Mercurial > repos > devteam > intersect
changeset 3:5f72be09cfd3 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:48:44 -0500 |
| parents | 77641d5731c8 |
| children | 8ddabc73af92 |
| files | gops_intersect.py intersect.xml operation_filter.py tool_dependencies.xml utils/__init__.py utils/gff_util.py utils/odict.py |
| diffstat | 6 files changed, 43 insertions(+), 574 deletions(-) [+] |
line wrap: on
line diff
--- a/gops_intersect.py Mon Apr 14 09:20:28 2014 -0400 +++ b/gops_intersect.py Wed Nov 11 12:48:44 2015 -0500 @@ -11,34 +11,34 @@ -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval """ -import sys, traceback, fileinput -from warnings import warn -from bx.intervals import * -from bx.intervals.io import * -from bx.intervals.operations.intersect import * +import fileinput +import sys +from bx.intervals.io import GenomicInterval, NiceReaderWrapper +from bx.intervals.operations.intersect import intersect from bx.cookbook import doc_optparse -from galaxy.tools.util.galaxyops import * +from bx.tabular.io import ParseError +from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff assert sys.version_info[:2] >= ( 2, 4 ) + def main(): mincols = 1 - upstream_pad = 0 - downstream_pad = 0 options, args = doc_optparse.parse( __doc__ ) try: chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) - chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) - if options.mincols: mincols = int( options.mincols ) + chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) + if options.mincols: + mincols = int( options.mincols ) pieces = bool( options.pieces ) in1_gff_format = bool( options.gff1 ) in2_gff_format = bool( options.gff2 ) in_fname, in2_fname, out_fname = args except: doc_optparse.exception() - + # Set readers to handle either GFF or default format. if in1_gff_format: in1_reader_wrapper = GFFReaderWrapper @@ -48,29 +48,29 @@ in2_reader_wrapper = GFFReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper - + g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ), - chrom_col=chr_col_1, - start_col=start_col_1, - end_col=end_col_1, - strand_col=strand_col_1, - fix_strand=True ) + chrom_col=chr_col_1, + start_col=start_col_1, + end_col=end_col_1, + strand_col=strand_col_1, + fix_strand=True ) if in1_gff_format: # Intersect requires coordinates in BED format. - g1.convert_to_bed_coord=True + g1.convert_to_bed_coord = True g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ), - chrom_col=chr_col_2, - start_col=start_col_2, - end_col=end_col_2, - strand_col=strand_col_2, - fix_strand=True ) + chrom_col=chr_col_2, + start_col=start_col_2, + end_col=end_col_2, + strand_col=strand_col_2, + fix_strand=True ) if in2_gff_format: # Intersect requires coordinates in BED format. - g2.convert_to_bed_coord=True - + g2.convert_to_bed_coord = True + out_file = open( out_fname, "w" ) try: - for feature in intersect( [g1,g2], pieces=pieces, mincols=mincols ): + for feature in intersect( [g1, g2], pieces=pieces, mincols=mincols ): if isinstance( feature, GFFFeature ): # Convert back to GFF coordinates since reader converted automatically. convert_bed_coords_to_gff( feature )
--- a/intersect.xml Mon Apr 14 09:20:28 2014 -0400 +++ b/intersect.xml Wed Nov 11 12:48:44 2015 -0500 @@ -32,7 +32,7 @@ <param format="interval,gff" name="input2" type="data" help="Second dataset"> <label>that intersect</label> </param> - <param name="min" size="4" type="integer" value="1" min="1" help="(bp)"> + <param name="min" type="integer" value="1" min="1" help="(bp)"> <label>for at least</label> </param> </inputs>
