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Remove excessive blank lines (PEP8 E303).

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commit 9c76921b919bc19e063168b295ad355b26e8357b 1 parent bfa8b25
@cbrueffer cbrueffer authored peterjc committed
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
3  Bio/Align/AlignInfo.py
@@ -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
1  Bio/Align/Generic.py
@@ -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
2  Bio/AlignIO/EmbossIO.py
@@ -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
1  Bio/AlignIO/FastaIO.py
@@ -591,7 +591,6 @@ def build_hsp():
"""
-
from StringIO import StringIO
alignments = list(FastaM10Iterator(StringIO(simple_example)))
View
2  Bio/AlignIO/StockholmIO.py
@@ -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
2  Bio/Alphabet/__init__.py
@@ -98,8 +98,6 @@ class RNAAlphabet(NucleotideAlphabet):
generic_rna = RNAAlphabet()
-
-
########### Other per-sequence encodings
class SecondaryStructure(SingleLetterAlphabet):
View
1  Bio/Blast/Applications.py
@@ -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"],
View
1  Bio/Blast/NCBIStandalone.py
@@ -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
1  Bio/Compass/__init__.py
@@ -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
1  Bio/Crystal/__init__.py
@@ -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
2  Bio/Data/CodonTable.py
@@ -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
2  Bio/FSSP/__init__.py
@@ -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
1  Bio/GenBank/__init__.py
@@ -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.
View
1  Bio/Graphics/BasicChromosome.py
@@ -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.
View
5 Bio/Graphics/GenomeDiagram/_AbstractDrawer.py
@@ -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)
View
14 Bio/Graphics/GenomeDiagram/_CircularDrawer.py
@@ -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):
View
5 Bio/Graphics/GenomeDiagram/_Colors.py
@@ -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)
@@ -153,7 +152,6 @@ def artemis_color(self, value):
else:
raise ValueError("Artemis color out of range: %d" % value)
-
def get_colorscheme(self):
""" get_colorscheme(self)
@@ -161,7 +159,6 @@ def get_colorscheme(self):
"""
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)
View
5 Bio/Graphics/GenomeDiagram/_Diagram.py
@@ -383,7 +383,6 @@ def del_track(self, track_level):
"""
del self.tracks[track_level]
-
def get_tracks(self):
""" get_tracks(self) -> list
@@ -391,7 +390,6 @@ def get_tracks(self):
"""
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)
View
2  Bio/Graphics/GenomeDiagram/_Feature.py
@@ -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
View
9 Bio/Graphics/GenomeDiagram/_FeatureSet.py
@@ -100,7 +100,6 @@ def __init__(self, set_id=None, name=None, parent=None):
self.features = {} # Holds features, keyed by ID
self.name = name # String describing the set
-
def add_feature(self, feature, **kwargs):
""" add_feature(self, feature, **args)
@@ -137,7 +136,6 @@ def del_feature(self, feature_id):
"""
del self.features[feature_id]
-
def set_all_features(self, attr, value):
""" set_all_features(self, attr, value)
@@ -160,7 +158,6 @@ def set_all_features(self, attr, value):
#if attr=="colour":
# self.set_all_feature("color",value)
-
def get_features(self, attribute=None, value=None, comparator=None):
""" get_features(self, attribute=None, value=None, comparator=None) ->
[Feature, Feature, ...]
@@ -207,8 +204,6 @@ def get_features(self, attribute=None, value=None, comparator=None):
# As a final option, just return an empty list
return []
-
-
def get_ids(self):
""" get_ids(self) -> [int, int, ...]
@@ -216,7 +211,6 @@ def get_ids(self):
"""
return self.features.keys()
-
def range(self):
""" range(self)
@@ -231,7 +225,6 @@ def range(self):
return (min(lows), max(highs)) # nothing in the set
return 0, 0
-
def to_string(self, verbose=0):
""" to_string(self, verbose=0) -> ""
@@ -256,7 +249,6 @@ def __len__(self):
"""
return len(self.features)
-
def __getitem__(self, key):
""" __getitem__(self, key) -> Feature
@@ -264,7 +256,6 @@ def __getitem__(self, key):
"""
return self.features[key]
-
def __str__(self):
""" __str__(self) -> ""
View
8 Bio/Graphics/GenomeDiagram/_Graph.py
@@ -151,7 +151,6 @@ def set_data(self, data):
for (pos, val) in data: # Fill data dictionary
self.data[pos] = val
-
def get_data(self):
""" get_data(self) -> [(int, float), (int, float), ...]
