Merge pull request #421 from jmchilton/lint_2

Pep-8 lint fixes (1)
2026-09-24 16:30:27 +08:00 · 2015-07-04 09:20:05 -05:00
parent 55f6ce0c1f 152ebeee10
commit 4d184f5a17
6 changed files with 118 additions and 113 deletions
@@ -8,6 +8,7 @@ from galaxy.exceptions import ActionInputError

 log = logging.getLogger( __name__ )

+
 class AdminActions( object ):
    """
    Mixin for controllers that provide administrative functionality.
@@ -22,7 +23,7 @@ class AdminActions( object ):
                create_amount = False
        if not params.name or not params.description:
            raise ActionInputError( "Enter a valid name and a description." )
-        elif self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name==params.name ).first():
+        elif self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name == params.name ).first():
            raise ActionInputError( "Quota names must be unique and a quota with that name already exists, so choose another name." )
        elif not params.get( 'amount', None ):
            raise ActionInputError( "Enter a valid quota amount." )
@@ -60,7 +61,7 @@ class AdminActions( object ):
    def _rename_quota( self, quota, params ):
        if not params.name:
            raise ActionInputError( 'Enter a valid name' )
-        elif params.name != quota.name and self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name==params.name ).first():
+        elif params.name != quota.name and self.sa_session.query( self.app.model.Quota ).filter( self.app.model.Quota.table.c.name == params.name ).first():
            raise ActionInputError( 'A quota with that name already exists' )
        else:
            old_name = quota.name
@@ -150,7 +151,7 @@ class AdminActions( object ):
        message += ', '.join( names )
        return message

-    def _undelete_quota( self, quota, params = None):
+    def _undelete_quota( self, quota, params=None):
        quotas = util.listify( quota )
        names = []
        for q in quotas:
@@ -197,4 +198,3 @@ class AdminActions( object ):
        self.sa_session.flush()
        message += ', '.join( names )
        return message
-
@@ -16,6 +16,7 @@ from galaxy.datatypes.metadata import MetadataElement

 log = logging.getLogger(__name__)

+
 class Amos( data.Text ):
    """Class describing the AMOS assembly file """
    edam_format = "format_2561"
@@ -53,17 +54,18 @@ class Amos( data.Text ):
            while not isAmos:
                line = fh.readline()
                if not line:
-                    break #EOF
+                    break  # EOF
                line = line.strip()
-                if line: #first non-empty line
+                if line:  # first non-empty line
                    if line.startswith( '{' ):
-                        if re.match(r'{(RED|CTG|TLE)$',line):
+                        if re.match(r'{(RED|CTG|TLE)$', line):
                            isAmos = True
            fh.close()
        except:
            pass
        return isAmos

+
 class Sequences( sequence.Fasta ):
    """Class describing the Sequences file generated by velveth """

@@ -83,24 +85,25 @@ class Sequences( sequence.Fasta ):
            while True:
                line = fh.readline()
                if not line:
-                    break #EOF
+                    break  # EOF
                line = line.strip()
-                if line: #first non-empty line
+                if line:  # first non-empty line
                    if line.startswith( '>' ):
-                        if not re.match(r'>[^\t]+\t\d+\t\d+$',line):
+                        if not re.match(r'>[^\t]+\t\d+\t\d+$', line):
                            break
-                        #The next line.strip() must not be '', nor startwith '>'
+                        # The next line.strip() must not be '', nor startwith '>'
                        line = fh.readline().strip()
                        if line == '' or line.startswith( '>' ):
                            break
                        return True
                    else:
-                        break #we found a non-empty line, but it's not a fasta header
+                        break  # we found a non-empty line, but it's not a fasta header
            fh.close()
        except:
            pass
        return False