--- a/operation_filter.py Mon Apr 14 09:20:28 2014 -0400 +++ b/operation_filter.py Wed Nov 11 12:48:44 2015 -0500 @@ -1,7 +1,4 @@ # runs after the job (and after the default post-filter) -import os -from galaxy import eggs -from galaxy import jobs from galaxy.tools.parameters import DataToolParameter from galaxy.jobs.handler import JOB_ERROR @@ -12,11 +9,6 @@ except: from sets import Set as set -#def exec_before_process(app, inp_data, out_data, param_dict, tool=None): -# """Sets the name of the data""" -# dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] ) -# if len(dbkeys) != 1: -# raise Exception, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>' def validate_input( trans, error_map, param_values, page_param_map ): dbkeys = set() @@ -25,7 +17,7 @@ for name, param in page_param_map.iteritems(): if isinstance( param, DataToolParameter ): # for each dataset parameter - if param_values.get(name, None) != None: + if param_values.get(name, None) is not None: dbkeys.add( param_values[name].dbkey ) data_params += 1 # check meta data @@ -34,17 +26,15 @@ if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ): # TODO: currently cannot validate GFF inputs b/c they are not derived from interval. pass - else: # Validate interval datatype. - startCol = int( param.metadata.startCol ) - endCol = int( param.metadata.endCol ) - chromCol = int( param.metadata.chromCol ) + else: # Validate interval datatype. + int( param.metadata.startCol ) + int( param.metadata.endCol ) + int( param.metadata.chromCol ) if param.metadata.strandCol is not None: - strandCol = int ( param.metadata.strandCol ) - else: - strandCol = 0 + int( param.metadata.strandCol ) except: error_msg = "The attributes of this dataset are not properly set. " + \ - "Click the pencil icon in the history item to set the chrom, start, end and strand columns." + "Click the pencil icon in the history item to set the chrom, start, end and strand columns." error_map[name] = error_msg data_param_names.add( name ) if len( dbkeys ) > 1: @@ -55,38 +45,33 @@ for name in data_param_names: error_map[name] = "A dataset of the appropriate type is required" + # Commented out by INS, 5/30/2007. What is the PURPOSE of this? def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): """Verify the output data after each run""" - items = out_data.items() - - for name, data in items: + for data in out_data.values(): try: if stderr and len( stderr ) > 0: raise Exception( stderr ) - except Exception, exc: + except Exception: data.blurb = JOB_ERROR data.state = JOB_ERROR -## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): -## pass - def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): exec_after_process( app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) # strip strand column if clusters were merged - items = out_data.items() - for name, data in items: - if param_dict['returntype'] == True: + for data in out_data.values(): + if param_dict['returntype'] is True: data.metadata.chromCol = 1 data.metadata.startCol = 2 data.metadata.endCol = 3 # merge always clobbers strand data.metadata.strandCol = None - + def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): exec_after_process( @@ -94,6 +79,5 @@ # strip strand column if clusters were merged if param_dict["returntype"] == '1': - items = out_data.items() - for name, data in items: + for data in out_data.values(): data.metadata.strandCol = None
--- a/tool_dependencies.xml Mon Apr 14 09:20:28 2014 -0400 +++ b/tool_dependencies.xml Wed Nov 11 12:48:44 2015 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="bx-python" version="0.7.1"> - <repository changeset_revision="41eb9d9f667d" name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2d0c08728bca" name="package_bx_python_0_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="galaxy-ops" version="1.0.0"> - <repository changeset_revision="4e39032e4ec6" name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9cbb20b85c01" name="package_galaxy_ops_1_0_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