@@ -164,7 +163,6 @@ def get_data(self):
data.sort()
return data
-
def add_point(self, point):
""" add_point(self, point)
@@ -175,7 +173,6 @@ def add_point(self, point):
pos, val = point
self.data[pos] = val
-
def quartiles(self):
""" quartiles(self) -> (float, float, float, float, float)
@@ -188,7 +185,6 @@ def quartiles(self):
return(data[0], data[datalen//4], data[datalen//2],
data[3*datalen//4], data[-1])
-
def range(self):
""" range(self) -> (int, int)
@@ -201,7 +197,6 @@ def range(self):
#print len(self.data)
return (positions[0], positions[-1])
-
def mean(self):
""" mean(self) -> Float
@@ -213,7 +208,6 @@ def mean(self):
sum += float(item)
return sum/len(data)
-
def stdev(self):
""" stdev(self) -> Float
@@ -235,7 +229,6 @@ def __len__(self):
"""
return len(self.data)
-
def __getitem__(self, index):
""" __getitem__(self, index) -> Float or list of tuples
@@ -266,7 +259,6 @@ def __getitem__(self, index):
else:
raise TypeError("Need an integer or a slice")
-
def __str__(self):
""" __str__(self) -> ""
View
10 Bio/Graphics/GenomeDiagram/_GraphSet.py
@@ -80,7 +80,6 @@ def __init__(self, name=None):
self._graphs = {} # Holds graphs, keyed by unique id
self.name = name # Holds description of graph
-
def new_graph(self, data, name=None, style='bar', color=colors.lightgreen,
altcolor=colors.darkseagreen, linewidth=1, center=None,
colour=None, altcolour=None, centre=None):
@@ -126,7 +125,6 @@ def new_graph(self, data, name=None, style='bar', color=colors.lightgreen,
self._next_id += 1 # increment next id
return graph
-
def del_graph(self, graph_id):
""" del_graph(self, graph_id)
@@ -136,7 +134,6 @@ def del_graph(self, graph_id):
"""
del self._graphs[graph_id]
-
def get_graphs(self):
""" get_graphs(self) -> [Graph, Graph, ...]
@@ -147,7 +144,6 @@ def get_graphs(self):
ids.sort()
return [self._graphs[id] for id in ids]
-
def get_ids(self):
""" get_ids(self) -> [int, int, ...]
@@ -155,7 +151,6 @@ def get_ids(self):
"""
return self._graphs.keys()
-
def range(self):
""" range(self) -> (int, int)
@@ -168,7 +163,6 @@ def range(self):
highs.append(high)
return (min(lows), max(highs))
-
def data_quartiles(self):
""" data_quartiles(self) -> (float, float, float, float, float)
@@ -183,7 +177,6 @@ def data_quartiles(self):
return(data[0], data[datalen/4], data[datalen/2],
data[3*datalen/4], data[-1])
-
def to_string(self, verbose=0):
""" to_string(self, verbose=0) -> ""
@@ -201,7 +194,6 @@ def to_string(self, verbose=0):
outstr.append("%s" % self._graphs[key])
return "\n".join(outstr)
-
def __len__(self):
""" __len__(self) -> int
@@ -209,7 +201,6 @@ def __len__(self):
"""
return len(self._graphs)
-
def __getitem__(self, key):
""" __getitem__(self, key) -> Graph
@@ -217,7 +208,6 @@ def __getitem__(self, key):
"""
return self._graphs[key]
-
def __str__(self):
""" __str__(self) -> ""
View
7 Bio/Graphics/GenomeDiagram/_LinearDrawer.py
@@ -246,7 +246,6 @@ def __init__(self, parent=None, pagesize='A3', orientation='landscape',
self.fragment_size = fragment_size
self.track_size = track_size
-
def draw(self):
""" draw(self)
@@ -309,7 +308,6 @@ def draw(self):
if self.tracklines: # Draw test tracks over top of diagram
self.draw_test_tracks()
-
def init_fragments(self):
""" init_fragments(self)
@@ -339,7 +337,6 @@ def init_fragments(self):
self.fragment_limits[fragment_count] = (marker, marker+fragment_step)
fragment_count += 1
-
def set_track_heights(self):
""" set_track_heights(self)
@@ -661,7 +658,6 @@ def draw_greytrack(self, track):
return greytrack_bgs, greytrack_labels
-
def draw_feature_set(self, set):
""" draw_feature_set(self, set) -> ([element, element,...], [element, element,...])
@@ -1078,7 +1074,6 @@ def draw_graph_set(self, set):
return elements, []
-
def draw_line_graph(self, graph):
""" draw_line_graph(self, graph) -> [element, element,...]
@@ -1145,7 +1140,6 @@ def draw_line_graph(self, graph):
return line_elements
-
def draw_heat_graph(self, graph):
""" draw_heat_graph(self, graph) -> [element, element,...]
@@ -1223,7 +1217,6 @@ def draw_heat_graph(self, graph):
return heat_elements
-
def draw_bar_graph(self, graph):
""" draw_bar_graph(self, graph) -> [element, element,...]
