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Remove excessive EOF blank lines (found with pep8 --select W391).

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commit 4576bea9a47daaa9554cb2ab54f7595605c5e75c 1 parent ea8acf7
@cbrueffer cbrueffer authored peterjc committed
Showing with 0 additions and 202 deletions.
  1. +0 −1  Bio/AlignIO/Interfaces.py
  2. +0 −1  Bio/Alphabet/__init__.py
  3. +0 −2  Bio/Blast/NCBIWWW.py
  4. +0 −3  Bio/Blast/ParseBlastTable.py
  5. +0 −1  Bio/FSSP/FSSPTools.py
  6. +0 −1  Bio/FSSP/__init__.py
  7. +0 −1  Bio/FSSP/fssp_rec.py
  8. +0 −1  Bio/File.py
  9. +0 −3  Bio/GA/Mutation/Simple.py
  10. +0 −1  Bio/GA/Repair/Stabilizing.py
  11. +0 −2  Bio/GA/Selection/Diversity.py
  12. +0 −1  Bio/GA/Selection/Tournament.py
  13. +0 −3  Bio/Graphics/DisplayRepresentation.py
  14. +0 −4 Bio/Graphics/GenomeDiagram/_Colors.py
  15. +0 −1  Bio/Graphics/GenomeDiagram/_Diagram.py
  16. +0 −1  Bio/Graphics/GenomeDiagram/_FeatureSet.py
  17. +0 −2  Bio/Graphics/GenomeDiagram/_Graph.py
  18. +0 −3  Bio/HMM/DynamicProgramming.py
  19. +0 −1  Bio/HMM/MarkovModel.py
  20. +0 −9 Bio/HMM/Trainer.py
  21. +0 −5 Bio/HMM/Utilities.py
  22. +0 −3  Bio/HotRand.py
  23. +0 −1  Bio/KDTree/KDTree.py
  24. +0 −1  Bio/Motif/MEME.py
  25. +0 −2  Bio/Motif/Parsers/AlignAce.py
  26. +0 −1  Bio/Motif/Parsers/MEME.py
  27. +0 −1  Bio/NeuralNetwork/Gene/Motif.py
  28. +0 −1  Bio/NeuralNetwork/Gene/Signature.py
  29. +0 −4 Bio/NeuralNetwork/Training.py
  30. +0 −1  Bio/Nexus/Trees.py
  31. +0 −1  Bio/PDB/AbstractPropertyMap.py
  32. +0 −1  Bio/PDB/Chain.py
  33. +0 −1  Bio/PDB/DSSP.py
  34. +0 −1  Bio/PDB/Dice.py
  35. +0 −1  Bio/PDB/FragmentMapper.py
  36. +0 −2  Bio/PDB/HSExposure.py
  37. +0 −1  Bio/PDB/MMCIF2Dict.py
  38. +0 −1  Bio/PDB/MMCIFParser.py
  39. +0 −1  Bio/PDB/Model.py
  40. +0 −1  Bio/PDB/NACCESS.py
  41. +0 −1  Bio/PDB/NeighborSearch.py
  42. +0 −4 Bio/PDB/PDBIO.py
  43. +0 −1  Bio/PDB/Polypeptide.py
  44. +0 −1  Bio/PDB/Residue.py
  45. +0 −1  Bio/PDB/ResidueDepth.py
  46. +0 −2  Bio/PDB/Structure.py
  47. +0 −1  Bio/PDB/StructureAlignment.py
  48. +0 −2  Bio/PDB/StructureBuilder.py
  49. +0 −3  Bio/Pathway/Rep/HashSet.py
  50. +0 −1  Bio/Phylo/Applications/_Phyml.py
  51. +0 −1  Bio/Phylo/Applications/_Raxml.py
  52. +0 −1  Bio/Phylo/BaseTree.py
  53. +0 −1  Bio/Phylo/Newick.py
  54. +0 −1  Bio/Phylo/NewickIO.py
  55. +0 −2  Bio/Phylo/PAML/yn00.py
  56. +0 −1  Bio/Phylo/PhyloXMLIO.py
  57. +0 −1  Bio/Phylo/_utils.py
  58. +0 −1  Bio/PopGen/Async/Local.py
  59. +0 −1  Bio/PopGen/FDist/Controller.py
  60. +0 −1  Bio/PopGen/FDist/Utils.py
  61. +0 −1  Bio/PopGen/FDist/__init__.py
  62. +0 −2  Bio/PopGen/GenePop/Controller.py
