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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
################################################################################
""" Track module
Provides:
o Track - Container for a single track on the diagram, containing
FeatureSet and GraphSet 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
"""
from __future__ import print_function
from reportlab.lib import colors
from Bio._py3k import range
# GenomeDiagram imports
from ._FeatureSet import FeatureSet
from ._GraphSet import GraphSet
class Track(object):
""" Track
Provides:
Methods:
o __init__(self, name=None, ...) Called on instantiation
o add_set(self, set) Add a FeatureSet or GraphSet to the diagram
o del_set(self, set_id) Delete a FeatureSet or GraphSet from the
diagram
o get_sets(self) Returns a list of the sets in the track
o get_ids(self) Returns a list of the ids for sets in the track
o range(self) Returns the base/position range covered by the data in
the track
o to_string(self, verbose=0) Returns a string describing the data in
the track
o __getitem__(self, key) Returns the set with the passed id
o __str__(self) Returns a formatted string describing the track
Attributes:
o height Int describing the relative height to other trackscale_fontsizes in the
diagram
o name String describing the track
o hide Boolean, 0 if the track is not to be drawn
o start, end Integers (or None) specifying start/end to draw just
a partial track.
o greytrack Boolean, 1 if a grey background to the track is to be
drawn
o greytrack_labels Int describing how many track-identifying labels
should be placed on the track at regular intervals
o greytrack_font String describing the font to use for the greytrack
labels
o greytrack_fontsize Int describing the font size to display the
labels on the grey track
o greytrack_font_rotation Int describing the angle through which to
rotate the grey track labels (Linear only)
o greytrack_font_color colors.Color describing the color to draw
the grey track labels
o scale Boolean, 1 if a scale is to be drawn on the track
o scale_format String, defaults to None, when scale values are written
as numerals. Setting this to 'SInt' invokes SI
unit-like multiples, such as Mbp, Kbp and so on.
o scale_color colors.Color to draw the elements of the scale
o scale_font String describing the font to use for the scale labels
o scale_fontsize Int describing the size of the scale label font
o scale_fontangle Int describing the angle at which to draw the scale
labels (linear only)
o scale_ticks Boolean, 1 if ticks should be drawn at all on the
scale
o scale_largeticks Float (0->1) describing the height of large
scale ticks relative to the track height.
o scale_smallticks Float (0->1) describing the height of large
scale ticks relative to the track height.
o scale_largetick_interval Int, describing the number of bases that
should separate large ticks
o scale_smalltick_interval Int, describing the number of bases that
should separate small ticks
o scale_largetick_labels Boolean describing whether position labels
should be written over large ticks
o scale_smalltick_labels Boolean describing whether position labels
should be written over small ticks
o axis_labels Boolean describing whether the value labels should
be placed on the Y axes
"""
def __init__(self, name=None, height=1, hide=0, greytrack=0,
greytrack_labels=5, greytrack_fontsize=8,
greytrack_font='Helvetica', greytrack_font_rotation=0,
greytrack_font_color=colors.Color(0.6, 0.6, 0.6),
scale=1, scale_format=None, scale_color=colors.black,
scale_font='Helvetica', scale_fontsize=6,
scale_fontangle=45, scale_largeticks=0.5, scale_ticks=1,
scale_smallticks=0.3, scale_largetick_interval=1e6,
scale_smalltick_interval=1e4, scale_largetick_labels=1,
scale_smalltick_labels=0, axis_labels=1,
start=None, end=None,
greytrack_font_colour=None, scale_colour=None):
""" __init__(self, name=None, ...)
o height Int describing the relative height to other tracks in the
diagram
o name String describing the track
o hide Boolean, 0 if the track is not to be drawn
o greytrack Boolean, 1 if a grey background to the track is to be
drawn
o greytrack_labels Int describing how many track-identifying labels
should be placed on the track at regular intervals
o greytrack_font String describing the font to use for the greytrack
labels
o greytrack_fontsize Int describing the font size to display the
labels on the grey track
o greytrack_font_rotation Int describing the angle through which to
rotate the grey track labels (Linear only)
o greytrack_font_color colors.Color describing the color to draw
the grey track labels (overridden by
backwards compatible argument with UK
spelling, colour).