View
7 Bio/Graphics/GenomeDiagram/_Track.py
@@ -268,7 +268,6 @@ def add_set(self, set):
self._sets[self._next_id] = set # Add set, keyed by unique id
self._next_id += 1 # Increment unique set ids
-
def new_set(self, type='feature', **args):
""" new_set(self, type='feature') -> FeatureSet or GraphSet
@@ -287,7 +286,6 @@ def new_set(self, type='feature', **args):
self._next_id += 1 # Increment unique set ids
return set
-
def del_set(self, set_id):
""" del_set(self, set_id)
@@ -297,7 +295,6 @@ def del_set(self, set_id):
"""
del self._sets[set_id]
-
def get_sets(self):
""" get_sets(self) -> FeatureSet or GraphSet
@@ -305,7 +302,6 @@ def get_sets(self):
"""
return self._sets.values()
-
def get_ids(self):
""" get_ids(self) -> [int, int, ...]
@@ -313,7 +309,6 @@ def get_ids(self):
"""
return self._sets.keys()
-
def range(self):
""" range(self) -> (int, int)
@@ -355,7 +350,6 @@ def to_string(self, verbose=0):
outstr.append("set: %s" % self._sets[key])
return "\n".join(outstr)
-
def __getitem__(self, key):
""" __getitem__(self, key) -> int
@@ -365,7 +359,6 @@ def __getitem__(self, key):
"""
return self._sets[key]
-
def __str__(self):
""" __str__(self) -> ""
View
2  Bio/HMM/MarkovModel.py
@@ -238,7 +238,6 @@ def set_equal_probabilities(self):
for key in self.emission_prob:
self.emission_prob[key] = new_emission_prob
-
def set_random_initial_probabilities(self):
"""Set all initial state probabilities to a randomly generated distribution.
Returns the dictionary containing the initial probabilities.
@@ -478,7 +477,6 @@ def __init__(self, initial_prob, transition_prob, emission_prob,
self._transitions_to = \
_calculate_to_transitions(self.transition_prob)
-
def get_blank_transitions(self):
"""Get the default transitions for the model.
View
1  Bio/HotRand.py
@@ -50,7 +50,6 @@ def next_num( self, num_digits = 4 ):
return byte_concat( hexdigits )
-
class HotRandom(object):
def __init__( self ):
View
1  Bio/KDTree/KDTree.py
@@ -185,7 +185,6 @@ def get_indices(self):
# Fixed radius search for all points
-
def all_search(self, radius):
"""All fixed neighbor search.
View
3  Bio/MarkovModel.py
@@ -36,8 +36,6 @@ def logaddexp(logx, logy):
minxy = min(logx, logy)
return minxy + numpy.log(numpy.exp(logx-minxy) + numpy.exp(logy-minxy))
-
-
def itemindex(values):
d = {}
entries = enumerate(values[::-1])
@@ -281,7 +279,6 @@ def _baum_welch_one(N, M, outputs,
# Normalize the probability for this time step.
lp_arc[:,:,t] = lp_traverse - _logsum(lp_traverse)
-
# Sum of all the transitions out of state i at time t.
lp_arcout_t = numpy.zeros((N, T))
for t in range(T):
View
2  Bio/Motif/MEME.py
@@ -8,8 +8,6 @@
from Bio import Seq
from Bio.Motif import Motif
-
-
def read(handle):
"""Parses the text output of the MEME program into MEME.Record object.
View
2  Bio/Motif/Parsers/MEME.py
@@ -18,8 +18,6 @@
from Bio import Seq
from Bio.Motif import Motif
-
-
def read(handle):
"""Parses the text output of the MEME program into MEME.Record object.
View
1  Bio/Motif/_Motif.py
@@ -680,7 +680,6 @@ def _from_jaspar_sites(self,stream):
self.set_mask("*"*len(instance))
return self
-
def __getitem__(self,index):
"""Returns the probability distribution over symbols at a given position, padding with background.
View
1  Bio/NMR/xpktools.py
@@ -174,7 +174,6 @@ def _find_start_entry(line,n):
infield=1
field=1
-
while (c<leng and field<n):
if (infield):
if (line[c]==" " and not (line[c-1]==" ")):
View
1  Bio/NeuralNetwork/Gene/Schema.py
@@ -608,7 +608,6 @@ def from_motifs(self, motif_repository, motif_percent, num_ambiguous):
# represented by this schema
all_motifs.remove(motif)
-
# all the schema info
schema_info[new_schema] = schema_counts
View
2  Bio/Nexus/Nexus.py
@@ -737,7 +737,6 @@ def _format(self,options):
if 'notokens' in options:
self.tokens=False
-
def _set(self,options):
self.set=options
@@ -1349,7 +1348,6 @@ def write_nexus_data(self, filename=None, matrix=None, exclude=[], delete=[],\
fh.write(self.append_sets(exclude=exclude,delete=delete,mrbayes=mrbayes))
return filename
-
def append_sets(self,exclude=[],delete=[],mrbayes=False,include_codons=True,codons_only=False):
"""Returns a sets block."""
if not self.charsets and not self.taxsets and not self.charpartitions:
View
2  Bio/Nexus/Trees.py
@@ -328,7 +328,6 @@ def collapse_genera(self,space_equals_underscore=True):
else: # for loop exhausted: no genera to collapse left
break # while
-
def sum_branchlength(self,root=None,node=None):
"""Adds up the branchlengths from root (default self.root) to node.