  63. +0 −1  Bio/PopGen/GenePop/FileParser.py
  64. +0 −1  Bio/PopGen/GenePop/LargeFileParser.py
  65. +0 −2  Bio/PopGen/GenePop/__init__.py
  66. +0 −2  Bio/PopGen/SimCoal/Controller.py
  67. +0 −2  Bio/PopGen/SimCoal/Template.py
  68. +0 −2  Bio/Restriction/RanaConfig.py
  69. +0 −1  Bio/Restriction/Restriction_Dictionary.py
  70. +0 −2  Bio/Restriction/_Update/RestrictionCompiler.py
  71. +0 −8 Bio/SCOP/Residues.py
  72. +0 −1  Bio/SeqIO/PdbIO.py
  73. +0 −1  Bio/SeqIO/UniprotIO.py
  74. +0 −1  Bio/SeqUtils/CodonUsage.py
  75. +0 −1  Bio/SeqUtils/ProtParam.py
  76. +0 −1  Bio/SubsMat/FreqTable.py
  77. +0 −2  Bio/UniGene/UniGene.py
  78. +0 −1  BioSQL/Loader.py
  79. +0 −1  BioSQL/__init__.py
  80. +0 −1  Doc/examples/clustal_run.py
  81. +0 −1  Doc/examples/fasta_iterator.py
  82. +0 −3  Doc/examples/getgene.py
  83. +0 −2  Doc/examples/local_blast.py
  84. +0 −1  Doc/examples/make_subsmat.py
  85. +0 −1  Doc/examples/swissprot.py
  86. +0 −2  Doc/examples/www_blast.py
  87. +0 −3  Scripts/GenBank/check_output_simple.py
  88. +0 −3  Scripts/GenBank/find_parser_problems.py
  89. +0 −1  Scripts/Performance/biosql_performance_load.py
  90. +0 −1  Scripts/debug/debug_blast_parser.py
  91. +0 −18 Scripts/scop_pdb.py
  92. +0 −2  Scripts/xbbtools/xbb_help.py
  93. +0 −3  Scripts/xbbtools/xbb_search.py
  94. +0 −2  Scripts/xbbtools/xbb_sequence.py
  95. +0 −1  Scripts/xbbtools/xbb_translations.py
  96. +0 −1  Scripts/xbbtools/xbbtools.py
  97. +0 −1  Tests/test_ColorSpiral.py
  98. +0 −1  Tests/test_Crystal.py
  99. +0 −1  Tests/test_FSSP.py
  100. +0 −1  Tests/test_HMMCasino.py
  101. +0 −1  Tests/test_Location.py
  102. +0 −1  Tests/test_Medline.py
  103. +0 −1  Tests/test_PAML_baseml.py
  104. +0 −1  Tests/test_ParserSupport.py
  105. +0 −1  Tests/test_Phd.py
  106. +0 −1  Tests/test_SeqIO_PdbIO.py
  107. +0 −2  Tests/test_SeqIO_online.py
  108. +0 −1  Tests/test_SeqUtils.py
  109. +0 −1  Tests/test_SubsMat.py
  110. +0 −2  Tests/test_TogoWS.py
  111. +0 −5 Tests/test_geo.py
  112. +0 −1  Tests/test_translate.py
View
1  Bio/AlignIO/Interfaces.py
@@ -144,4 +144,3 @@ def write_alignment(self, alignment):
# You SHOULD subclass this, to write the alignment #
# objecta to the file handle #
#####################################################
-
View
1  Bio/Alphabet/__init__.py
@@ -400,4 +400,3 @@ def _verify_alphabet(sequence):
if letter not in letters:
return False
return True
-
View
2  Bio/Blast/NCBIWWW.py
@@ -243,5 +243,3 @@ def _parse_qblast_ref_page(handle):
except ValueError:
raise ValueError("A non-integer RTOE found in " \
+"the 'please wait' page, %s" % repr(rtoe))
-
-
View
3  Bio/Blast/ParseBlastTable.py
@@ -98,6 +98,3 @@ def _parse_fields(self, inline):
