Scripts: Some more PEP8 whitespace cleanup.

Scripts/GenBank/check_output.py

@@ -48,7 +48,7 @@ def do_comparison(good_record, test_record):
 
 
 def write_format(file):
-    record_parser = GenBank.RecordParser(debug_level = 2)
+    record_parser = GenBank.RecordParser(debug_level=2)
 
     print "Testing GenBank writing for %s..." % os.path.basename(file)
     # be able to handle gzipped files

Scripts/GenBank/check_output_simple.py

@@ -19,7 +19,7 @@
     print "Usage ./check_output.py <GenBank file to parse>"
     sys.exit()
 
-parser = GenBank.FeatureParser(debug_level = 2)
+parser = GenBank.FeatureParser(debug_level=2)
 
 handle = open(sys.argv[1], 'r')
 

Scripts/GenBank/find_parser_problems.py

@@ -19,11 +19,11 @@
     print "Usage ./find_parser_problems <GenBank file to parse>"
     sys.exit()
 
-feature_parser = GenBank.FeatureParser(debug_level = 0)
+feature_parser = GenBank.FeatureParser(debug_level=0)
 parser = GenBank.ErrorParser(feature_parser)
 
 handle = open(sys.argv[1], 'r')
-iterator = GenBank.Iterator(handle, parser, has_header = 1)
+iterator = GenBank.Iterator(handle, parser, has_header=1)
 
 while 1:
     have_record = 0

Scripts/PDB/generate_three_to_one_dict.py

@@ -71,7 +71,7 @@
         one = line.strip().split()[-1]
         found_one = True
     if line.startswith('_chem_comp.three_letter_code'):
-        three = '%-3s' % (line.strip().split()[-1],) # make it three-letter
+        three = '%-3s' % (line.strip().split()[-1],)  # make it three-letter
         found_three = True
 
     if found_one and found_three:
@@ -96,7 +96,7 @@
     line = fh.readline()
 
 if len(current_line) < 5:
-    three_to_one_buf[-1] = three_to_one_buf[:-1] # remove the last comma
+    three_to_one_buf[-1] = three_to_one_buf[:-1]  # remove the last comma
     three_to_one_buf.append('}')
 else:
     three_to_one_buf.append('%s }' % (current_line[:-1]))

Scripts/Performance/biosql_performance_load.py

@@ -5,8 +5,8 @@
 # set up the connection
 from Bio import GenBank
 from BioSQL import BioSeqDatabase
-server = BioSeqDatabase.open_database(host = "192.168.0.192", user = "root",
-                                       passwd = "", db = "pythonloadtest")
+server = BioSeqDatabase.open_database(host="192.168.0.192", user="root",
+                                       passwd="", db="pythonloadtest")
 
 # remove the database if it already exists
 db_name = "testload"

Scripts/Performance/biosql_performance_read.py

@@ -4,8 +4,8 @@
 import time
 # set up the connection
 from BioSQL import BioSeqDatabase
-server = BioSeqDatabase.open_database(host = "192.168.0.192", user = "root",
-                                       passwd = "", db = "test_biosql")
+server = BioSeqDatabase.open_database(host="192.168.0.192", user="root",
+                                       passwd="", db="test_biosql")
 db = server["embl_rod"]
 
 # -- do the fasta-only timing part

Scripts/Restriction/ranacompiler.py

@@ -12,7 +12,7 @@
 from Bio.Restriction._Update.RestrictionCompiler import DictionaryBuilder
 
 
-def standalone() :
+def standalone():
     parser = optparse.OptionParser()
     add = parser.add_option
 
@@ -37,12 +37,12 @@ def standalone() :
     options, args = parser.parse_args()
     return options, args
 
-if __name__ == '__main__' :
+if __name__ == '__main__':
     options, args = standalone()
     Builder = DictionaryBuilder(options.rebase_password, options.ftp_proxy)
     Builder.build_dict()
-    if options.i :
+    if options.i:
         Builder.install_dict()
-    else :
+    else:
         Builder.no_install()
     sys.exit()