@@ -412,7 +411,6 @@ def common_ancestor(self,node1,node2):
l2=[self.root]+self.trace(self.root,node2)
return [n for n in l1 if n in l2][-1]
-
def distance(self,node1,node2):
"""Add and return the sum of the branchlengths between two nodes.
dist = distance(self,node1,node2)
View
2  Bio/PDB/Atom.py
@@ -106,7 +106,6 @@ def _assign_atom_mass(self):
else:
return float('NaN')
-
# Special methods
def __repr__(self):
@@ -174,7 +173,6 @@ def set_anisou(self, anisou_array):
"""
self.anisou_array=anisou_array
-
# Public methods
def flag_disorder(self):
View
1  Bio/PDB/Chain.py
@@ -117,7 +117,6 @@ def has_id(self, id):
id=self._translate_id(id)
return Entity.has_id(self, id)
-
# Public
def get_residues(self):
View
1  Bio/PDB/Dice.py
@@ -67,7 +67,6 @@ def extract(structure, chain_id, start, end, filename):
io.save(filename, sel)
-
if __name__=="__main__":
from Bio.PDB.PDBParser import PDBParser
View
1  Bio/PDB/FragmentMapper.py
@@ -328,7 +328,6 @@ def __getitem__(self, res):
m=s[0]
fm=FragmentMapper(m, 10, 5, "levitt_data")
-
for r in Selection.unfold_entities(m, "R"):
print r,
View
1  Bio/PDB/HSExposure.py
@@ -132,7 +132,6 @@ def _get_gly_cb_vector(self, residue):
return cb_at_origin_v
-
class HSExposureCA(_AbstractHSExposure):
"""
Class to calculate HSE based on the approximate CA-CB vectors,
View
3  Bio/PDB/PDBList.py
@@ -79,7 +79,6 @@ def __init__(self,server='ftp://ftp.wwpdb.org', pdb=os.getcwd(), obsolete_pdb=No
self.overwrite = 0
self.flat_tree = 0
-
def get_status_list(self,url):
"""Retrieves a list of pdb codes in the weekly pdb status file
from the given URL. Used by get_recent_files.
@@ -96,7 +95,6 @@ def get_status_list(self,url):
handle.close()
return answer
-
def get_recent_changes(self):
"""Returns three lists of the newest weekly files (added,mod,obsolete).
@@ -295,7 +293,6 @@ def update_pdb(self):
else:
print "Obsolete file %s is missing" % old_file
-
def download_entire_pdb(self, listfile=None):
"""Retrieve all PDB entries not present in the local PDB copy.
View
1  Bio/PDB/ResidueDepth.py
@@ -168,6 +168,5 @@ def __init__(self, model, pdb_file):
rd=ResidueDepth(model, sys.argv[1])
-
for item in rd:
print item
View
1  Bio/Phylo/PhyloXML.py
@@ -508,7 +508,6 @@ def __init__(self,
self.absent=absent or []
-
class CladeRelation(PhyloElement):
"""Expresses a typed relationship between two clades.
View
1  Bio/Phylo/PhyloXMLIO.py
@@ -591,7 +591,6 @@ def uri(self, elem):
type=elem.get('type'))
-
# ---------------------------------------------------------
# OUTPUT
# ---------------------------------------------------------
View
2  Bio/PopGen/FDist/Controller.py
@@ -3,8 +3,6 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-
-
"""
This module allows to control fdist.
View
3  Bio/PopGen/FDist/__init__.py
@@ -18,9 +18,6 @@
"""
-
-
-
def read(handle):
"""Parses FDist data into a Record object.
View
4 Bio/PopGen/GenePop/Controller.py
@@ -3,8 +3,6 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-
-
"""
This module allows to control GenePop.
@@ -259,7 +257,6 @@ def _run_genepop(self, extensions, option, fname, opts={}):
self._remove_garbage(None)
return
-
def _test_pop_hz_both(self, fname, type, ext, enum_test = True,
dememorization = 10000, batches = 20, iterations = 5000):
"""Hardy-Weinberg test for heterozygote deficiency/excess.