return 0
def _Parse(self, method_name, inline):
return getattr(self,method_name)(inline)
-
-
-
View
1  Bio/FSSP/FSSPTools.py
@@ -89,4 +89,3 @@ def name_filter(sum_dict, align_dict, name_list):
new_align_dict.abs(pos_num).pos_align_dict[prot_num] = \
align_dict.abs(pos_num).pos_align_dict[prot_num]
return new_sum_dict, new_align_dict
-
View
1  Bio/FSSP/__init__.py
@@ -264,4 +264,3 @@ def read_fssp(fssp_handle):
del i.PosAlignList
align_dict.build_resnum_list()
return (header, sum_dict, align_dict)
-
View
1  Bio/FSSP/fssp_rec.py
@@ -31,4 +31,3 @@ class align(object):
turn5 = (20,22)
acc = (34,37)
start_aa_list = 42
-
View
1  Bio/File.py
@@ -682,4 +682,3 @@ def close(self):
proxies = self._proxies
while proxies:
proxies.popitem()[1]._handle.close()
-
View
3  Bio/GA/Mutation/Simple.py
@@ -83,6 +83,3 @@ def mutate(self, organism):
mutated_org.genome[gene_index] = new_letter
return mutated_org
-
-
-
View
1  Bio/GA/Repair/Stabilizing.py
@@ -56,4 +56,3 @@ def repair(self, organism):
new_org.genome[to_change] = new_gene
return new_org
-
View
2  Bio/GA/Selection/Diversity.py
@@ -94,5 +94,3 @@ def select(self, population):
# return the new population, which should have the same number
# of individuals we started with.
return new_population[:len(population)]
-
-
View
1  Bio/GA/Selection/Tournament.py
@@ -72,4 +72,3 @@ def select(self, population):
new_population.extend([new_org_1, new_org_2])
return new_population
-
View
3  Bio/Graphics/DisplayRepresentation.py
@@ -179,6 +179,3 @@ def _color_from_count(self, count):
# if we got here we didn't find a color for the count
raise ValueError("Count value %s was not found in the color scheme."
% count)
-
-
-
View
4 Bio/Graphics/GenomeDiagram/_Colors.py
@@ -224,7 +224,3 @@ def float1_color(self, values):
print gdct.translate((1, 75, 240))
print gdct.translate(7)
print gdct.translate(2)
-
-
-
-
View
1  Bio/Graphics/GenomeDiagram/_Diagram.py
@@ -485,4 +485,3 @@ def __str__(self):
outstr.append("Track %d: %s\n" % (level, self.tracks[level]))
outstr = '\n'.join(outstr)
return outstr
-
View
1  Bio/Graphics/GenomeDiagram/_FeatureSet.py
@@ -298,4 +298,3 @@ def __str__(self):
#for feature in gdfs.get_features():
# print feature.id, feature.start, feature.end
#print gdfs[500]
-
View
2  Bio/Graphics/GenomeDiagram/_Graph.py
@@ -280,5 +280,3 @@ def __str__(self):
outstr.append("Minimum: %s\n1Q: %s\n2Q: %s\n3Q: %s\nMaximum: %s" % self.quartiles())
outstr.append("Sequence Range: %s..%s" % self.range())
return "\n".join(outstr)
-
-
View
3  Bio/HMM/DynamicProgramming.py
@@ -323,6 +323,3 @@ class LogDPAlgorithms(AbstractDPAlgorithms):
"""
def __init__(self, markov_model, sequence):
raise NotImplementedError("Haven't coded this yet...")