+
 class Roadmaps( data.Text ):
    """Class describing the Sequences file generated by velveth """
    edam_format = "format_2561"
@@ -119,23 +122,24 @@ class Roadmaps( data.Text ):
            while True:
                line = fh.readline()
                if not line:
-                    break #EOF
+                    break  # EOF
                line = line.strip()
-                if line: #first non-empty line
-                    if not re.match(r'\d+\t\d+\t\d+$',line):
+                if line:  # first non-empty line
+                    if not re.match(r'\d+\t\d+\t\d+$', line):
                        break
-                    #The next line.strip() should be 'ROADMAP 1'
+                    # The next line.strip() should be 'ROADMAP 1'
                    line = fh.readline().strip()
-                    if not re.match(r'ROADMAP \d+$',line):
+                    if not re.match(r'ROADMAP \d+$', line):
                        break
                    return True
                else:
-                    break #we found a non-empty line, but it's not a fasta header
+                    break  # we found a non-empty line, but it's not a fasta header
            fh.close()
        except:
            pass
        return False

+
 class Velvet( Html ):
    MetadataElement( name="base_name", desc="base name for velveth dataset", default="velvet", readonly=True, set_in_upload=True)
    MetadataElement( name="paired_end_reads", desc="has paired-end reads", default="False", readonly=False, set_in_upload=True)
@@ -147,17 +151,17 @@ class Velvet( Html ):

    def __init__( self, **kwd ):
        Html.__init__( self, **kwd )
-        self.add_composite_file( 'Sequences', mimetype = 'text/html', description = 'Sequences', substitute_name_with_metadata = None, is_binary = False )
-        self.add_composite_file( 'Roadmaps', mimetype = 'text/html', description = 'Roadmaps', substitute_name_with_metadata = None, is_binary = False )
-        self.add_composite_file( 'Log', mimetype = 'text/html', description = 'Log', optional = 'True', substitute_name_with_metadata = None, is_binary = False )
+        self.add_composite_file( 'Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False )
+        self.add_composite_file( 'Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False )
+        self.add_composite_file( 'Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=False )

-    def generate_primary_file( self, dataset = None ):
-        log.debug( "Velvet log info  %s %s" % ('JJ generate_primary_file',dataset))
+    def generate_primary_file( self, dataset=None ):
+        log.debug( "Velvet log info  %s %s" % ('JJ generate_primary_file', dataset))
        rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
-        for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
+        for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
            fn = composite_name
-            log.debug( "Velvet log info  %s %s %s" % ('JJ generate_primary_file',fn,composite_file))
+            log.debug( "Velvet log info  %s %s %s" % ('JJ generate_primary_file', fn, composite_file))
            opt_text = ''
            if composite_file.optional:
                opt_text = ' (optional)'
@@ -168,7 +172,7 @@ class Velvet( Html ):
        rval.append( '</ul></div></html>' )
        return "\n".join( rval )

-    def regenerate_primary_file(self,dataset):
+    def regenerate_primary_file(self, dataset):
        """
        cannot do this until we are setting metadata
        """
@@ -176,23 +180,23 @@ class Velvet( Html ):
        gen_msg = ''
        try:
            efp = dataset.extra_files_path
-            log_path = os.path.join(efp,'Log')
-            f = open(log_path,'r')
+            log_path = os.path.join(efp, 'Log')
+            f = open(log_path, 'r')
            log_content = f.read(1000)
            f.close()
-            log_msg = re.sub('/\S*/','',log_content)
+            log_msg = re.sub('/\S*/', '', log_content)
            log.debug( "Velveth log info  %s" % log_msg)
-            paired_end_reads = re.search('-(short|long)Paired', log_msg) != None
+            paired_end_reads = re.search('-(short|long)Paired', log_msg) is not None
            dataset.metadata.paired_end_reads = paired_end_reads
-            long_reads = re.search('-long', log_msg) != None
+            long_reads = re.search('-long', log_msg) is not None
            dataset.metadata.long_reads = long_reads
-            short2_reads = re.search('-short(Paired)?2', log_msg) != None
+            short2_reads = re.search('-short(Paired)?2', log_msg) is not None
            dataset.metadata.short2_reads = short2_reads
-            dataset.info = re.sub('.*velveth \S+','hash_length',re.sub('\n',' ',log_msg))
+            dataset.info = re.sub('.*velveth \S+', 'hash_length', re.sub('\n', ' ', log_msg))
            if paired_end_reads:
-                 gen_msg = gen_msg + ' Paired-End Reads'
+                gen_msg = gen_msg + ' Paired-End Reads'
            if long_reads:
-                 gen_msg = gen_msg + ' Long Reads'
+                gen_msg = gen_msg + ' Long Reads'
            if len(gen_msg) > 0:
                gen_msg = 'Uses: ' + gen_msg
        except:
@@ -200,12 +204,12 @@ class Velvet( Html ):
        log.debug( "Velveth log info  %s" % gen_msg)
        rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
        # rval.append('<div>Generated:<p/><code> %s </code></div>' %(re.sub('\n','<br>',log_msg)))
-        rval.append('<div>Generated:<p/> %s </div>' %(gen_msg))
+        rval.append('<div>Generated:<p/> %s </div>' % (gen_msg))
        rval.append('<div>Velveth dataset:<p/><ul>')
-        for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
+        for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
            fn = composite_name
-            log.debug( "Velvet log info  %s %s %s" % ('JJ regenerate_primary_file',fn,composite_file))
-            if re.search('Log',fn) == None:
+            log.debug( "Velvet log info  %s %s %s" % ('JJ regenerate_primary_file', fn, composite_file))
+            if re.search('Log', fn) is None:
                opt_text = ''
                if composite_file.optional:
                    opt_text = ' (optional)'
@@ -214,7 +218,7 @@ class Velvet( Html ):
                else:
                    rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) )
        rval.append( '</ul></div></html>' )
-        f = file(dataset.file_name,'w')
+        f = file(dataset.file_name, 'w')
        f.write("\n".join( rval ))
        f.write('\n')
        f.close()
@@ -11,7 +11,6 @@ import shutil
 import struct
 import subprocess
 import tempfile
-import re
 import warnings
 import zipfile

