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# Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Contact: Leighton Pritchard, Scottish Crop Research Institute,
# Invergowrie, Dundee, Scotland, DD2 5DA, UK
# L.Pritchard@scri.ac.uk
################################################################################
#
# Thanks to Peter Cock for the impetus to write the get_features() code to
# subselect Features.
#
################################################################################
""" FeatureSet module
Provides:
o FeatureSet - container for Feature objects
For drawing capabilities, this module uses reportlab to draw and write
the diagram:
http://www.reportlab.com
For dealing with biological information, the package expects BioPython
objects:
http://www.biopython.org
"""
#------------------------------------------------------------------------------
# IMPORTS
# ReportLab
from __future__ import print_function
from reportlab.pdfbase import _fontdata
from reportlab.lib import colors
# GenomeDiagram
from ._Feature import Feature
# Builtins
import re
#------------------------------------------------------------------------------
# CLASSES
#------------------------------------------------------------
# FeatureSet
class FeatureSet(object):
""" FeatureSet
Provides:
Methods:
o __init__(self, set_id=None, name=None) Called on instantiation
o add_feature(self, feature, color=colors.lightgreen) Add a Feature
object to the set
o del_feature(self, feature_id) Remove a feature from the set, by id
o set_all_features(self, attr, value) Set the passed attribute to the
passed value in all features in the set
o get_features(self) Returns a list of Features from the set
o get_ids(self) Returns a list of unique ids for features in the set
o range(self) Returns the range of bases covered by features in
the set
o to_string(self, verbose=0) Returns a string describing the set
o __len__(self) Returns the length of sequence covered by the set
o __getitem__(self, key) Returns a feature from the set, keyed by id
o __str__(self) Returns a string describing the set
Attributes:
o id Unique id for the set
o name String describing the set
"""
def __init__(self, set_id=None, name=None, parent=None):
""" __init__(self, set_id=None, name=None)
o set_id Unique id for the set
o name String identifying the feature set
"""
self.parent = parent
self.id = id # Unique id for the set
self.next_id = 0 # counter for unique feature ids
self.features = {} # Holds features, keyed by ID
self.name = name # String describing the set
def add_feature(self, feature, **kwargs):
""" add_feature(self, feature, **args)
o feature Bio.SeqFeature object
o **kwargs Keyword arguments for Feature. Named attributes
of the Feature
Add a Bio.SeqFeature object to the diagram (will be stored
internally in a Feature wrapper
"""
id = self.next_id # get id number
f = Feature(self, id, feature)
self.features[id] = f # add feature
for key in kwargs:
if key == "colour" or key == "color":
#Deal with "colour" as a special case by also mapping to color.
#If Feature.py used a python property we wouldn't need to call
#set_color explicitly. However, this is important to make sure
#every color gets mapped to a colors object - for example color
#numbers, or strings (may not matter for PDF, but does for PNG).
self.features[id].set_color(kwargs[key])
continue
setattr(self.features[id], key, kwargs[key])
self.next_id += 1 # increment next id
return f
def del_feature(self, feature_id):
""" del_feature(self, feature_id)
o feature_id Unique id of the feature to delete
Remove a feature from the set, indicated by its id
"""
del self.features[feature_id]
def set_all_features(self, attr, value):
""" set_all_features(self, attr, value)
o attr An attribute of the Feature class
o value The value to set that attribute
Set the passed attribute of all features in the set to the
passed value
"""
changed = 0
for feature in self.features.values():
# If the feature has the attribute, and the value should change
if hasattr(feature, attr):
if getattr(feature, attr) != value:
setattr(feature, attr, value) # set it to the passed value
#For backwards compatibility, we support both colour and color.
#As a quick hack, make "colour" set both "colour" and "color".
#if attr=="colour":
# self.set_all_feature("color",value)
def get_features(self, attribute=None, value=None, comparator=None):
""" get_features(self, attribute=None, value=None, comparator=None) ->
[Feature, Feature, ...]
o attribute String, attribute of a Feature object
o value The value desired of the attribute
o comparator String, how to compare the Feature attribute to the
passed value
If no attribute or value is given, return a list of all features in the
feature set. If both an attribute and value are given, then depending
on the comparator, then a list of all features in the FeatureSet
matching (or not) the passed value will be returned. Allowed comparators
are: 'startswith', 'not', 'like'.
The user is expected to make a responsible decision about which feature
attributes to use with which passed values and comparator settings.
"""
# If no attribute or value specified, return all features
if attribute is None or value is None:
return list(self.features.values())
# If no comparator is specified, return all features where the attribute
# value matches that passed
if comparator is None:
return [feature for feature in self.features.values() if
getattr(feature, attribute) == value]
# If the comparator is 'not', return all features where the attribute
# value does not match that passed
elif comparator == 'not':
return [feature for feature in self.features.values() if
getattr(feature, attribute) != value]
# If the comparator is 'startswith', return all features where the attribute
# value does not match that passed
elif comparator == 'startswith':
return [feature for feature in self.features.values() if
getattr(feature, attribute).startswith(value)]
# If the comparator is 'like', use a regular expression search to identify
# features
elif comparator == 'like':
return [feature for feature in self.features.values() if
re.search(value, getattr(feature, attribute))]
# As a final option, just return an empty list
return []
def get_ids(self):
""" get_ids(self) -> [int, int, ...]
Return a list of all ids for the feature set
"""
return list(self.features.keys())
def range(self):
""" range(self)
Returns the lowest and highest base (or mark) numbers as a tuple
"""
lows, highs = [], []
for feature in self.features.values():
for start, end in feature.locations:
lows.append(start)
highs.append(end)
if len(lows) != 0 and len(highs) != 0: # Default in case there is
return (min(lows), max(highs)) # nothing in the set
return 0, 0
def to_string(self, verbose=0):
""" to_string(self, verbose=0) -> ""
o verbose Boolean indicating whether a short or complete
account of the set is required
Returns a formatted string with information about the set
"""
if not verbose: # Short account only required
return "%s" % self
else: # Long account desired
outstr = ["\n<%s: %s>" % (self.__class__, self.name)]
outstr.append("%d features" % len(self.features))
for key in self.features:
outstr.append("feature: %s" % self.features[key])
return "\n".join(outstr)
def __len__(self):
""" __len__(self) -> int
Return the number of features in the set
"""
return len(self.features)
def __getitem__(self, key):
""" __getitem__(self, key) -> Feature
Return a feature, keyed by id
"""
return self.features[key]
def __str__(self):
""" __str__(self) -> ""
Returns a formatted string with information about the feature set
"""
outstr = ["\n<%s: %s %d features>" % (self.__class__, self.name,
len(self.features))]
return "\n".join(outstr)
################################################################################
# RUN AS SCRIPT
################################################################################
if __name__ == '__main__':
from Bio import SeqIO
genbank_entry = SeqIO.read('/data/Genomes/Bacteria/Nanoarchaeum_equitans/NC_005213.gbk', 'gb')
# Test code
gdfs = FeatureSet(0, 'Nanoarchaeum equitans CDS')
for feature in genbank_entry.features:
if feature.type == 'CDS':
gdfs.add_feature(feature)
#print len(gdfs)
#print gdfs.get_ids()
#gdfs.del_feature(560)
#print gdfs.get_ids()
#print gdfs.get_features()
#for feature in gdfs.get_features():
# print feature.id, feature.start, feature.end
#print gdfs[500]
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