@@ -402,7 +399,6 @@ def test_global_hz_deficiency(self, fname, enum_test = True,
return self._test_global_hz_both(fname, 4, ".DG", enum_test,
dememorization, batches, iterations)
-
#1.5
def test_global_hz_excess(self, fname, enum_test = True,
dememorization = 10000, batches = 20, iterations = 5000):
View
3  Bio/PopGen/GenePop/EasyController.py
@@ -3,8 +3,6 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-
-
"""
This module allows to control GenePop through an easier interface.
@@ -142,7 +140,6 @@ def get_allele_frequency(self, pop_pos, locus_name):
allele_freq[alleles[i]] = freqs[i]
return total, allele_freq
-
def get_multilocus_f_stats(self):
""" Returns the multilocus F stats
View
1  Bio/PopGen/GenePop/FileParser.py
@@ -105,7 +105,6 @@ def __str__(self):
self.seek_position(current_pop, current_ind)
return "".join(rep)
-
def start_read(self):
"""Starts parsing a file containing a GenePop file.
"""
View
1  Bio/PopGen/GenePop/__init__.py
@@ -191,7 +191,6 @@ def split_in_loci(self, gp):
gp_loci[gp_pop.loci_list[0]] = gp_pop
return gp_loci
-
def remove_population(self, pos):
"""Removes a population (by position).
"""
View
1  Bio/PopGen/SimCoal/Cache.py
@@ -26,7 +26,6 @@ def __init__(self, data_dir, simcoal_dir):
self.cacheDir = os.sep.join([data_dir, 'SimCoal', 'cache'])
self.simcoalDir = simcoal_dir
-
def run_simcoal(self, par_file, num_sims, ploydi = '1', parDir = None):
if parDir is None:
parDir = os.sep.join([self.dataDir, 'SimCoal', 'runs'])
View
1  Bio/Restriction/Restriction.py
@@ -2211,7 +2211,6 @@ def overhang5(self, dct=None):
dct = self.mapping
return dict([(k,v) for k,v in dct.iteritems() if k.is_5overhang()])
-
def overhang3(self, dct=None):
"""A.Overhang3([dct]) -> dict.
View
2  Bio/SCOP/Cla.py
@@ -17,8 +17,6 @@
"""
-
-
import Residues
View
1  Bio/SCOP/Des.py
@@ -65,7 +65,6 @@ def _process(self, line):
self.name = ''
self.sunid = int(sunid)
-
def __str__(self):
s = []
s.append(self.sunid)
View
1  Bio/SCOP/Dom.py
@@ -55,7 +55,6 @@ def _process(self, line):
self.residues = Residues(res)
self.residues.pdbid =pdbid
-
def __str__(self):
s = []
s.append(self.sid)
View
2  Bio/SCOP/Hie.py
@@ -66,7 +66,6 @@ def _process(self, line):
children = children.split(',')
self.children = map(int, children)
-
def __str__(self):
s = []
s.append(str(self.sunid))
@@ -79,7 +78,6 @@ def __str__(self):
else:
s.append('-')
-
if self.children:
child_str = map(str, self.children)
s.append(",".join(child_str))
View
2  Bio/SCOP/Raf.py
@@ -89,7 +89,6 @@ def __getitem__(self, key):
f.close()
return record
-
def getSeqMap(self, residues):
"""Get the sequence map for a collection of residues.
@@ -192,7 +191,6 @@ def _process(self, line):
self.res.append(r)
-
def index(self, resid, chainid="_"):
for i in range(0, len(self.res)):
if self.res[i].resid == resid and self.res[i].chainid == chainid:
View
2  Bio/SCOP/Residues.py
@@ -33,14 +33,12 @@ class Residues(object):
"""
-
def __init__(self, str=None):
self.pdbid = ''
self.fragments = ()
if str is not None:
self._parse(str)
-
def _parse(self, str):
str = str.strip()
View
10 Bio/SCOP/__init__.py
@@ -275,7 +275,6 @@ def __init__(self, cla_handle=None, des_handle=None, hie_handle=None,
def getRoot(self):
return self.getNodeBySunid(0)
-
def getDomainBySid(self, sid):
"""Return a domain from its sid"""
if sid in self._sidDict:
@@ -287,7 +286,6 @@ def getDomainBySid(self, sid):
else:
return None
-
def getNodeBySunid(self, sunid):
"""Return a node from its sunid"""
if sunid in self._sunidDict:
@@ -314,7 +312,6 @@ def write_hie(self, handle):
for n in nodes:
handle.write(str(n.toHieRecord()))
-
def write_des(self, handle):
"""Build a DES SCOP parsable file from this object"""