@@ -35,6 +34,7 @@ log = logging.getLogger(__name__)

 # Currently these supported binary data types must be manually set on upload

+
 class Binary( data.Data ):
    """Binary data"""
    edam_format = "format_2333"
@@ -89,7 +89,7 @@ class Binary( data.Data ):
        to_ext = dataset.extension
        valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
        fname = ''.join(c in valid_chars and c or '_' for c in dataset.name)[0:150]
-        trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename
+        trans.response.set_content_type( "application/octet-stream" )  # force octet-stream so Safari doesn't append mime extensions to filename
        trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext)
        return open( dataset.file_name )

@@ -100,7 +100,7 @@ class Ab1( Binary ):

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
-            dataset.peek  = "Binary ab1 sequence file"
+            dataset.peek = "Binary ab1 sequence file"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
@@ -134,7 +134,6 @@ class Idat( Binary ):
 Binary.register_sniffable_binary_format("idat", "idat", Idat)


-
 class CompressedArchive( Binary ):
    """
        Class describing an compressed binary file
@@ -145,7 +144,7 @@ class CompressedArchive( Binary ):

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
-            dataset.peek  = "Compressed binary file"
+            dataset.peek = "Compressed binary file"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
@@ -209,7 +208,7 @@ class Bam( Binary ):
        if stderr:
            if exit_code != 0:
                shutil.rmtree(tmp_dir)  # clean up
-                raise Exception, "Error merging BAM files: %s" % stderr
+                raise Exception( "Error merging BAM files: %s" % stderr )
            else:
                print stderr
        os.unlink(stderr_name)
@@ -243,11 +242,11 @@ class Bam( Binary ):
            # seconds to index with samtools, and 45 minutes to sort, so indexing is relatively inexpensive.
            if self._is_coordinate_sorted( file_name ):
                return False
-            index_name = tempfile.NamedTemporaryFile( prefix = "bam_index" ).name
-            stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
+            index_name = tempfile.NamedTemporaryFile( prefix="bam_index" ).name
+            stderr_name = tempfile.NamedTemporaryFile( prefix="bam_index_stderr" ).name
            command = 'samtools index %s %s' % ( file_name, index_name )
            proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
-            exit_code = proc.wait()
+            proc.wait()
            stderr = open( stderr_name ).read().strip()
            if stderr:
                try:
@@ -276,28 +275,28 @@ class Bam( Binary ):
        on an output dataset after the content is initially generated.
        """
        # Use samtools to sort the Bam file
-        ##$ samtools sort
-        ##Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>
-        ## Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created.
-        ## This command may also create temporary files <out.prefix>.%d.bam when the
-        ## whole alignment cannot be fitted into memory ( controlled by option -m ).
-        #do this in a unique temp directory, because of possible <out.prefix>.%d.bam temp files
+        # $ samtools sort
+        # Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>
+        # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created.
+        # This command may also create temporary files <out.prefix>.%d.bam when the
+        # whole alignment cannot be fitted into memory ( controlled by option -m ).
+        # do this in a unique temp directory, because of possible <out.prefix>.%d.bam temp files
        if not self.dataset_content_needs_grooming( file_name ):
            # Don't re-sort if already sorted
            return
        tmp_dir = tempfile.mkdtemp()
        tmp_sorted_dataset_file_name_prefix = os.path.join( tmp_dir, 'sorted' )
-        stderr_name = tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "bam_sort_stderr" ).name
-        samtools_created_sorted_file_name = "%s.bam" % tmp_sorted_dataset_file_name_prefix #samtools accepts a prefix, not a filename, it always adds .bam to the prefix