--- a/utils/gff_util.py Mon Apr 14 09:20:28 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,430 +0,0 @@ -""" -Provides utilities for working with GFF files. -""" - -import copy -from bx.intervals.io import * -from bx.tabular.io import Header, Comment -from utils.odict import odict - -class GFFInterval( GenomicInterval ): - """ - A GFF interval, including attributes. If file is strictly a GFF file, - only attribute is 'group.' - """ - def __init__( self, reader, fields, chrom_col=0, feature_col=2, start_col=3, end_col=4, \ - strand_col=6, score_col=5, default_strand='.', fix_strand=False ): - # HACK: GFF format allows '.' for strand but GenomicInterval does not. To get around this, - # temporarily set strand and then unset after initing GenomicInterval. - unknown_strand = False - if not fix_strand and fields[ strand_col ] == '.': - unknown_strand = True - fields[ strand_col ] = '+' - GenomicInterval.__init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, \ - default_strand, fix_strand=fix_strand ) - if unknown_strand: - self.strand = '.' - self.fields[ strand_col ] = '.' - - # Handle feature, score column. - self.feature_col = feature_col - if self.feature_col >= self.nfields: - raise MissingFieldError( "No field for feature_col (%d)" % feature_col ) - self.feature = self.fields[ self.feature_col ] - self.score_col = score_col - if self.score_col >= self.nfields: - raise MissingFieldError( "No field for score_col (%d)" % score_col ) - self.score = self.fields[ self.score_col ] - - # GFF attributes. - self.attributes = parse_gff_attributes( fields[8] ) - - def copy( self ): - return GFFInterval(self.reader, list( self.fields ), self.chrom_col, self.feature_col, self.start_col, - self.end_col, self.strand_col, self.score_col, self.strand) - -class GFFFeature( GFFInterval ): - """ - A GFF feature, which can include multiple intervals. - """ - def __init__( self, reader, chrom_col=0, feature_col=2, start_col=3, end_col=4, \ - strand_col=6, score_col=5, default_strand='.', fix_strand=False, intervals=[], \ - raw_size=0 ): - # Use copy so that first interval and feature do not share fields. - GFFInterval.__init__( self, reader, copy.deepcopy( intervals[0].fields ), chrom_col, feature_col, \ - start_col, end_col, strand_col, score_col, default_strand, \ - fix_strand=fix_strand ) - self.intervals = intervals - self.raw_size = raw_size - # Use intervals to set feature attributes. - for interval in self.intervals: - # Error checking. NOTE: intervals need not share the same strand. - if interval.chrom != self.chrom: - raise ValueError( "interval chrom does not match self chrom: %s != %s" % \ - ( interval.chrom, self.chrom ) ) - # Set start, end of interval. - if interval.start < self.start: - self.start = interval.start - if interval.end > self.end: - self.end = interval.end - - def name( self ): - """ Returns feature's name. """ - name = None - # Preference for name: GTF, GFF3, GFF. - for attr_name in [ - # GTF: - 'gene_id', 'transcript_id', - # GFF3: - 'ID', 'id', - # GFF (TODO): - 'group' ]: - name = self.attributes.get( attr_name, None ) - if name is not None: - break - return name - - def copy( self ): - intervals_copy = [] - for interval in self.intervals: - intervals_copy.append( interval.copy() ) - return GFFFeature(self.reader, self.chrom_col, self.feature_col, self.start_col, self.end_col, self.strand_col, - self.score_col, self.strand, intervals=intervals_copy ) - - def lines( self ): - lines = [] - for interval in self.intervals: - lines.append( '\t'.join( interval.fields ) ) - return lines - - -class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ): - """ - Reader wrapper that reads GFF intervals/lines and automatically converts - them to BED format. - """ - - def parse_row( self, line ): - # HACK: this should return a GFF interval, but bx-python operations - # require GenomicInterval objects and subclasses will not work. - interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, \ - self.end_col, self.strand_col, self.default_strand, \ - fix_strand=self.fix_strand ) - interval = convert_gff_coords_to_bed( interval ) - return interval - -class GFFReaderWrapper( NiceReaderWrapper ): - """ - Reader wrapper for GFF files. - - Wrapper has two major functions: - - 1. group entries for GFF file (via group column), GFF3 (via id attribute), - or GTF (via gene_id/transcript id); - 2. convert coordinates from GFF format--starting and ending coordinates - are 1-based, closed--to the 'traditional'/BED interval format--0 based, - half-open. This is useful when using GFF files as inputs to tools that - expect traditional interval format. - """ - - def __init__( self, reader, chrom_col=0, feature_col=2, start_col=3, \ - end_col=4, strand_col=6, score_col=5, fix_strand=False, convert_to_bed_coord=False, **kwargs ): - NiceReaderWrapper.