-
-
-
View
1  Bio/HMM/MarkovModel.py
@@ -655,4 +655,3 @@ def _log_transform(self, probability):
log_prob[key] = neg_inf
return log_prob
-
View
9 Bio/HMM/Trainer.py
@@ -418,12 +418,3 @@ def _count_transitions(self, state_seq, transition_counts):
(cur_state, next_state))
return transition_counts
-
-
-
-
-
-
-
-
-
View
5 Bio/HMM/Utilities.py
@@ -50,8 +50,3 @@ def pretty_print_prediction(emissions, real_state, predicted_state,
break
cur_position += seq_length
-
-
-
-
-
View
3  Bio/HotRand.py
@@ -71,6 +71,3 @@ def hot_rand( self, high, low = 0 ):
nums = [ '0000', 'abcd', '1234', '5555', '4321', 'aaaa', 'ffff' ]
for num in nums:
print hex_convert( num )
-
-
-
View
1  Bio/KDTree/KDTree.py
@@ -259,4 +259,3 @@ def all_get_radii(self):
x, y, z=center
print "Found %i points in radius %f around center (%.2f, %.2f, %.2f)." % (len(indices), query_radius, x, y, z)
-
View
1  Bio/Motif/MEME.py
@@ -396,4 +396,3 @@ def __skip_unused_lines(handle):
raise ValueError("Unexpected end of stream: Expected to find line starting with '***'")
if not line.startswith('***'):
raise ValueError("Line does not start with '***':\n%s" % line)
-
View
2  Bio/Motif/Parsers/AlignAce.py
@@ -61,5 +61,3 @@ def read(handle):
else:
raise ValueError(line)
return record
-
-
View
1  Bio/Motif/Parsers/MEME.py
@@ -363,4 +363,3 @@ def __skip_unused_lines(handle):
raise ValueError("Unexpected end of stream: Expected to find line starting with '***'")
if not line.startswith('***'):
raise ValueError("Line does not start with '***':\n%s" % line)
-
View
1  Bio/NeuralNetwork/Gene/Motif.py
@@ -209,4 +209,3 @@ def representation(self, sequence):
motif_amounts.append(seq_motifs[motif])
return motif_amounts
-
View
1  Bio/NeuralNetwork/Gene/Signature.py
@@ -215,4 +215,3 @@ def representation(self, sequence):
sig_amounts.append(sequence_sigs[sig])
return sig_amounts
-
View
4 Bio/NeuralNetwork/Training.py
@@ -83,7 +83,3 @@ def add_examples(self, training_examples):
self.validation_examples.append(example)
else:
self.test_examples.append(example)
-
-
-
-
View
1  Bio/Nexus/Trees.py
@@ -852,4 +852,3 @@ def consensus(trees, threshold=0.5,outgroup=None):
if alltaxa != set(consensus.get_taxa()):
raise TreeError('FATAL ERROR: consensus tree is corrupt')
return consensus
-
View
1  Bio/PDB/AbstractPropertyMap.py
@@ -131,4 +131,3 @@ def _translate_id(self, ent_id):
if isinstance(res_id, int):
ent_id=(chain_id, (' ', res_id, ' '), atom_name, icode)
return ent_id
-
View
1  Bio/PDB/Chain.py
@@ -128,4 +128,3 @@ def get_atoms(self):
for r in self:
for a in r:
yield a
-
View
1  Bio/PDB/DSSP.py
@@ -323,4 +323,3 @@ def resid2code(res_id):
print s[0]['A'][1].xtra
# Secondary structure
print ''.join(d[key][1] for key in d.keys())
-
View
1  Bio/PDB/Dice.py
@@ -78,4 +78,3 @@ def extract(structure, chain_id, start, end, filename):
s=p.get_structure("scr", sys.argv[1])
extract(s, " ", 1, 100, "out.pdb")
-
View
1  Bio/PDB/FragmentMapper.py
@@ -336,4 +336,3 @@ def __getitem__(self, res):
print fm[r]
else:
print
-
View
2  Bio/PDB/HSExposure.py
@@ -344,5 +344,3 @@ def __init__(self, model, radius=12.0, offset=0):
print r.xtra['PCB_CB_ANGLE']
except:
pass
-
-
View
1  Bio/PDB/MMCIF2Dict.py
@@ -149,4 +149,3 @@ def _make_mmcif_dict(self):
print value
except KeyError:
print "No such key found."
