flake8 lib/galaxy_utils/

.ci/flake8_blacklist.txt

@@ -8,7 +8,6 @@ lib/galaxy/model/migrate/versions/
 lib/galaxy/model/tool_shed_install/migrate/versions/
 lib/galaxy/util/pastescript/serve.py
 lib/galaxy/webapps/tool_shed/model/migrate/versions/
-lib/galaxy_utils/
 lib/pkg_resources.py
 lib/tool_shed/
 scripts/api/

lib/galaxy_utils/sequence/fasta.py

@@ -1,22 +1,28 @@
-#Dan Blankenberg
+# Dan Blankenberg
+
 
 class fastaSequence( object ):
     def __init__( self ):
         self.identifier = None
-        self.sequence = '' #holds raw sequence string: no whitespace
+        self.sequence = ''  # holds raw sequence string: no whitespace
+
     def __len__( self ):
         return len( self.sequence )
+
     def __str__( self ):
         return "%s\n%s\n" % ( self.identifier, self.sequence )
 
+
 class fastaReader( object ):
     def __init__( self, fh ):
         self.file = fh
+
     def close( self ):
         return self.file.close()
+
     def next( self ):
         line = self.file.readline()
-        #remove header comment lines
+        # remove header comment lines
         while line and line.startswith( '#' ):
             line = self.file.readline()
         if not line:
@@ -29,29 +35,33 @@ def next( self ):
             line = self.file.readline()
             if not line or line.startswith( '>' ):
                 if line:
-                    self.file.seek( offset ) #this causes sequence id lines to be read twice, once to determine previous sequence end and again when getting actual sequence; can we cache this to prevent it from being re-read?
+                    self.file.seek( offset )  # this causes sequence id lines to be read twice, once to determine previous sequence end and again when getting actual sequence; can we cache this to prevent it from being re-read?
                 return rval
-            #454 qual test data that was used has decimal scores that don't have trailing spaces
-            #so we'll need to parse and build these sequences not based upon de facto standards
-            #i.e. in a less than ideal fashion
+            # 454 qual test data that was used has decimal scores that don't have trailing spaces
+            # so we'll need to parse and build these sequences not based upon de facto standards
+            # i.e. in a less than ideal fashion
             line = line.rstrip()
             if ' ' in rval.sequence or ' ' in line:
                 rval.sequence = "%s%s " % ( rval.sequence, line )
             else:
                 rval.sequence += line
             offset = self.file.tell()
+
     def __iter__( self ):
         while True:
             yield self.next()
 
+
 class fastaNamedReader( object ):
     def __init__( self, fh ):
         self.file = fh
         self.reader = fastaReader( self.file )
         self.offset_dict = {}
         self.eof = False
+
     def close( self ):
         return self.file.close()
+
     def get( self, sequence_id ):
         if not isinstance( sequence_id, basestring ):
             sequence_id = sequence_id.identifier
@@ -71,7 +81,7 @@ def get( self, sequence_id ):
                     fasta_seq = self.reader.next()
                 except StopIteration:
                     self.eof = True
-                    break #eof, id not found, will return None
+                    break  # eof, id not found, will return None
                 if fasta_seq.identifier == sequence_id:
                     rval = fasta_seq
                     break
@@ -80,8 +90,9 @@ def get( self, sequence_id ):
                         self.offset_dict[ fasta_seq.identifier ] = []
                     self.offset_dict[ fasta_seq.identifier ].append( offset )
         return rval
+
     def has_data( self ):
-        #returns a string representation of remaining data, or empty string (False) if no data remaining
+        # returns a string representation of remaining data, or empty string (False) if no data remaining
         eof = self.eof
         count = 0
         rval = ''
@@ -90,7 +101,7 @@ def has_data( self ):
         if not eof:
             offset = self.file.tell()
             try:
-                fasta_seq = self.reader.next()
+                self.reader.next()
             except StopIteration:
                 eof = True
             self.file.seek( offset )
@@ -100,11 +111,14 @@ def has_data( self ):
             rval = "%s%s" % ( rval, "An additional unknown number of sequences exist in the input that were not utilized." )
         return rval
 
+
 class fastaWriter( object ):
     def __init__( self, fh ):
         self.file = fh
+
     def write( self, fastq_read ):
-        #this will include color space adapter base if applicable
+        # this will include color space adapter base if applicable
         self.file.write( ">%s\n%s\n" % ( fastq_read.identifier[1:], fastq_read.sequence ) )
+
     def close( self ):
         return self.file.close()