Scripts/Restriction/rebase_update.py

@@ -11,7 +11,7 @@
 import optparse
 from Bio.Restriction._Update.Update import *
 
-if __name__ == '__main__' :
+if __name__ == '__main__':
     parser = optparse.OptionParser()
     add = parser.add_option
 

Scripts/query_pubmed.py

@@ -52,7 +52,7 @@ def print_usage():
 
     if count_only:
         handle = Entrez.esearch(db="pubmed", term=query)
-    else :
+    else:
         handle = Entrez.esearch(db="pubmed", term=query, usehistory="Y")
     search_results = Entrez.read(handle)
     ids = search_results["IdList"]
@@ -65,7 +65,7 @@ def print_usage():
     webenv = search_results["WebEnv"]
     query_key = search_results["QueryKey"]
     batch_size = 3
-    for start in range(0, count, batch_size) :
+    for start in range(0, count, batch_size):
         end = min(count, start + batch_size)
         #print "Going to download record %i to %i" % (start+1, end)
         fetch_handle = Entrez.efetch(db="pubmed", rettype="medline",

Scripts/scop_pdb.py

@@ -113,7 +113,7 @@ def main():
         sids = args[2:]
     elif input == '-':
         sids = sys.stdin.xreadlines()
-    else :
+    else:
         in_handle = open(input)
         sids = in_handle.xreadlines()
 

Scripts/xbbtools/nextorf.py

@@ -80,7 +80,7 @@ def ReadFile(self):
                 CDS.extend(self.GetCDS(self.seq))
             if minus:
                 self.rseq = self.seq.reverse_complement()
-                CDS.extend(self.GetCDS(self.rseq, strand = -1))
+                CDS.extend(self.GetCDS(self.rseq, strand=-1))
             self.Output(CDS)
 
     def ToFasta(self, header, seq):
@@ -98,7 +98,7 @@ def Gc(self, seq):
 
     def Gc2(self, seq):
         l = len(seq)
-        d= {}
+        d = {}
         for nt in ['A', 'T', 'G', 'C']:
             d[nt] = [0, 0, 0]
 
@@ -150,7 +150,7 @@ def GetOrfCoordinates(self, seq):
             frame_coordinates.append(coordinates)
         return frame_coordinates
 
-    def GetCDS(self, seq, strand = 1):
+    def GetCDS(self, seq, strand=1):
         frame_coordinates = self.GetOrfCoordinates(seq)
         START, STOP = 1, 0
         so = self.options
@@ -180,7 +180,7 @@ def GetCDS(self, seq, strand = 1):
                             start_site = start_site + f - 1
                         if codon == 'XXX':
                             stop = start_site + 3*((int((stop-1)-start_site)/3))
-                        s = seq[start_site -1 : stop]
+                        s = seq[start_site-1:stop]
                         CDS.append((start_site, stop, length, s, strand*f))
                         start_site = 0
                         if nostart == '1':

Scripts/xbbtools/xbb_blast.py

@@ -18,7 +18,7 @@
 
 
 class BlastIt:
-    def __init__(self, seq, parent = None):
+    def __init__(self, seq, parent=None):
         self.seq = seq
         self.parent = parent
         self.toplevel = Toplevel(parent)
@@ -46,29 +46,29 @@ def GetBlasts(self):
     def Choices(self):
         self.GetBlasts()
         self.cf = Frame(self.toplevel)
-        self.cf.pack(side = TOP, expand = 1, fill = X)
+        self.cf.pack(side=TOP, expand=1, fill=X)
         self.dbs = Pmw.ComboBox(self.cf,
-                                label_text = 'Blast Databases:',
-                                labelpos = 'nw',
-                                scrolledlist_items = self.nin + self.pin,
-                                selectioncommand = self.Validate
+                                label_text='Blast Databases:',
+                                labelpos='nw',
+                                scrolledlist_items=self.nin + self.pin,
+                                selectioncommand=self.Validate
                                 )
         self.blasts = Pmw.ComboBox(self.cf,
-                                   label_text = 'Blast Programs:',
-                                   labelpos = 'nw',
-                                   scrolledlist_items = ['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx'],
-                                   selectioncommand = self.Validate
+                                   label_text='Blast Programs:',
+                                   labelpos='nw',
+                                   scrolledlist_items=['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx'],
+                                   selectioncommand=self.Validate
                                    )
-        self.dbs.pack(side = LEFT, expand = 1, fill = X)
-        self.blasts.pack(side = LEFT, expand = 1, fill = X)
+        self.dbs.pack(side=LEFT, expand=1, fill=X)
+        self.blasts.pack(side=LEFT, expand=1, fill=X)
 