-
View
1  Bio/PDB/MMCIFParser.py
@@ -171,4 +171,3 @@ def _get_icode(self, resseq):
for chain in model.get_list():
print chain
print "Found %d residues." % len(chain.get_list())
-
View
1  Bio/PDB/Model.py
@@ -67,4 +67,3 @@ def get_atoms(self):
for r in self.get_residues():
for a in r:
yield a
-
View
1  Bio/PDB/NACCESS.py
@@ -181,4 +181,3 @@ def __init__(self, model, pdb_file = None,
n = NACCESS(model, sys.argv[1])
for e in n.get_iterator():
print e
-
View
1  Bio/PDB/NeighborSearch.py
@@ -137,4 +137,3 @@ def get_coord(self):
ns=NeighborSearch(al)
print "Found ", len(ns.search_all(5.0))
-
View
4 Bio/PDB/PDBIO.py
@@ -188,7 +188,3 @@ def save(self, file, select=Select(), write_end=0):
io.set_structure(s2)
io.save(fp, write_end=1)
fp.close()
-
-
-
-
View
1  Bio/PDB/Polypeptide.py
@@ -473,4 +473,3 @@ def _test_dist(self, c, n):
print pp.get_sequence()
for pp in ppb.build_peptides(s[0]["A"]):
print pp.get_sequence()
-
View
1  Bio/PDB/Residue.py
@@ -160,4 +160,3 @@ def disordered_add(self, residue):
assert(not self.disordered_has_id(resname))
self[resname]=residue
self.disordered_select(resname)
-
View
1  Bio/PDB/ResidueDepth.py
@@ -171,4 +171,3 @@ def __init__(self, model, pdb_file):
for item in rd:
print item
-
View
2  Bio/PDB/Structure.py
@@ -51,5 +51,3 @@ def get_atoms(self):
for r in self.get_residues():
for a in r:
yield a
-
-
View
1  Bio/PDB/StructureAlignment.py
@@ -132,4 +132,3 @@ def get_iterator(self):
# Print aligned pairs (r is None if gap)
for (r1,r2) in al.get_iterator():
print r1, r2
-
View
2  Bio/PDB/StructureBuilder.py
@@ -253,5 +253,3 @@ def get_structure(self):
def set_symmetry(self, spacegroup, cell):
pass
-
-
View
3  Bio/Pathway/Rep/HashSet.py
@@ -99,6 +99,3 @@ def cartesian(self,s):
for j in s.list():
p.append((i,j))
return HashSet(p)
-
-
-
View
1  Bio/Phylo/Applications/_Phyml.py
@@ -255,4 +255,3 @@ def __init__(self, cmd='phyml', **kwargs):
),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
-
View
1  Bio/Phylo/Applications/_Raxml.py
@@ -368,4 +368,3 @@ def __init__(self, cmd='raxmlHPC', **kwargs):
# ENH: enforce -s, -n and -m
if not self.parsimony_seed:
self.parsimony_seed = 10000
-
View
1  Bio/Phylo/BaseTree.py
@@ -1152,4 +1152,3 @@ def __repr__(self):
def __str__(self):
"""Show the color's RGB values."""
return "(%d, %d, %d)" % (self.red, self.green, self.blue)
-
View
1  Bio/Phylo/Newick.py
@@ -29,4 +29,3 @@ def __init__(self, branch_length=1.0, name=None, clades=None,
BaseTree.Clade.__init__(self, branch_length=branch_length,
name=name, clades=clades, confidence=confidence)
self.comment = comment
-
View
1  Bio/Phylo/NewickIO.py
@@ -243,4 +243,3 @@ def make_info_string(clade, terminal=False):
) % (clade.confidence, clade.branch_length or 0.0)
return make_info_string
-
View
2  Bio/Phylo/PAML/yn00.py
@@ -132,5 +132,3 @@ def read(results_file):
if len(results) == 0:
raise ValueError("Invalid results file.")