nodes = self._sunidDict.values()
@@ -324,7 +321,6 @@ def write_des(self, handle):
if n != self.root:
handle.write(str(n.toDesRecord()))
-
def write_cla(self, handle):
"""Build a CLA SCOP parsable file from this object"""
nodes = self._sidDict.values()
@@ -333,7 +329,6 @@ def write_cla(self, handle):
for n in nodes:
handle.write(str(n.toClaRecord()))
-
def getDomainFromSQL(self, sunid=None, sid=None):
"""Load a node from the SQL backend using sunid or sid"""
if sunid is None and sid is None:
@@ -406,7 +401,6 @@ def getDescendentsFromSQL(self, node, type):
des_list = []
-
# SQL cla table knows nothing about 'ro'
if node.type == 'ro':
for c in node.getChildren():
@@ -473,7 +467,6 @@ def write_hie_sql(self, handle):
for c in p.children:
cur.execute("INSERT INTO hie VALUES (%s,%s)" % (p.sunid, c.sunid))
-
def write_cla_sql(self, handle):
"""Write CLA data to SQL database"""
cur = handle.cursor()
@@ -747,7 +740,6 @@ def domainsClusteredByEv(self,id):
self.EvDatasets[id] = self.getAstralDomainsFromFile(filename)
return self.EvDatasets[id]
-
def domainsClusteredById(self,id):
"""get domains clustered by percent id"""
if id not in self.IdDatasets:
@@ -763,7 +755,6 @@ def domainsClusteredById(self,id):
self.IdDatasets[id] = self.getAstralDomainsFromFile(filename)
return self.IdDatasets[id]
-
def getAstralDomainsFromFile(self,filename=None,file_handle=None):
"""Get the scop domains from a file containing a list of sids"""
if file_handle is None and filename is None:
@@ -807,7 +798,6 @@ def getSeq(self,domain):
"""Return seq associated with domain"""
return self.getSeqBySid(domain.sid)
-
def hashedDomainsById(self,id):
"""Get domains clustered by sequence identity in a dict"""
if id not in self.IdDatahash:
View
1  Bio/Search.py
@@ -62,7 +62,6 @@ def __len__(self):
return self.length
-
# >GB_PL:ATF18F4 AL021637 Arabidopsis thaliana DNA chromosome 4, BAC clone
# F18F4 (ESSAII project). 2/98
# Length = 93,646
View
1  Bio/Seq.py
@@ -561,7 +561,6 @@ def endswith(self, suffix, start=0, end=sys.maxint):
suffix_str = self._get_seq_str_and_check_alphabet(suffix)
return str(self).endswith(suffix_str, start, end)
-
def split(self, sep=None, maxsplit=-1):
"""Split method, like that of a python string.
View
1  Bio/SeqFeature.py
@@ -804,7 +804,6 @@ def nofuzzy_end(self):
"""
return int(self._end)
-
def extract(self, parent_sequence):
"""Extract feature sequence from the supplied parent sequence."""
if self.ref or self.ref_db:
View
1  Bio/SeqIO/UniprotIO.py
@@ -292,7 +292,6 @@ def _parse_comment(element):
ann_key = 'comment_%s_xml' % element.attrib['type'].replace(' ', '')
append_to_annotations(ann_key, ElementTree.tostring(element))
-
def _parse_dbReference(element):
self.ParsedSeqRecord.dbxrefs.append(element.attrib['type'] + ':' + element.attrib['id'])
#e.g.
View
1  Bio/SeqRecord.py
@@ -549,7 +549,6 @@ def __contains__(self, char):
"""
return char in self.seq
-
def __str__(self):
"""A human readable summary of the record and its annotation (string).
View
2  Bio/SeqUtils/CodonUsage.py
@@ -101,7 +101,6 @@ def generate_index(self, fasta_file):
for i in range(len(codons)):
self.index[codons[i]] = rcsu[i] / rcsu_max
-
def cai_for_gene(self, dna_sequence):
"""Calculate the CAI (float) for the provided DNA sequence (string).
@@ -128,7 +127,6 @@ def cai_for_gene(self, dna_sequence):
return math.exp(cai_value / (cai_length - 1.0))
-
def _count_codons(self, fasta_file):
handle = open(fasta_file, 'r')
View
1  Bio/SeqUtils/ProtParam.py
@@ -178,7 +178,6 @@ def gravy(self):
return total_gravy / self.length
-
def _weight_list(self, window, edge):
"""Makes a list of relative weight of the
window edges compared to the window center. The weights are linear.