+        stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir, prefix="bam_sort_stderr" ).name
+        samtools_created_sorted_file_name = "%s.bam" % tmp_sorted_dataset_file_name_prefix  # samtools accepts a prefix, not a filename, it always adds .bam to the prefix
        command = "samtools sort %s %s" % ( file_name, tmp_sorted_dataset_file_name_prefix )
        proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
        exit_code = proc.wait()
-        #Did sort succeed?
+        # Did sort succeed?
        stderr = open( stderr_name ).read().strip()
        if stderr:
            if exit_code != 0:
-                shutil.rmtree( tmp_dir) #clean up
-                raise Exception, "Error Grooming BAM file contents: %s" % stderr
+                shutil.rmtree( tmp_dir)  # clean up
+                raise Exception( "Error Grooming BAM file contents: %s" % stderr )
            else:
                print stderr
        # Move samtools_created_sorted_file_name to our output dataset location
@@ -309,20 +308,20 @@ class Bam( Binary ):
    def init_meta( self, dataset, copy_from=None ):
        Binary.init_meta( self, dataset, copy_from=copy_from )

-    def set_meta( self, dataset, overwrite = True, **kwd ):
+    def set_meta( self, dataset, overwrite=True, **kwd ):
        """ Creates the index for the BAM file. """
        # These metadata values are not accessible by users, always overwrite
        index_file = dataset.metadata.bam_index
        if not index_file:
-            index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset )
+            index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset=dataset )
        # Create the Bam index
-        ##$ samtools index
-        ##Usage: samtools index <in.bam> [<out.index>]
-        stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
+        # $ samtools index
+        # Usage: samtools index <in.bam> [<out.index>]
+        stderr_name = tempfile.NamedTemporaryFile( prefix="bam_index_stderr" ).name
        command = [ 'samtools', 'index', dataset.file_name, index_file.file_name ]
        proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
        exit_code = proc.wait()
-        #Did index succeed?
+        # Did index succeed?
        if exit_code == -6:
            # SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter.
            dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ),
@@ -339,8 +338,8 @@ class Bam( Binary ):
        stderr = open( stderr_name ).read().strip()
        if stderr:
            if exit_code != 0:
-                os.unlink( stderr_name ) #clean up
-                raise Exception, "Error Setting BAM Metadata: %s" % stderr
+                os.unlink( stderr_name )  # clean up
+                raise Exception( "Error Setting BAM Metadata: %s" % stderr )
            else:
                print stderr
        dataset.metadata.bam_index = index_file
@@ -371,7 +370,7 @@ class Bam( Binary ):

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
-            dataset.peek  = "Binary bam alignments file"
+            dataset.peek = "Binary bam alignments file"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
@@ -383,14 +382,12 @@ class Bam( Binary ):
        except:
            return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) )

-
-
    # ------------- Dataproviders
    # pipe through samtools view
-    #ALSO: (as Sam)
+    # ALSO: (as Sam)
    # bam does not use '#' to indicate comments/headers - we need to strip out those headers from the std. providers
-    #TODO:?? seems like there should be an easier way to do/inherit this - metadata.comment_char?
-    #TODO: incorporate samtools options to control output: regions first, then flags, etc.
+    # TODO:?? seems like there should be an easier way to do/inherit this - metadata.comment_char?
+    # TODO: incorporate samtools options to control output: regions first, then flags, etc.
    @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.line.FilteredLineDataProvider.settings )
    def line_dataprovider( self, dataset, **settings ):
        samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset )
@@ -417,13 +414,13 @@ class Bam( Binary ):