return results
-
-
View
1  Bio/Phylo/PhyloXMLIO.py
@@ -856,4 +856,3 @@ def domain(self, obj):
symbol = _handle_simple('symbol')
synonym = _handle_simple('synonym')
type = _handle_simple('type')
-
View
1  Bio/Phylo/_utils.py
@@ -415,4 +415,3 @@ def draw_clade(clade, x_start, color, lw):
axes.set_ylim(max(y_posns.itervalues()) + 0.8, 0.2)
if do_show:
plt.show()
-
View
1  Bio/PopGen/Async/Local.py
@@ -63,4 +63,3 @@ def start_work(self):
self.done[id] = ret_code, output_files
self.cores_used -= 1
self.access_ds.release()
-
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1  Bio/PopGen/FDist/Controller.py
@@ -315,4 +315,3 @@ def run_pv(self, out_file='probs.dat', data_dir='.',
os.remove(data_dir + os.sep + in_name)
os.remove(data_dir + os.sep + out_name)
return result
-
View
1  Bio/PopGen/FDist/Utils.py
@@ -208,4 +208,3 @@ def approximate_fst(desired_fst, simulated_fst, parameter_fst,
min_run_fst = parameter_fst
next_parameter_fst = (max_run_fst + parameter_fst)/2
return next_parameter_fst, max_run_fst, min_run_fst
-
View
1  Bio/PopGen/FDist/__init__.py
@@ -84,4 +84,3 @@ def __str__(self):
rep.append('\n')
rep.append('\n')
return "".join(rep)
-
View
2  Bio/PopGen/GenePop/Controller.py
@@ -864,5 +864,3 @@ def calc_ibd_haplo(self, fname, stat="a", scale="Log", min_dist=0.00001):
the individual name has to be the sample coordinates.
"""
return self._calc_ibd(fname, 6, stat, scale, min_dist)
-
-
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1  Bio/PopGen/GenePop/FileParser.py
@@ -337,4 +337,3 @@ def remove_loci_by_name(self, names, fname):
self.remove_loci_by_position(positions, fname)
#If here than locus not existent... Maybe raise exception?
# Although it should be Ok... Just a boolean return, maybe?
-
View
1  Bio/PopGen/GenePop/LargeFileParser.py
@@ -113,4 +113,3 @@ def data_generator(self):
clean_list.append(tuple(mk_real))
yield indiv_name, clean_list
raise StopIteration()
-
View
2  Bio/PopGen/GenePop/__init__.py
@@ -216,5 +216,3 @@ def remove_locus_by_name(self, name):
return
#If here than locus not existent... Maybe raise exception?
# Although it should be Ok... Just a boolean return, maybe?
-
-
View
2  Bio/PopGen/SimCoal/Controller.py
@@ -57,5 +57,3 @@ def run_simcoal(self, par_file, num_sims, ploydi = '1', par_dir = '.'):
cmd += ' >/dev/null 2>&1'
os.system(cmd)
os.chdir(curr_dir)
-
-
View
2  Bio/PopGen/SimCoal/Template.py
@@ -215,5 +215,3 @@ def generate_simcoal_from_template(model, chrs, params, out_dir = '.', tp_dir=No
par_stream = open(out_dir + sep + 'tmp.par', 'r')
generate_model(par_stream, model, params, out_dir = out_dir)
par_stream.close()
-
-
View
2  Bio/Restriction/RanaConfig.py
@@ -79,5 +79,3 @@
Rebase_name = 'anonymous'
Rebase_password = ''
#Rebase_password = 'your_address@somewhere.something'
-
-
View
1  Bio/Restriction/Restriction_Dictionary.py
@@ -16902,4 +16902,3 @@ def _temp():
typedict['type288'] = _temp()
del _temp
-
View
2  Bio/Restriction/_Update/RestrictionCompiler.py
@@ -972,5 +972,3 @@ def information_mixer(self, file1, file2, file3):
t = i.strip().split(' ', 1)
suppliersdict[t[0]] = (t[1], [])
return
-
-
View
8 Bio/SCOP/Residues.py
@@ -85,11 +85,3 @@ def __str__(self):
if start: s.append("%s-%s" % (start, end))
strs.append("".join(s))
return prefix+ ",".join(strs)
-
-
-
-
-
-
-
-
View
1  Bio/SeqIO/PdbIO.py
@@ -215,4 +215,3 @@ def restype(residue):
with open(fname) as handle:
records = parser(handle)
SeqIO.write(records, sys.stdout, 'fasta')
-
View
1  Bio/SeqIO/UniprotIO.py
@@ -517,4 +517,3 @@ def _parse_sequence(element):
self.ParsedSeqRecord.id = self.ParsedSeqRecord.annotations['accessions'][0]
return self.ParsedSeqRecord
-
View
1  Bio/SeqUtils/CodonUsage.py
@@ -155,4 +155,3 @@ def print_index(self):
"""Prints out the index used."""