__init__( self, reader, chrom_col=chrom_col, start_col=start_col, end_col=end_col, \ - strand_col=strand_col, fix_strand=fix_strand, **kwargs ) - self.feature_col = feature_col - self.score_col = score_col - self.convert_to_bed_coord = convert_to_bed_coord - self.last_line = None - self.cur_offset = 0 - self.seed_interval = None - self.seed_interval_line_len = 0 - - def parse_row( self, line ): - interval = GFFInterval( self, line.split( "\t" ), self.chrom_col, self.feature_col, \ - self.start_col, self.end_col, self.strand_col, self.score_col, \ - self.default_strand, fix_strand=self.fix_strand ) - return interval - - def next( self ): - """ Returns next GFFFeature. """ - - # - # Helper function. - # - - def handle_parse_error( parse_error ): - """ Actions to take when ParseError found. """ - if self.outstream: - if self.print_delegate and hasattr(self.print_delegate,"__call__"): - self.print_delegate( self.outstream, e, self ) - self.skipped += 1 - # no reason to stuff an entire bad file into memmory - if self.skipped < 10: - self.skipped_lines.append( ( self.linenum, self.current_line, str( e ) ) ) - - # For debugging, uncomment this to propogate parsing exceptions up. - # I.e. the underlying reason for an unexpected StopIteration exception - # can be found by uncommenting this. - # raise e - - # - # Get next GFFFeature - # - raw_size = self.seed_interval_line_len - - # If there is no seed interval, set one. Also, if there are no more - # intervals to read, this is where iterator dies. - if not self.seed_interval: - while not self.seed_interval: - try: - self.seed_interval = GenomicIntervalReader.next( self ) - except ParseError, e: - handle_parse_error( e ) - # TODO: When no longer supporting python 2.4 use finally: - #finally: - raw_size += len( self.current_line ) - - # If header or comment, clear seed interval and return it with its size. - if isinstance( self.seed_interval, ( Header, Comment ) ): - return_val = self.seed_interval - return_val.raw_size = len( self.current_line ) - self.seed_interval = None - self.seed_interval_line_len = 0 - return return_val - - # Initialize feature identifier from seed. - feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF - # For GFF3 - feature_id = self.seed_interval.attributes.get( 'ID', None ) - feature_parent_id = self.seed_interval.attributes.get( 'Parent', None ) - # For GTF. - feature_gene_id = self.seed_interval.attributes.get( 'gene_id', None ) - feature_transcript_id = self.seed_interval.attributes.get( 'transcript_id', None ) - - # Read all intervals associated with seed. - feature_intervals = [] - feature_intervals.append( self.seed_interval ) - while True: - try: - interval = GenomicIntervalReader.next( self ) - raw_size += len( self.current_line ) - except StopIteration, e: - # No more intervals to read, but last feature needs to be - # returned. - interval = None - raw_size += len( self.current_line ) - break - except ParseError, e: - handle_parse_error( e ) - raw_size += len( self.current_line ) - continue - # TODO: When no longer supporting python 2.4 use finally: - #finally: - #raw_size += len( self.current_line ) - - # Ignore comments. - if isinstance( interval, Comment ): - continue - - # Determine if interval is part of feature. - part_of = False - group = interval.attributes.get( 'group', None ) - # GFF test: - if group and feature_group == group: - part_of = True - # GFF3 test: - parent_id = interval.attributes.get( 'Parent', None ) - cur_id = interval.attributes.get( 'ID', None ) - if ( cur_id and cur_id == feature_id ) or ( parent_id and parent_id == feature_id ): - part_of = True - # GTF test: - transcript_id = interval.attributes.get( 'transcript_id', None ) - if transcript_id and transcript_id == feature_transcript_id: - part_of = True - - # If interval is not part of feature, clean up and break. - if not part_of: - # Adjust raw size because current line is not part of feature. - raw_size -= len( self.current_line ) - break - - # Interval associated with feature. - feature_intervals.append( interval ) - - # Last interval read is the seed for the next interval. - self.seed_interval = interval - self.seed_interval_line_len = len( self.current_line ) - - # Return feature. - feature = GFFFeature( self, self.chrom_col, self.feature_col, self.start_col, \ - self.end_col, self.strand_col, self.score_col, \ - self.default_strand, fix_strand=self.fix_strand, \ - intervals=feature_intervals, raw_size=raw_size ) - - # Convert to BED coords? - if self.convert_to_bed_coord: - convert_gff_coords_to_bed( feature ) - - return feature - -def convert_bed_coords_to_gff( interval ): - """ - Converts an interval object's coordinates from BED format to GFF format. - Accepted object types include GenomicInterval and list (where the first - element in the list is the interval's start, and the second element is - the interval's end). - """ - if isinstance( interval, GenomicInterval ): - interval.start += 1 - if isinstance( interval, GFFFeature ): - for subinterval in interval.intervals: - convert_bed_coords_to_gff( subinterval ) - elif type ( interval ) is list: - interval[ 0 ] += 1 - return interval - -def convert_gff_coords_to_bed( interval ): - """ - Converts an interval object's coordinates from GFF format to BED format. - Accepted object types include GFFFeature, GenomicInterval, and list (where - the first element in the list is the interval's start, and the second - element is the interval's end). - """ - if isinstance( interval, GenomicInterval ): - interval.start -= 1 - if isinstance( interval, GFFFeature ): - for subinterval in interval.intervals: - convert_gff_coords_to_bed( subinterval ) - elif type ( interval ) is list: - interval[ 0 ] -= 1 - return interval - -def parse_gff_attributes( attr_str ): - """ - Parses a GFF/GTF attribute string and returns a dictionary of name-value - pairs. The general format for a GFF3 attributes string is - - name1=value1;name2=value2 - - The general format for a GTF attribute string is - - name1 "value1" ; name2 "value2" - - The general format for a GFF attribute string is a single string that - denotes the interval's group; in this case, method returns a dictionary - with a single key-value pair, and key name is 'group' - """ - attributes_list = attr_str.split(";") - attributes = {} - for name_value_pair in attributes_list: - # Try splitting by '=' (GFF3) first because spaces are allowed in GFF3 - # attribute; next, try double quotes for GTF. - pair = name_value_pair.strip().split("=") - if len( pair ) == 1: - pair = name_value_pair.strip().split("\"") - if len( pair ) == 1: - # Could not split for some reason -- raise exception? - continue - if pair == '': - continue - name = pair[0].strip() - if name == '': - continue - # Need to strip double quote from values - value = pair[1].strip(" \"") - attributes[ name ] = value - - if len( attributes ) == 0: - # Could not split attributes string, so entire string must be - # 'group' attribute. This is the case for strictly GFF files. - attributes['group'] = attr_str - return attributes - -def gff_attributes_to_str( attrs, gff_format ): - """ - Convert GFF attributes to string. Supported formats are GFF3, GTF. - """ - if gff_format == 'GTF': - format_string = '%s "%s"' - # Convert group (GFF) and ID, parent (GFF3) attributes to transcript_id, gene_id - id_attr = None - if 'group' in attrs: - id_attr = 'group' - elif 'ID' in attrs: - id_attr = 'ID' - elif 'Parent' in attrs: - id_attr = 'Parent' - if id_attr: - attrs['transcript_id'] = attrs['gene_id'] = attrs[id_attr] - elif gff_format == 'GFF3': - format_string = '%s=%s' - attrs_strs = [] - for name, value in attrs.items(): - attrs_strs.append( format_string % ( name, value ) ) - return " ; ".join( attrs_strs ) - -def read_unordered_gtf( iterator, strict=False ): - """ - Returns GTF features found in an iterator. GTF lines need not be ordered - or clustered for reader to work. Reader returns GFFFeature objects sorted - by transcript_id, chrom, and start position. - """ - - # -- Get function