         self.alternative_f = Frame(self.cf)
         self.alternative = Entry(self.alternative_f)
-        self.alternative_f.pack(side = TOP, fill = X, expand = 1)
-        self.alternative.pack(side = LEFT, fill = X, expand = 1)
-        self.ok = Button(self.alternative_f, text = 'Run',
-                         command = self._Run)
-        self.ok.pack(side = RIGHT)
+        self.alternative_f.pack(side=TOP, fill=X, expand=1)
+        self.alternative.pack(side=LEFT, fill=X, expand=1)
+        self.ok = Button(self.alternative_f, text='Run',
+                         command=self._Run)
+        self.ok.pack(side=RIGHT)
 
         self.dbs.selectitem(0)
         self.blasts.selectitem(0)
@@ -83,8 +83,8 @@ def Validate(self, *args):
         elif (prog in ['blastp', 'blastx']) == (db in self.pin):
             color = 'green'
 
-        self.dbs.component('entry').configure(bg = color)
-        self.blasts.component('entry').configure(bg = color)
+        self.dbs.component('entry').configure(bg=color)
+        self.blasts.component('entry').configure(bg=color)
 
     def _Run(self):
         alternative_command = self.alternative.get()

Scripts/xbbtools/xbb_blastbg.py

@@ -18,7 +18,7 @@
 
 
 class BlastDisplayer:
-    def __init__(self, command, text_id = None):
+    def __init__(self, command, text_id=None):
         self.command = command
         self.tid = text_id
 

Scripts/xbbtools/xbb_help.py

@@ -12,20 +12,20 @@ class xbbtools_help(Toplevel):
     def __init__(self, *args):
         Toplevel.__init__(self)
         self.tid = ScrolledText(self)
-        self.tid.pack(fill = BOTH, expand = 1)
+        self.tid.pack(fill=BOTH, expand=1)
         self.Styles()
         self.Show()
 
     def Styles(self):
         for c in ['red', 'blue', 'magenta', 'yellow', 'green', 'red4', 'green4', 'blue4']:
-            self.tid.tag_configure(c, foreground = c)
+            self.tid.tag_configure(c, foreground=c)
 
-        self.tid.tag_config('underline', underline =1)
-        self.tid.tag_config('italic', font = ('Courier', 6, 'italic'))
-        self.tid.tag_config('bold', font = ('Courier', 8, 'bold'))
-        self.tid.tag_config('title', font = ('Courier', 12, 'bold'))
-        self.tid.tag_config('small', font = ('Courier', 6, ''))
-        self.tid.tag_config('highlight', background = 'gray')
+        self.tid.tag_config('underline', underline=1)
+        self.tid.tag_config('italic', font=('Courier', 6, 'italic'))
+        self.tid.tag_config('bold', font=('Courier', 8, 'bold'))
+        self.tid.tag_config('title', font=('Courier', 12, 'bold'))
+        self.tid.tag_config('small', font=('Courier', 6, ''))
+        self.tid.tag_config('highlight', background='gray')
 
     def Show(self):
         t = self.tid

Scripts/xbbtools/xbb_search.py

@@ -51,11 +51,11 @@ def IUPAC2regex(self, s):
                 rx += r
         return rx
 