    # these can't be used directly - may need BamColumn, BamDict (Bam metadata -> column/dict)
    # OR - see genomic_region_dataprovider
-    #@dataproviders.decorators.dataprovider_factory( 'dataset-column', dataproviders.column.ColumnarDataProvider.settings )
-    #def dataset_column_dataprovider( self, dataset, **settings ):
+    # @dataproviders.decorators.dataprovider_factory( 'dataset-column', dataproviders.column.ColumnarDataProvider.settings )
+    # def dataset_column_dataprovider( self, dataset, **settings ):
    #    settings[ 'comment_char' ] = '@'
    #    return super( Sam, self ).dataset_column_dataprovider( dataset, **settings )

-    #@dataproviders.decorators.dataprovider_factory( 'dataset-dict', dataproviders.column.DictDataProvider.settings )
-    #def dataset_dict_dataprovider( self, dataset, **settings ):
+    # @dataproviders.decorators.dataprovider_factory( 'dataset-dict', dataproviders.column.DictDataProvider.settings )
+    # def dataset_dict_dataprovider( self, dataset, **settings ):
    #    settings[ 'comment_char' ] = '@'
    #    return super( Sam, self ).dataset_dict_dataprovider( dataset, **settings )

@@ -443,10 +440,10 @@ class Bam( Binary ):
    @dataproviders.decorators.dataprovider_factory( 'genomic-region', dataproviders.column.ColumnarDataProvider.settings )
    def genomic_region_dataprovider( self, dataset, **settings ):
        # GenomicRegionDataProvider currently requires a dataset as source - may not be necc.
-        #TODO:?? consider (at least) the possible use of a kwarg: metadata_source (def. to source.dataset),
+        # TODO:?? consider (at least) the possible use of a kwarg: metadata_source (def. to source.dataset),
        #   or remove altogether...
-        #samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset )
-        #return dataproviders.dataset.GenomicRegionDataProvider( samtools_source, metadata_source=dataset,
+        # samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset )
+        # return dataproviders.dataset.GenomicRegionDataProvider( samtools_source, metadata_source=dataset,
        #                                                        2, 3, 3, **settings )

        # instead, set manually and use in-class column gen
@@ -469,6 +466,7 @@ class Bam( Binary ):

 Binary.register_sniffable_binary_format("bam", "bam", Bam)

+
 class Bcf( Binary):
    """Class describing a BCF file"""
    edam_format = "format_3020"
@@ -487,21 +485,21 @@ class Bcf( Binary):
        except:
            return False

-    def set_meta( self, dataset, overwrite = True, **kwd ):
+    def set_meta( self, dataset, overwrite=True, **kwd ):
        """ Creates the index for the BCF file. """
        # These metadata values are not accessible by users, always overwrite
        index_file = dataset.metadata.bcf_index
        if not index_file:
-            index_file = dataset.metadata.spec['bcf_index'].param.new_file( dataset = dataset )
+            index_file = dataset.metadata.spec['bcf_index'].param.new_file( dataset=dataset )
        # Create the bcf index
-        ##$ bcftools index
-        ##Usage: bcftools index <in.bcf>
+        # $ bcftools index
+        # Usage: bcftools index <in.bcf>

        dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ),
                    '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) )
        os.symlink( dataset.file_name, dataset_symlink )

-        stderr_name = tempfile.NamedTemporaryFile( prefix = "bcf_index_stderr" ).name
+        stderr_name = tempfile.NamedTemporaryFile( prefix="bcf_index_stderr" ).name
        command = [ 'bcftools', 'index', dataset_symlink ]
        proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
        exit_code = proc.wait()
@@ -510,8 +508,8 @@ class Bcf( Binary):
        stderr = open( stderr_name ).read().strip()
        if stderr:
            if exit_code != 0:
-                os.unlink( stderr_name ) #clean up
-                raise Exception, "Error Setting BCF Metadata: %s" % stderr
+                os.unlink( stderr_name )  # clean up
+                raise Exception( "Error Setting BCF Metadata: %s" % stderr )
            else:
                print stderr
        dataset.metadata.bcf_index = index_file
@@ -527,7 +525,7 @@ class H5( Binary ):