that generates line/feature key. -- - - get_transcript_id = lambda fields: parse_gff_attributes( fields[8] )[ 'transcript_id' ] - if strict: - # Strict GTF parsing uses transcript_id only to group lines into feature. - key_fn = get_transcript_id - else: - # Use lenient parsing where chromosome + transcript_id is the key. This allows - # transcripts with same ID on different chromosomes; this occurs in some popular - # datasources, such as RefGenes in UCSC. - key_fn = lambda fields: fields[0] + '_' + get_transcript_id( fields ) - - - # Aggregate intervals by transcript_id and collect comments. - feature_intervals = odict() - comments = [] - for count, line in enumerate( iterator ): - if line.startswith( '#' ): - comments.append( Comment( line ) ) - continue - - line_key = key_fn( line.split('\t') ) - if line_key in feature_intervals: - feature = feature_intervals[ line_key ] - else: - feature = [] - feature_intervals[ line_key ] = feature - feature.append( GFFInterval( None, line.split( '\t' ) ) ) - - # Create features. - chroms_features = {} - for count, intervals in enumerate( feature_intervals.values() ): - # Sort intervals by start position. - intervals.sort( lambda a,b: cmp( a.start, b.start ) ) - feature = GFFFeature( None, intervals=intervals ) - if feature.chrom not in chroms_features: - chroms_features[ feature.chrom ] = [] - chroms_features[ feature.chrom ].append( feature ) - - # Sort features by chrom, start position. - chroms_features_sorted = [] - for chrom_features in chroms_features.values(): - chroms_features_sorted.append( chrom_features ) - chroms_features_sorted.sort( lambda a,b: cmp( a[0].chrom, b[0].chrom ) ) - for features in chroms_features_sorted: - features.sort( lambda a,b: cmp( a.start, b.start ) ) - - # Yield comments first, then features. - # FIXME: comments can appear anywhere in file, not just the beginning. - # Ideally, then comments would be associated with features and output - # just before feature/line. - for comment in comments: - yield comment - - for chrom_features in chroms_features_sorted: - for feature in chrom_features: - yield feature -
--- a/utils/odict.py Mon Apr 14 09:20:28 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -""" -Ordered dictionary implementation. -""" - -from UserDict import UserDict - -class odict(UserDict): - """ - http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/107747 - - This dictionary class extends UserDict to record the order in which items are - added. Calling keys(), values(), items(), etc. will return results in this - order. - """ - def __init__( self, dict = None ): - self._keys = [] - UserDict.__init__( self, dict ) - - def __delitem__( self, key ): - UserDict.__delitem__( self, key ) - self._keys.remove( key ) - - def __setitem__( self, key, item ): - UserDict.__setitem__( self, key, item ) - if key not in self._keys: - self._keys.append( key ) - - def clear( self ): - UserDict.clear( self ) - self._keys = [] - - def copy(self): - new = odict() - new.update( self ) - return new - - def items( self ): - return zip( self._keys, self.values() ) - - def keys( self ): - return self._keys[:] - - def popitem( self ): - try: - key = self._keys[-1] - except IndexError: - raise KeyError( 'dictionary is empty' ) - val = self[ key ] - del self[ key ] - return ( key, val ) - - def setdefault( self, key, failobj=None ): - if key not in self._keys: - self._keys.append( key ) - return UserDict.setdefault( self, key, failobj ) - - def update( self, dict ): - for ( key, val ) in dict.items(): - self.__setitem__( key, val ) - - def values( self ): - return map( self.get, self._keys ) - - def iterkeys( self ): - return iter( self._keys ) - - def itervalues( self ): - for key in self._keys: - yield self.get( key ) - - def iteritems( self ): - for key in self._keys: - yield key, self.get( key ) - - def __iter__( self ): - for key in self._keys: - yield key - - def reverse( self ): - self._keys.reverse() - - def insert( self, index, key, item ): - if key not in self._keys: - self._keys.insert( index, key ) - UserDict.__setitem__( self, key, item )