View
1  Bio/SubsMat/MatrixInfo.py
@@ -1854,7 +1854,6 @@ def _temp():
del _temp
-
# http://www.embl-heidelberg.de/~vogt/matrices/levin.cmp
def _temp():
return {
View
9 Bio/UniGene/UniGene.py
@@ -30,7 +30,6 @@
import Bio.File
-
class UniGeneParser( sgmllib.SGMLParser ):
def reset( self ):
@@ -71,8 +70,6 @@ def feed( self, handle ):
sgmllib.SGMLParser.feed( self, text )
-
-
def handle_data(self, newtext ):
newtext = string.strip( newtext )
self.text = self.text + newtext
@@ -134,8 +131,6 @@ def extract_key( self ):
self.queue[ key ] = UserDict.UserDict()
self.master_key = key
-
-
def start_table( self, attrs ):
self.open_tag_stack.append( self.open_tag )
self.open_tag = 'open_table'
@@ -175,11 +170,8 @@ def end_tr( self ):
except:
self.queue[ self.master_key ][ self.key_waiting ] = text
-
self.key_waiting = ''
-
-
def start_td( self, attrs ):
self.open_tag_stack.append( self.open_tag )
self.open_tag = 'open_table_data'
@@ -215,7 +207,6 @@ def print_tags( self ):
self.print_item( self.queue[ key ] )
-
if( __name__ == '__main__' ):
handle = open( 'Hs13225.htm')
undo_handle = Bio.File.UndoHandle( handle )
View
1  Bio/_py3k/__init__.py
@@ -21,7 +21,6 @@ def _as_unicode(s):
#Note ISO-8859-1 aka Latin-1 preserves first 256 chars
return codecs.latin_1_decode(s)[0]
-
def _as_bytes(s):
"""Turn byte string or unicode string into a bytes string.
View
4 BioSQL/Loader.py
@@ -182,7 +182,6 @@ def _get_taxon_id(self, record):
# Cropping it now should help in getting a match when searching,
# and avoids an error if we try and add these to the database.
-
if ncbi_taxon_id:
#Good, we have the NCBI taxon to go on - this is unambiguous :)
#Note that the scientific name and common name will only be
@@ -489,7 +488,6 @@ def _get_taxon_id_from_ncbi_lineage(self, taxonomic_lineage):
scientific_name[:255]))
return taxon_id
-
def _load_bioentry_table(self, record):
"""Fill the bioentry table with sequence information (PRIVATE).
@@ -680,7 +678,6 @@ def _load_annotations(self, record, bioentry_id):
#print "Ignoring annotation '%s' entry of type '%s'" \
# % (key, type(value))
-
def _load_reference(self, reference, rank, bioentry_id):
"""Record a SeqRecord's annotated references in the database (PRIVATE).
@@ -903,7 +900,6 @@ def _load_seqfeature_qualifiers(self, qualifiers, seqfeature_id):
self._load_seqfeature_dbxref(qualifiers[qualifier_key],
seqfeature_id)
-
def _load_seqfeature_dbxref(self, dbxrefs, seqfeature_id):
"""Add database crossreferences of a SeqFeature to the database (PRIVATE).
View
2  Doc/examples/getgene.py
@@ -257,8 +257,6 @@ def Get_Keywords(self, id):
break
return keywords
-
-
def help(exit = 0):
name = os.path.basename(sys.argv[0])
print 'Usage: %s <db> <gene ID>' % name
View
26 Doc/examples/nmr/simplepredict.py
@@ -40,11 +40,6 @@
# This script generates a human readable standard output version of the
# NOE coordinates as well as an nmrview peaklist out_example.xpk.
-
-
-
-
-
# ***********************************************************************
# ***** LOAD MODULES *****
@@ -70,18 +65,12 @@
relayatom="N15" # J-coupling from here to detected atom
fromatom="15N2" # The other labelled nucleus
-
-
-
# *-*-* First the peaklist is read into a data class from xpktools
# *-*-* that contains methods for easily extracting information from
# *-*-* the peaklist file
peaklist=xpktools.Peaklist(infn) # infn is the name of the xpk file
-
-
-
# *-*-* The class attribute residue_dict allows the data lines
# *-*-* to be separated from the header and returned here to
# *-*-* the dictionary <dict> as a list indexed by the assignment
@@ -90,28 +79,19 @@
dict=peaklist.residue_dict(detectatom)
-
-
-
# *-*-* As well as the data, the dictionary contains two other entries,
# *-*-* corresponding to the maximum and minimum residues indexed
MAXRES=dict["maxres"]
MINRES=dict["minres"]
-
-
#****** CALCULATE AND WRITE CROSSPEAK PEAKLIST *****
-
-
# *-*-* The peaklist class has a method for writing out the header
# *-*-* information in a format recognizable by nmrview
peaklist.write_header(outfn) # Write the header to the output file
-
-