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
-            dataset.peek  = "Binary h5 file"
+            dataset.peek = "Binary h5 file"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
@@ -549,7 +547,7 @@ class Scf( Binary ):

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
-            dataset.peek  = "Binary scf sequence file"
+            dataset.peek = "Binary scf sequence file"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
@@ -585,7 +583,7 @@ class Sff( Binary ):

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
-            dataset.peek  = "Binary sff file"
+            dataset.peek = "Binary sff file"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
@@ -627,7 +625,7 @@ class BigWig(Binary):

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
-            dataset.peek  = "Binary UCSC %s file" % self._name
+            dataset.peek = "Binary UCSC %s file" % self._name
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
@@ -699,7 +697,7 @@ class SQlite ( Binary ):
    def init_meta( self, dataset, copy_from=None ):
        Binary.init_meta( self, dataset, copy_from=copy_from )

-    def set_meta( self, dataset, overwrite = True, **kwd ):
+    def set_meta( self, dataset, overwrite=True, **kwd ):
        try:
            tables = []
            columns = dict()
@@ -708,7 +706,7 @@ class SQlite ( Binary ):
            c = conn.cursor()
            tables_query = "SELECT name,sql FROM sqlite_master WHERE type='table' ORDER BY name"
            rslt = c.execute(tables_query).fetchall()
-            for table,sql in rslt:
+            for table, sql in rslt:
                tables.append(table)
                try:
                    col_query = 'SELECT * FROM %s LIMIT 0' % table
@@ -742,12 +740,12 @@ class SQlite ( Binary ):

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
-            dataset.peek  = "SQLite Database"
+            dataset.peek = "SQLite Database"
            lines = ['SQLite Database']
            if dataset.metadata.tables:
                for table in dataset.metadata.tables:
                    try:
-                        lines.append('%s [%s]' % (table,dataset.metadata.table_row_count[table]))
+                        lines.append('%s [%s]' % (table, dataset.metadata.table_row_count[table]))
                    except:
                        continue
            dataset.peek = '\n'.join(lines)
@@ -762,7 +760,6 @@ class SQlite ( Binary ):
        except:
            return "SQLite Database (%s)" % ( data.nice_size( dataset.get_size() ) )

-
    @dataproviders.decorators.dataprovider_factory( 'sqlite', dataproviders.dataset.SQliteDataProvider.settings )
    def sqlite_dataprovider( self, dataset, **settings ):
        dataset_source = dataproviders.dataset.DatasetDataProvider( dataset )
@@ -779,7 +776,7 @@ class SQlite ( Binary ):
        return dataproviders.dataset.SQliteDataDictProvider( dataset_source, **settings )


-#Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)
+# Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)


 class GeminiSQLite( SQlite ):
@@ -788,8 +785,8 @@ class GeminiSQLite( SQlite ):
                     readonly=True, visible=True, no_value='0.10.0' )
    file_ext = "gemini.sqlite"

-    def set_meta( self, dataset, overwrite = True, **kwd ):
-        super( GeminiSQLite, self ).set_meta( dataset, overwrite = overwrite, **kwd )
+    def set_meta( self, dataset, overwrite=True, **kwd ):
+        super( GeminiSQLite, self ).set_meta( dataset, overwrite=overwrite, **kwd )
        try:
            conn = sqlite.connect( dataset.file_name )
            c = conn.cursor()
@@ -821,7 +818,7 @@ class GeminiSQLite( SQlite ):

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
-            dataset.peek  = "Gemini SQLite Database, version %s" % ( dataset.metadata.gemini_version or 'unknown' )
+            dataset.peek = "Gemini SQLite Database, version %s" % ( dataset.metadata.gemini_version or 'unknown' )
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
@@ -841,7 +838,8 @@ Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)

 class Xlsx(Binary):
    """Class for Excel 2007 (xlsx) files"""
-    file_ext="xlsx"
+    file_ext = "xlsx"
+
    def sniff( self, filename ):
        # Xlsx is compressed in zip format and must not be uncompressed in Galaxy.
        try:
@@ -878,7 +876,7 @@ class Sra( Binary ):

    def set_peek(self, dataset, is_multi_byte=False):
        if not dataset.dataset.purged:
-            dataset.peek  = 'Binary sra file'
+            dataset.peek = 'Binary sra file'
            dataset.blurb = data.nice_size(dataset.get_size())
        else:
            dataset.peek = 'file does not exist'
@@ -1,4 +1,3 @@
-import os
 import re
 import bz2
 import gzip
@@ -18,8 +17,9 @@ except ImportError:
    except:
        PIL = None

