Fix whitespace before and after operators (PEP8 E221 and E222).

Whitespace was left intact in places where it helps readability.

Bio/Affy/CelFile.py

@@ -42,7 +42,7 @@ def read(handle):
             section = "HEADER"
         elif line[:11]=="[INTENSITY]":
             section = "INTENSITY"
-            record.intensities  = numpy.zeros((record.nrows, record.ncols))
+            record.intensities = numpy.zeros((record.nrows, record.ncols))
             record.stdevs = numpy.zeros((record.nrows, record.ncols))
             record.npix = numpy.zeros((record.nrows, record.ncols), int)
         elif line[0]=="[":
@@ -58,7 +58,7 @@ def read(handle):
                 continue
             words = line.split()
             y, x = map(int, words[:2])
-            record.intensities[x,y]  = float(words[2])
+            record.intensities[x,y] = float(words[2])
             record.stdevs[x,y] = float(words[3])
-            record.npix[x,y]  = int(words[4])
+            record.npix[x,y] = int(words[4])
     return record

Bio/Align/AlignInfo.py

@@ -179,7 +179,7 @@ def _guess_consensus_alphabet(self, ambiguous):
         #Now check its compatible with all the rest of the sequences
         for record in self.alignment:
             #Get the (un-gapped version of) the sequence's alphabet
-            alt =  Alphabet._get_base_alphabet(record.seq.alphabet)
+            alt = Alphabet._get_base_alphabet(record.seq.alphabet)
             if not isinstance(alt, a.__class__):
                 raise ValueError("Alignment contains a sequence with \
                                 an incompatible alphabet.")

Bio/AlignIO/FastaIO.py

@@ -45,13 +45,13 @@ def _extract_alignment_region(alignment_seq_with_flanking, annotation):
     if int(annotation['al_start']) <= int(annotation['al_stop']):
         start = int(annotation['al_start']) \
               - display_start
-        end   = int(annotation['al_stop']) \
+        end = int(annotation['al_stop']) \
               - display_start + 1
     else:
         #FASTA has flipped this sequence...
         start = display_start \
               - int(annotation['al_start'])
-        end   = display_start \
+        end = display_start \
               - int(annotation['al_stop']) + 1
     end += align_stripped.count("-")
     assert 0 <= start and start < end and end <= len(align_stripped), \

Bio/Alphabet/Reduced.py

@@ -79,7 +79,7 @@ class Murphy10(Alphabet.ProteinAlphabet):
    size = 10
 murphy_10 = Murphy10()
 
-murphy_8_tab  = {"L": "L",
+murphy_8_tab = {"L": "L",
              "V": "L",
              "I": "L",
              "M": "L",
@@ -105,7 +105,7 @@ class Murphy8(Alphabet.ProteinAlphabet):
    size = 8
 murphy_8 = Murphy8()
 
-murphy_4_tab  = {"L": "L",
+murphy_4_tab = {"L": "L",
              "V": "L",
              "I": "L",
              "M": "L",
@@ -157,7 +157,7 @@ class HPModel(Alphabet.ProteinAlphabet):
    size = 2
 hp_model = HPModel()
 
-pc_5_table  = {"I": "A", # Aliphatic
+pc_5_table = {"I": "A", # Aliphatic
          "V": "A",
          "L": "A",
          "F": "R", # Aromatic

Bio/Crystal/__init__.py

@@ -231,15 +231,15 @@ def __repr__(self):
         keys = self.data.keys()
         keys.sort()
         for key in keys:
-            output = output +  '%s : %s\n' % (key, self.data[ key ])
+            output = output + '%s : %s\n' % (key, self.data[ key ])
         return output
 
     def __str__(self):
         output = ''
         keys = self.data.keys()
         keys.sort()
         for key in keys:
-            output = output +  '%s : %s\n' % (key, self.data[ key ])
+            output = output + '%s : %s\n' % (key, self.data[ key ])
         return output
 
     def tostring(self):

Bio/FSSP/__init__.py

@@ -80,7 +80,7 @@ def __repr__(self):
          outstring = self.aa+self.ss.lower()
       return outstring
 
