ def set_bounds(self, start, end):
self.start, self.end = int(start), int(end)
self.length = self.end - self.start + 1
-
def is_in_bounds(self, value):
""" is_in_bounds(self, value)
@@ -540,7 +536,6 @@ def is_in_bounds(self, value):
return 1
return 0
-
def __len__(self):
""" __len__(self)
@@ -236,7 +236,6 @@ def __init__(self, parent=None, pagesize='A3', orientation='landscape',
else:
self.sweep = 1
-
def set_track_heights(self):
""" set_track_heights(self)
@@ -333,7 +332,6 @@ def draw(self):
if self.tracklines: # Draw test tracks over top of diagram
self.draw_test_tracks()
-
def draw_track(self, track):
""" draw_track(self, track) -> ([element, element,...], [element, element,...])
@@ -355,7 +353,6 @@ def draw_track(self, track):
track_labels += labels
return track_elements, track_labels
-
def draw_feature_set(self, set):
""" draw_feature_set(self, set) -> ([element, element,...], [element, element,...])
@@ -408,7 +405,6 @@ def draw_feature(self, feature):
return feature_elements, label_elements
-
def get_feature_sigil(self, feature, locstart, locend, **kwargs):
""" get_feature_sigil(self, feature, x0, x1, fragment) -> (element, element)
@@ -565,7 +561,6 @@ def draw_cross_link(self, cross_link):
startangleB, endangleB,
cross_link.color, cross_link.border, cross_link.flip)]
-
def draw_graph_set(self, set):
""" draw_graph_set(self, set) -> ([element, element,...], [element, element,...])
@@ -588,7 +583,6 @@ def draw_graph_set(self, set):
return elements, []
-
def draw_line_graph(self, graph):
""" draw_line_graph(self, graph, center) -> [element, element,...]
@@ -706,8 +700,6 @@ def draw_bar_graph(self, graph):
pos1angle, barcolor))
return bar_elements
-
-
def draw_heat_graph(self, graph):
""" draw_heat_graph(self, graph) -> [element, element,...]
@@ -750,7 +742,6 @@ def draw_heat_graph(self, graph):
heat, border=heat))
return heat_elements
-
def draw_scale(self, track):
""" draw_scale(self, track) -> ([element, element,...], [element, element,...])
@@ -908,7 +899,6 @@ def draw_scale(self, track):
return scale_elements, scale_labels
-
def draw_tick(self, tickpos, ctr, ticklen, track, draw_label):
""" draw_tick(self, tickpos, ctr, ticklen) -> (element, element)
@@ -960,7 +950,6 @@ def draw_tick(self, tickpos, ctr, ticklen, track, draw_label):
labelgroup = None
return tick, labelgroup
-
def draw_test_tracks(self):
""" draw_test_tracks(self)
@@ -981,7 +970,6 @@ def draw_test_tracks(self):
strokeColor=colors.blue,
fillColor=None)) # bottom line
-
def draw_greytrack(self, track):
""" draw_greytrack(self)
@@ -1044,7 +1032,6 @@ def draw_greytrack(self, track):
return greytrack_bgs, greytrack_labels
-
def canvas_angle(self, base):
""" canvas_angle(self, base) -> (float, float, float)
"""
@@ -1269,7 +1256,6 @@ def _draw_sigil_cut_corner_box(self, bottom, center, top,
p.closePath()
return p
-
def _draw_sigil_arrow(self, bottom, center, top,
startangle, endangle, strand,
**kwargs):
@@ -59,7 +59,6 @@ def __init__(self, filename=None):
else:
self._colorscheme = self._artemis_colorscheme
-
def translate(self, color=None, colour=None):
""" translate(self, color)
@@ -153,15 +152,13 @@ def artemis_color(self, value):
else:
raise ValueError("Artemis color out of range: %d" % value)
-
def get_colorscheme(self):
""" get_colorscheme(self)
Return the user-defined color scheme as a dictionary
"""
return self._colorscheme
-
def scheme_color(self, value):
""" scheme_color(self, value)
@@ -176,7 +173,6 @@ def scheme_color(self, value):
else:
raise ValueError("Scheme color out of range: %d" % value)
-
def int255_color(self, values):
""" int255_color(self, values)
@@ -191,7 +187,6 @@ def int255_color(self, values):
red, green, blue = red * factor, green * factor, blue * factor
return colors.Color(red, green, blue)
-
def float1_color(self, values):
""" float1_color(self, values)
@@ -383,15 +383,13 @@ def del_track(self, track_level):
"""
del self.tracks[track_level]
-
def get_tracks(self):
""" get_tracks(self) -> list
Returns a list of the tracks contained in the diagram
"""
return self.tracks.values()
-
def move_track(self, from_level, to_level):
""" move_track(self, from_level, to_level)
@@ -406,7 +404,6 @@ def move_track(self, from_level, to_level):
del self.tracks[from_level]
self.add_track(aux, to_level)
-
def renumber_tracks(self, low=1, step=1):
""" renumber_tracks(self, low=1, step=1)
@@ -436,7 +433,6 @@ def get_levels(self):
levels.sort()
return levels
-
def get_drawn_levels(self):
""" get_drawn_levels(self) -> [int, int, ...]
@@ -448,7 +444,6 @@ def get_drawn_levels(self):
drawn_levels.sort()
return drawn_levels
-
def range(self):
""" range(self) -> (int, int)
@@ -159,7 +159,6 @@ def set_feature(self, feature):
self._feature = feature
self.__process_feature()
-
def __process_feature(self):
""" __process_feature(self)
@@ -202,7 +201,6 @@ def __process_feature(self):
#Note will be 0 to N for origin wrapping feature on genome of length N
self.start, self.end = min(bounds), max(bounds)
-
def get_feature(self):
""" get_feature(self) -> Bio.SeqFeature
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