for i in sorted(self.index):
print "%s\t%.3f" % (i, self.index[i])
-
View
1  Bio/SeqUtils/ProtParam.py
@@ -291,4 +291,3 @@ def secondary_structure_fraction (self):
sheet = sum([aa_percentages[r] for r in 'EMAL'])
return helix, turn, sheet
-
View
1  Bio/SubsMat/FreqTable.py
@@ -87,4 +87,3 @@ def read_freq(f):
key, value = line.strip().split()
freq_dict[key] = float(value)
return FreqTable(freq_dict,FREQ)
-
View
2  Bio/UniGene/UniGene.py
@@ -222,5 +222,3 @@ def print_tags( self ):
unigene_parser = UniGeneParser()
unigene_parser.parse( handle )
unigene_parser.print_tags()
-
-
View
1  BioSQL/Loader.py
@@ -1064,4 +1064,3 @@ def remove(self):
self.adaptor.execute(sql, (self.dbid,))
sql = r"DELETE FROM biodatabase WHERE biodatabase_id = %s"
self.adaptor.execute(sql, (self.dbid,))
-
View
1  BioSQL/__init__.py
@@ -12,4 +12,3 @@
http://biopython.org/wiki/BioSQL
http://www.biosql.org/
"""
-
View
1  Doc/examples/clustal_run.py
@@ -64,4 +64,3 @@
freq_table_info)
print "relative info content:", info_content
-
View
1  Doc/examples/fasta_iterator.py
@@ -57,4 +57,3 @@ def extract_organisms(file_to_parse):
all_species = extract_organisms("ls_orchid.fasta")
print "number of species:", len(all_species)
print 'species names:', all_species
-
View
3  Doc/examples/getgene.py
@@ -262,6 +262,3 @@ def help(exit = 0):
for id in ids:
#print db_index.Get(id)
print func(id)
-
-
-
View
2  Doc/examples/local_blast.py
@@ -48,5 +48,3 @@
print hsp.query[0:75] + dots
print hsp.match[0:75] + dots
print hsp.sbjct[0:75] + dots
-
-
View
1  Doc/examples/make_subsmat.py
@@ -29,4 +29,3 @@
print 'log_odds_mat:', my_lom
my_lom.print_mat()
-
View
1  Doc/examples/swissprot.py
@@ -17,4 +17,3 @@
print "classification:", record.organism_classification
print
-
View
2  Doc/examples/www_blast.py
@@ -49,5 +49,3 @@
print hsp.query[0:75] + '...'
print hsp.match[0:75] + '...'
print hsp.sbjct[0:75] + '...'