-   __str__  = __repr__
+   __str__ = __repr__
 
 
 
@@ -129,7 +129,7 @@ def __init__(self,in_fff_rec):
       # print in_fff_rec
       self.abs_res_num = int(in_fff_rec[fssp_rec.align.abs_res_num])
       self.pdb_res_num = in_fff_rec[fssp_rec.align.pdb_res_num].strip()
-      self.chain_id  = in_fff_rec[fssp_rec.align.chain_id]
+      self.chain_id = in_fff_rec[fssp_rec.align.chain_id]
       if self.chain_id == ' ':
          self.chain_id = '0'
       self.res_name = in_fff_rec[fssp_rec.align.res_name]

Bio/GA/Crossover/GeneralPoint.py

@@ -49,7 +49,7 @@ def __init__(self, points, crossover_prob = .1):
         """
         self._crossover_prob = crossover_prob
 
-        self._sym     = points % 2 # odd n, gets a symmetry flag
+        self._sym = points % 2 # odd n, gets a symmetry flag
         self._npoints = (points + self._sym)//2 # (N or N+1)//2
 
     def do_crossover(self, org_1, org_2):
@@ -62,7 +62,7 @@ def do_crossover(self, org_1, org_2):
         if crossover_chance <= self._crossover_prob:
 
             # pre-compute bounds (len(genome))
-            bound  = (len(new_org[0].genome), len(new_org[1].genome))
+            bound = (len(new_org[0].genome), len(new_org[1].genome))
 
             mbound = min(bound)
             # can't have more than 0,x_0...x_n,bound locations
@@ -82,7 +82,7 @@ def do_crossover(self, org_1, org_2):
                     y_locs = self._generate_locs( bound[1] )
                 else:
                     y_locs = x_locs
-                    xlocs  = self._generate_locs( bound[0] )
+                    xlocs = self._generate_locs( bound[0] )
 
             # copy new genome strings over
             tmp = self._crossover(0, new_org, (x_locs,y_locs))

Bio/GA/Crossover/Uniform.py

@@ -27,7 +27,7 @@ def __init__(self, crossover_prob = .1, uniform_prob = 0.7):
         """Initialize to do uniform crossover at the specified probability and frequency.
         """
         self._crossover_prob = crossover_prob
-        self._uniform_prob   = uniform_prob
+        self._uniform_prob = uniform_prob
         return
 
     def do_crossover(self, org_1, org_2):

Bio/GenBank/Record.py

@@ -334,7 +334,7 @@ def _keywords_line(self):
         """
         output = ""
         if len(self.keywords) >= 0:
-            output +=  Record.BASE_FORMAT % "KEYWORDS"
+            output += Record.BASE_FORMAT % "KEYWORDS"
             keyword_info = ""
             for keyword in self.keywords:
                 keyword_info += "%s; " % keyword

Bio/Geo/Record.py

@@ -84,6 +84,6 @@ def __str__( self ):
 def out_block( text, prefix = '' ):
     output = ''
     for j in range( 0, len( text ), 80 ):
-        output = output + '%s%s\n'  % ( prefix, text[ j: j + 80 ] )
+        output = output + '%s%s\n' % ( prefix, text[ j: j + 80 ] )
     output = output + '\n'
     return output

Bio/Graphics/GenomeDiagram/_GraphSet.py

@@ -122,7 +122,7 @@ def new_graph(self, data, name=None, style='bar', color=colors.lightgreen,
         id = self._next_id                              # get id number
         graph = GraphData(id, data, name, style, color, altcolor, center)
         graph.linewidth = linewidth
-        self._graphs[id] =  graph                       # add graph data
+        self._graphs[id] = graph                        # add graph data
         self._next_id += 1                              # increment next id
         return graph
 

Bio/HMM/Trainer.py

@@ -199,7 +199,7 @@ def train(self, training_seqs, stopping_criteria,
                 # calculate the forward and backward variables
                 DP = dp_method(self._markov_model, training_seq)
                 forward_var, seq_prob = DP.forward_algorithm()
-                backward_var =  DP.backward_algorithm()
+                backward_var = DP.backward_algorithm()
 
                 all_probabilities.append(seq_prob)
 
