# HG changeset patch
# User devteam
# Date 1447264124 18000
# Node ID 5f72be09cfd3c289b872d6008b87666ac873f90a
# Parent 77641d5731c845f9674943f3ccf5836e25092d83
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit a1517c9d22029095120643bbe2c8fa53754dd2b7
diff -r 77641d5731c8 -r 5f72be09cfd3 gops_intersect.py
--- 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 )
diff -r 77641d5731c8 -r 5f72be09cfd3 intersect.xml
--- 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 @@
-
+
diff -r 77641d5731c8 -r 5f72be09cfd3 operation_filter.py
--- 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, 'Both Queries must be from the same genome build
'
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
diff -r 77641d5731c8 -r 5f72be09cfd3 tool_dependencies.xml
--- 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 @@
-
+
-
+
diff -r 77641d5731c8 -r 5f72be09cfd3 utils/__init__.py
diff -r 77641d5731c8 -r 5f72be09cfd3 utils/gff_util.py
--- 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
-
diff -r 77641d5731c8 -r 5f72be09cfd3 utils/odict.py
--- 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 )