-    def _Search(self, start = 0):
+    def _Search(self, start=0):
         pos = self.rx.search(self.sequence, start)
         return pos
 
-    def Search(self, start = 0):
+    def Search(self, start=0):
         pos = self.rx.search(self.sequence, start)
         if pos:
             return pos.start()
@@ -78,7 +78,7 @@ def SearchAll(self):
 
 
 class XDNAsearch(Toplevel, DNAsearch):
-    def __init__(self, seq= '', master= None, highlight = 0):
+    def __init__(self, seq='', master=None, highlight=0):
         DNAsearch.__init__(self)
         self.master = master
         self.highlight = highlight
@@ -90,28 +90,28 @@ def __init__(self, seq= '', master= None, highlight = 0):
     def init_graphics(self):
         Toplevel.__init__(self, self.master)
         self.frame = Frame(self)
-        self.frame.pack(fill = BOTH, expand = 1)
+        self.frame.pack(fill=BOTH, expand=1)
 
         self.search_entry = Entry(self.frame)
-        self.search_entry.pack(fill = BOTH, expand = 1)
+        self.search_entry.pack(fill=BOTH, expand=1)
 
         f2 = Frame(self.frame)
-        f2.pack(side = TOP, fill = BOTH, expand = 1)
+        f2.pack(side=TOP, fill=BOTH, expand=1)
 
         f = f2
-        self.forward = Button(f, text = 'Search +', command = self.do_search)
-        self.forward.pack(side = LEFT)
-        self.forward = Button(f, text = 'Search -',
-                              command = lambda x=self.do_search: x(other_strand=1))
-        self.forward.pack(side = LEFT)
-        self.cancel = Button(f, text = 'Cancel', command = self.exit)
-        self.cancel.pack(side = LEFT)
+        self.forward = Button(f, text='Search +', command=self.do_search)
+        self.forward.pack(side=LEFT)
+        self.forward = Button(f, text='Search -',
+                              command=lambda x=self.do_search: x(other_strand=1))
+        self.forward.pack(side=LEFT)
+        self.cancel = Button(f, text='Cancel', command=self.exit)
+        self.cancel.pack(side=LEFT)
         self.current_color = 'cyan'
-        self.colorb = Button(f, text = 'Color', command = self.change_color, foreground = self.current_color)
-        self.colorb.pack(side = LEFT)
+        self.colorb = Button(f, text='Color', command=self.change_color, foreground=self.current_color)
+        self.colorb.pack(side=LEFT)
         self.config_color(self.current_color)
 
-    def config_color(self, color = None):
+    def config_color(self, color=None):
         if not self.highlight:
             return
         if not color:
@@ -122,19 +122,19 @@ def config_color(self, color = None):
         self.current_color = color
         self.current_tag = 'searched_%s' % self.current_color
         self.master.tag_config(self.current_tag, background=self.current_color)
-        self.master.tag_config(self.current_tag + 'R', background=self.current_color, underline = 1)
+        self.master.tag_config(self.current_tag + 'R', background=self.current_color, underline=1)
         self.colors.append(color)
 
     def change_color(self):
         self.config_color()
-        self.colorb.configure(foreground = self.current_color)
+        self.colorb.configure(foreground=self.current_color)
         self.colorb.update()
 
     def get_pattern(self):
         pattern = self.search_entry.get()
         return pattern
 
-    def do_search(self, other_strand = 0):
+    def do_search(self, other_strand=0):
         pattern = self.get_pattern()
         if other_strand:
             pattern = reverse_complement(pattern)
@@ -165,6 +165,6 @@ def showcolor(self):
 if __name__ == '__main__':
     seq = 'ATGGTGTGTGTGTACGATCGCCCCCCCCAGTCGATCGATGCATCGTA'
     win = Tk()
-    xtest = XDNAsearch(seq = seq, master = win)
+    xtest = XDNAsearch(seq=seq, master=win)
 
     win.mainloop()