@@ -221,7 +221,7 @@ def train(self, training_seqs, stopping_criteria,
             self._markov_model.transition_prob = ml_transitions
             self._markov_model.emission_prob = ml_emissions
 
-            cur_log_likelihood =  self.log_likelihood(all_probabilities)
+            cur_log_likelihood = self.log_likelihood(all_probabilities)
 
             # if we have previously calculated the log likelihood (ie.
             # not the first round), see if we can finish

Bio/KEGG/Compound/__init__.py

@@ -61,7 +61,7 @@ def __str__(self):
         Returns a string representation of this Record.
         """
         return self._entry() + \
-               self._name()  + \
+               self._name() + \
                self._formula() + \
                self._mass() + \
                self._pathway() + \

Bio/KEGG/Enzyme/__init__.py

@@ -80,7 +80,7 @@ def __str__(self):
         Returns a string representation of this Record.
         """
         return self._entry() + \
-               self._name()  + \
+               self._name() + \
                self._classname() + \
                self._sysname() + \
                self._reaction() + \

Bio/KEGG/__init__.py

@@ -33,9 +33,9 @@ def _wrap_kegg(line, max_width = KEGG_DATA_LENGTH, wrap_rule = _default_wrap):
     """
     s = ""
     wrapped_line = ""
-    indent =  " " * wrap_rule[0]
+    indent = " " * wrap_rule[0]
     connect = wrap_rule[1]
-    rules =   wrap_rule[2:]
+    rules = wrap_rule[2:]
     while 1:
         if len(line) <= max_width:
             wrapped_line = wrapped_line + line

Bio/NMR/xpktools.py

@@ -26,7 +26,7 @@ class XpkEntry(object):
     def __init__(self,entry,headline):
        self.fields={}   # Holds all fields from input line in a dictionary
                         # keys are data labels from the .xpk header 
-       datlist  = entry.split()
+       datlist = entry.split()
        headlist = headline.split()
 
        i=0  

Bio/NaiveBayes.py

@@ -72,7 +72,7 @@ def calculate(nb, observation, scale=0):
                          % (len(observation), nb.dimensionality))
 
     # Calculate log P(observation|class) for every class.
-    n  = len(nb.classes)
+    n = len(nb.classes)
     lp_observation_class = numpy.zeros(n)   # array of log P(observation|class)
     for i in range(n):
         # log P(observation|class) = SUM_i log P(observation_i|class)

Bio/Pathway/__init__.py

@@ -75,8 +75,8 @@ def __init__(self, reactants = {}, catalysts = [],
         for r, value in reactants.iteritems():
             if value == 0:
                 del self.reactants[r]
-        self.catalysts  = sorted(set(catalysts))
-        self.data       = data
+        self.catalysts = sorted(set(catalysts))
+        self.data = data
         self.reversible = reversible
 
     def __eq__(self, r):
@@ -107,7 +107,7 @@ def __repr__(self):
     def __str__(self):
         """Returns a string representation of self."""
         substrates = ""
-        products   = ""
+        products = ""
         all_species = sorted(self.reactants)
         for species in all_species:
             stoch = self.reactants[species]

Bio/PopGen/FDist/Async.py

@@ -106,7 +106,7 @@ def monitor(self):
         while(True):
             sleep(1)
             self.async.access_ds.acquire()
-            keys =  self.async.done.keys()[:]
+            keys = self.async.done.keys()[:]
             self.async.access_ds.release()
             for done in keys:
                 self.async.access_ds.acquire()

Bio/PopGen/FDist/Controller.py

@@ -269,7 +269,7 @@ def run_cplot(self, ci= 0.95, data_dir='.', version = 1, smooth=0.04):
             cplot_name = "cplot"
         else:
             cplot_name = "cplot2"
-        os.system('cd ' + data_dir + ' && '  +
+        os.system('cd ' + data_dir + ' && ' +
             self._get_path(cplot_name) + ' < ' + in_name + ' > ' + out_name)
         os.remove(data_dir + os.sep + in_name)
         os.remove(data_dir + os.sep + out_name)