+
 def check_image( file_path ):
-    if PIL != None:
+    if PIL is not None:
        try:
            im = PIL.open( file_path )
        except:
@@ -28,10 +28,11 @@ def check_image( file_path ):
            return im
        return False
    else:
-        if imghdr.what( file_path ) != None:
+        if imghdr.what( file_path ) is not None:
            return True
        return False

+
 def check_html( file_path, chunk=None ):
    if chunk is None:
        temp = open( file_path, "U" )
@@ -58,6 +59,7 @@ def check_html( file_path, chunk=None ):
        temp.close()
    return False

+
 def check_binary( name, file_path=True ):
    # Handles files if file_path is True or text if file_path is False
    is_binary = False
@@ -65,7 +67,6 @@ def check_binary( name, file_path=True ):
        temp = open( name, "U" )
    else:
        temp = StringIO( name )
-    chars_read = 0
    try:
        for char in temp.read( 100 ):
            if util.is_binary( char ):
@@ -75,6 +76,7 @@ def check_binary( name, file_path=True ):
        temp.close( )
    return is_binary

+
 def check_gzip( file_path ):
    # This method returns a tuple of booleans representing ( is_gzipped, is_valid )
    # Make sure we have a gzipped file
@@ -95,7 +97,7 @@ def check_gzip( file_path ):
            return ( True, True )
    except:
        return( False, False )
-    CHUNK_SIZE = 2**15 # 32Kb
+    CHUNK_SIZE = 2 ** 15  # 32Kb
    gzipped_file = gzip.GzipFile( file_path, mode='rb' )
    chunk = gzipped_file.read( CHUNK_SIZE )
    gzipped_file.close()
@@ -104,6 +106,7 @@ def check_gzip( file_path ):
        return ( True, False )
    return ( True, True )

+
 def check_bz2( file_path ):
    try:
        temp = open( file_path, "U" )
@@ -113,7 +116,7 @@ def check_bz2( file_path ):
            return ( False, False )
    except:
        return( False, False )
-    CHUNK_SIZE = 2**15 # reKb
+    CHUNK_SIZE = 2 ** 15  # reKb
    bzipped_file = bz2.BZ2File( file_path, mode='rb' )
    chunk = bzipped_file.read( CHUNK_SIZE )
    bzipped_file.close()
@@ -122,15 +125,18 @@ def check_bz2( file_path ):
        return ( True, False )
    return ( True, True )

+
 def check_zip( file_path ):
    if zipfile.is_zipfile( file_path ):
        return True
    return False

+
 def is_bz2( file_path ):
    is_bz2, is_valid = check_bz2( file_path )
    return is_bz2

+
 def is_gzip( file_path ):
    is_gzipped, is_valid = check_gzip( file_path )
    return is_gzipped
@@ -7,4 +7,3 @@ class ChromInfo( Tabular ):
    file_ext = "len"
    MetadataElement( name="chrom", default=1, desc="Chrom column", param=metadata.ColumnParameter )
    MetadataElement( name="length", default=2, desc="Length column", param=metadata.ColumnParameter )
-
@@ -13,6 +13,7 @@ from galaxy.datatypes.tabular import Tabular

 log = logging.getLogger(__name__)

+
 class LastzCoverage( Tabular ):
    file_ext = "coverage"

@@ -28,7 +29,6 @@ class LastzCoverage( Tabular ):
        """
        # Maybe if we import here people will still be able to use Galaxy when numpy kills it
        eggs.require("numpy>=1.2.1")
-        #from numpy.lib import format
        import numpy

        range = end - start
@@ -55,5 +55,3 @@ class LastzCoverage( Tabular ):
        resolution = min( resolution, 10000 )
        resolution = max( resolution, 1 )
        return resolution
-
-