# *-*-* Predict the i->i+inc and i->i-inc noe positions if possible
# *-*-* Write each one to the output file as they are calculated
@@ -119,11 +99,8 @@
res=MINRES # minimum residue number in the set
outlist=[] # Holds the output data
-
while (res<=MAXRES):
-
-
# *-*-* Predicting the NOE positions based on peak assignment data
# *-*-* is done by supplying the peaklist to and specifying the label
# *-*-* of the origin and detected atom in the NOE transfer as well as
@@ -132,8 +109,6 @@
noe1=NOEtools.predictNOE(peaklist,"15N2","H1",res,res+inc)
noe2=NOEtools.predictNOE(peaklist,"15N2","H1",res,res-inc)
-
-
# *-*-* The output of predictNOE is in the form of an xpk entry line
# *-*-* suitable for printing to an output file
# *-*-* Additionally, it is possible to extract information easily from
@@ -152,7 +127,6 @@
print string.split(entry1.fields["15N2.L"],".")[0], "-->", string.split(entry1.fields["N15.L"],".")[0], "\t", entry1.fields["H1.P"], entry1.fields["N15.P"], entry1.fields["15N2.P"],entry1.fields["int"]
-
noe1=noe1+"\012"
noe1=xpktools.replace_entry(noe1,1,count)
outlist.append(noe1)
View
2  Scripts/scop_pdb.py
@@ -55,8 +55,6 @@ def usage() :
sid -- A SCOP domain identifier. e.g. d3hbib_
"""
-
-
default_pdb_url = "http://www.rcsb.org/pdb/cgi/export.cgi/somefile.pdb?" \
"format=PDB&pdbId=%s&compression=None"
#default_pdb_url = "file://usr/local/db/pdb/data/010331/snapshot/all/pdb%s.ent"
View
1  Scripts/xbbtools/nextorf.py
@@ -46,7 +46,6 @@ def makeTableX(table):
table.stop_codons)
-
class NextOrf:
def __init__(self, file, options):
self.options = options
View
1  Scripts/xbbtools/xbb_blast.py
@@ -152,7 +152,6 @@ def Exit(self, *args):
sys.exit(0)
-
if __name__ == '__main__':
seq = sys.argv[1]
win = Tk()
View
2  Scripts/xbbtools/xbb_sequence.py
@@ -13,7 +13,5 @@ class xbb_sequence(Sequence):
def __init__(self):
""
-
-
if __name__ == '__main__':
test = xbb_sequence()
View
3  Scripts/xbbtools/xbb_widget.py
@@ -100,7 +100,6 @@ def init_colors(self):
'ComboBox.Label':'lightblue',
}
-
def init_optionsdb(self):
# does anybody know a better way of defining colors ?
# how would one implement Tk's -class ?
@@ -162,7 +161,6 @@ def create_menu(self, parent):
menu.add_radiobutton(label=table, command = self.set_codon_table, variable = self.current_codon_table)
self.translation_menu.add_cascade(label="Genetic Codes", menu=self.gencode_menu)
-
self.menubar.add_cascade(label="Translations", menu=self.translation_menu)
# Tools menu
@@ -206,7 +204,6 @@ def create_seqinfo(self, parent):
for i in ['id', 'from_id', 'to_id', 'length_id', 'label']:
d[i].pack(side = LEFT, fill = BOTH, expand = 1)
-
self.seq_info2 = Frame(parent, relief = RIDGE,
borderwidth = 5, height = 30)
self.seq_info2.pack(fill = BOTH, expand = 1, side = TOP)
View
1  Tests/test_AlignIO_FastaIO.py
@@ -46,7 +46,6 @@
"Expected %i records per alignment, got %i" \
% (t_per, len(alignment))
-
#Print the alignment
for i,alignment in enumerate(alignments):
print "="*78
View
3  Tests/test_CAPS.py
@@ -29,7 +29,6 @@ def test_trivial(self):
self.assertEqual(map.dcuts[0].cuts_in, [0])
self.assertEqual(map.dcuts[0].blocked_in, [1])
-
def test(self):
alignment = [
"""\
@@ -68,7 +67,6 @@ def test(self):
self.assertEqual(map.dcuts[1].cuts_in, [1,2])
self.assertEqual(map.dcuts[1].blocked_in, [0])
-
def testNoCAPS(self):
alignment = ["aaaaaaaaaaaaaaaaaaaa",
"aaaaaaaaaaaaaaaaaaaa",
@@ -78,7 +76,6 @@ def testNoCAPS(self):
map = CAPS.CAPSMap(align, enzymes)
self.assertEqual(map.dcuts, [])
-
def test_uneven(self):
alignment = ["aaaaaaaaaaaaaa",
"aaaaaaaaaaaaaa", #we'll change this below
View
1  Tests/test_Cluster.py
@@ -262,7 +262,6 @@ def test_clusterdistance(self):
method='a', transpose=0)
self.assertAlmostEqual(distance, 0.360, places=3)
-
def test_treecluster(self):
if TestCluster.module=='Bio.Cluster':
from Bio.Cluster import treecluster
View
12 Tests/test_Crystal.py
@@ -52,7 +52,6 @@ def testEquals(self):
second = Chain(self.f)
self.assertNotEqual(first, second)
-
def testLen(self):
chain = Chain(self.a)
elements = self.a.strip().split()
@@ -69,7 +68,6 @@ def testLen(self):
num_elements = len(elements)