-
-
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3  Scripts/GenBank/check_output_simple.py
@@ -50,6 +50,3 @@
print feature
handle.close()
-
-
-
View
3  Scripts/GenBank/find_parser_problems.py
@@ -53,6 +53,3 @@
print feature
handle.close()
-
-
-
View
1  Scripts/Performance/biosql_performance_load.py
@@ -30,4 +30,3 @@
print "Loading"
print "\tDid %s records in %s seconds for\n\t%f records per second" % \
(num_records, elapsed_time, float(num_records) / float(elapsed_time))
-
View
1  Scripts/debug/debug_blast_parser.py
@@ -242,4 +242,3 @@ def test_blast_output(outfile):
print >>sys.stderr, "-p and -n not implemented yet"
sys.exit(-1)
test_blast_output(TESTFILE)
-
View
18 Scripts/scop_pdb.py
@@ -158,21 +158,3 @@ def main():
if __name__ == "__main__":
main()
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
View
2  Scripts/xbbtools/xbb_help.py
@@ -64,5 +64,3 @@ def Show(self):
N: GATC
""", 'small')
-
-
View
3  Scripts/xbbtools/xbb_search.py
@@ -166,6 +166,3 @@ def showcolor(self):
xtest = XDNAsearch(seq = seq, master = win)
win.mainloop()
-
-
-
View
2  Scripts/xbbtools/xbb_sequence.py
@@ -17,5 +17,3 @@ def __init__(self):
if __name__ == '__main__':
test = xbb_sequence()
-
-
View
1  Scripts/xbbtools/xbb_translations.py
@@ -122,4 +122,3 @@ def gcframe(self, seq, translation_table = 1):
# for i in Translate.unambiguous_dna_by_id.keys():
# print Translate.unambiguous_dna_by_id[i].table.names[0]
-
View
1  Scripts/xbbtools/xbbtools.py
@@ -25,4 +25,3 @@
pass
win.mainloop()
-
View
1  Tests/test_ColorSpiral.py
@@ -110,4 +110,3 @@ def test_dict(self):
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner = runner)
-
View
1  Tests/test_Crystal.py
@@ -517,4 +517,3 @@ def testEquals(self):
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
-
View
1  Tests/test_FSSP.py
@@ -51,4 +51,3 @@
ks.sort()
for key in ks:
f.write("%s : %s\n" % (key, dict[key]))
-
View
1  Tests/test_HMMCasino.py
@@ -198,4 +198,3 @@ def stop_training(log_likelihood_change, num_iterations):
if VERBOSE:
print "Prediction probability:", prob
Utilities.pretty_print_prediction(test_rolls, test_states, predicted_states)
-
View
1  Tests/test_Location.py
@@ -40,4 +40,3 @@
print "Location:", location
print " Non-Fuzzy Start:", location.nofuzzy_start
print " Non-Fuzzy End:", location.nofuzzy_end
-
View
1  Tests/test_Medline.py
@@ -183,4 +183,3 @@ def test_parse(self):
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
-
View
1  Tests/test_PAML_baseml.py
@@ -296,4 +296,3 @@ def testParseSEs(self):
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
-
View
1  Tests/test_ParserSupport.py
@@ -159,4 +159,3 @@ def m(line):
print arac(h, m, start="foobar") # 0
print arac(h, m, blank=1) # 0
print arac(h, m, end="LVSVKEQ") # 1
-
View
1  Tests/test_Phd.py
@@ -363,4 +363,3 @@ def test_check_SeqIO(self):
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
-
View
1  Tests/test_SeqIO_PdbIO.py
@@ -98,4 +98,3 @@ def test_atom_noheader(self):
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
-
View
2  Tests/test_SeqIO_online.py
@@ -92,5 +92,3 @@ def funct(d, f, e, l, c):
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
-
-
View
1  Tests/test_SeqUtils.py
@@ -137,4 +137,3 @@ def windowed_LCC(s):
assert value == checksum(Seq(seq_str, single_letter_alphabet))
#Finally check it works with a MutableSeq object
assert value == checksum(MutableSeq(seq_str, single_letter_alphabet))
-
View
1  Tests/test_SubsMat.py
@@ -82,4 +82,3 @@
#test into two, and have one raise MissingExternalDependencyError cheat:
f.write("BLOSUM30 & BLOSUM90 0.88\n")
f.write("BLOSUM90 & BLOSUM30 0.88\n")
-
View
2  Tests/test_TogoWS.py
@@ -496,5 +496,3 @@ def test_genbank_to_embl(self):
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
-
-
View
5 Tests/test_geo.py
@@ -28,8 +28,3 @@
for record in records:
print record
print "\n"
-
-
-
-
-
View
1  Tests/test_translate.py
@@ -115,4 +115,3 @@
print str(stop_protein)
# XXX (Backwards with ambiguity code is unfinished!)
-
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