Bio/PopGen/GenePop/Controller.py

@@ -609,13 +609,13 @@ def pop_parser(self):
 
                 while "Expected number of ho" not in l:
                     l = self.stream.readline()
-                expHo =  _gp_float(l[38:])
+                expHo = _gp_float(l[38:])
                 l = self.stream.readline()
-                obsHo =  _gp_int(l[38:])
+                obsHo = _gp_int(l[38:])
                 l = self.stream.readline()
-                expHe =  _gp_float(l[38:])
+                expHe = _gp_float(l[38:])
                 l = self.stream.readline()
-                obsHe =  _gp_int(l[38:])
+                obsHe = _gp_int(l[38:])
                 l = self.stream.readline()
 
                 while "Sample count" not in l:

Bio/PopGen/GenePop/EasyController.py

@@ -157,7 +157,7 @@ def get_f_stats(self, locus_name):
 
             Returns Fis(CW), Fst, Fit, Qintra, Qinter
         """
-        loci_iter =  self._controller.calc_fst_all(self._fname)[1]
+        loci_iter = self._controller.calc_fst_all(self._fname)[1]
         for name, fis, fst, fit, qintra, qinter in loci_iter:
             if name == locus_name:
                 return fis, fst, fit, qintra, qinter

Bio/PopGen/GenePop/FileParser.py

@@ -62,9 +62,9 @@ class FileRecord(object):
 
     """
     def __init__(self, fname):
-        self.comment_line    = ""
-        self.loci_list       = []
-        self.fname           = fname
+        self.comment_line = ""
+        self.loci_list = []
+        self.fname = fname
         self.start_read()
 
     def __str__(self):
@@ -74,7 +74,7 @@ def __str__(self):
            Marker length will be 3.
         """
         marker_len = 3
-        rep  = [self.comment_line + '\n']
+        rep = [self.comment_line + '\n']
         rep.append('\n'.join(self.loci_list) + '\n')
         current_pop = self.current_pop
         current_ind = self.current_ind

Bio/PopGen/GenePop/LargeFileParser.py

@@ -86,13 +86,13 @@ class Record(object):
     
     """
     def __init__(self, handle):
-        self.handle          = handle
-        self.marker_len      = 0
-        self.comment_line    = ""
-        self.loci_list       = []
-        self.populations     = []
-        self.data_generator  = None
-        self.stack           = [] 
+        self.handle = handle
+        self.marker_len = 0
+        self.comment_line = ""
+        self.loci_list = []
+        self.populations = []
+        self.data_generator = None
+        self.stack = []
 
     def data_generator(self):
         for handle in [self.stack, self.handle]:

Bio/PopGen/GenePop/__init__.py

@@ -121,11 +121,11 @@ class Record(object):
     
     """
     def __init__(self):
-        self.marker_len      = 0
-        self.comment_line    = ""
-        self.loci_list       = []
-        self.pop_list        = []
-        self.populations     = []
+        self.marker_len = 0
+        self.comment_line = ""
+        self.loci_list = []
+        self.pop_list = []
+        self.populations = []
 
     def __str__(self):
         """Returns (reconstructs) a GenePop textual representation.

Bio/PopGen/SimCoal/Template.py

@@ -37,7 +37,7 @@ def process_para(in_string, out_file_prefix, para_list, curr_values):
         f = open(f_name + '.par', 'w')
         #executed_template = template
         executed_template = exec_template(template)
-        clean_template =  executed_template.replace('\r\n','\n').replace('\n\n','\n')
+        clean_template = executed_template.replace('\r\n','\n').replace('\n\n','\n')
         f.write(clean_template)
         f.close()
         return [f_name]

Bio/Restriction/PrintFormat.py

@@ -260,7 +260,7 @@ def _make_number_only(self, ls, title, nc = [], s1 =''):
             return title
         ls.sort(lambda x,y : cmp(len(x[1]), len(y[1])))
         iterator = iter(ls)
-        cur_len  = 1
+        cur_len = 1
         new_sect = []
         for name, sites in iterator:
             l = len(sites)