o scale Boolean, 1 if a scale is to be drawn on the track
o scale_color colors.Color to draw the elements of the scale
(overridden by backwards compatible argument with UK
spelling, colour).
o scale_font String describing the font to use for the scale labels
o scale_fontsize Int describing the size of the scale label font
o scale_fontangle Int describing the angle at which to draw the scale
labels (linear only)
o scale_ticks Boolean, 1 if ticks should be drawn at all on the
scale
o scale_largeticks Float (0->1) describing the height of large
scale ticks relative to the track height.
o scale_smallticks Float (0->1) describing the height of large
scale ticks relative to the track height.
o scale_largetick_interval Int, describing the number of bases that
should separate large ticks
o scale_smalltick_interval Int, describing the number of bases that
should separate small ticks
o scale_largetick_labels Boolean describing whether position labels
should be written over large ticks
o scale_smalltick_labels Boolean describing whether position labels
should be written over small ticks
o name String to help identify the track
o height Relative height to draw the track
o axis_labels Boolean describing whether the value labels should
be placed on the Y axes
"""
# Let the UK spelling (colour) override the USA spelling (color)
if greytrack_font_colour is not None:
greytrack_font_color = greytrack_font_colour
if scale_colour is not None:
scale_color = scale_colour
self._next_id = 0 # This will count sets as they are added to the track
self._sets = {} # Holds sets, keyed by unique ID
# Assign attribute values from instantiation
self.height = height
if name is not None:
self.name = str(name)
else:
self.name = "Track"
self.hide = hide
self.start = start
self.end = end
# Attributes for the grey track background and labels
self.greytrack = greytrack
self.greytrack_labels = greytrack_labels
self.greytrack_fontsize = greytrack_fontsize
self.greytrack_font = greytrack_font
self.greytrack_font_rotation = greytrack_font_rotation
self.greytrack_fontcolor = greytrack_font_color
# Attributes for the track scale
self.scale = scale
self.scale_format = scale_format
self.scale_color = scale_color
self.scale_font = scale_font
self.scale_fontsize = scale_fontsize
self.scale_fontangle = scale_fontangle
self.scale_ticks = scale_ticks
self.scale_largeticks = scale_largeticks
self.scale_smallticks = scale_smallticks
self.scale_largetick_interval = scale_largetick_interval
self.scale_smalltick_interval = scale_smalltick_interval
self.scale_largetick_labels = scale_largetick_labels
self.scale_smalltick_labels = scale_smalltick_labels
self.axis_labels = axis_labels
def add_set(self, set):
""" add_set(self, set)
o set A FeatureSet or GraphSet object
Add a preexisting FeatureSet or GraphSet object to the track
"""
set.id = self._next_id # Assign unique id to set
set.parent = self # Make set's parent this track
self._sets[self._next_id] = set # Add set, keyed by unique id
self._next_id += 1 # Increment unique set ids
def new_set(self, type='feature', **args):
""" new_set(self, type='feature') -> FeatureSet or GraphSet
Create a new FeatureSet or GraphSet object, add it to the
track, and return for user manipulation
"""
type_dict = {'feature': FeatureSet,
'graph': GraphSet
}
set = type_dict[type]()
for key in args:
setattr(set, key, args[key])
set.id = self._next_id # Assign unique id to set
set.parent = self # Make set's parent this track
self._sets[self._next_id] = set # Add set, keyed by unique id
self._next_id += 1 # Increment unique set ids
return set
def del_set(self, set_id):
""" del_set(self, set_id)
o set_id The unique id for the set in this track
Remove the set with the passed id from the track
"""
del self._sets[set_id]
def get_sets(self):
""" get_sets(self) -> FeatureSet or GraphSet
Return the sets contained in this track
"""
return list(self._sets.values())
def get_ids(self):
""" get_ids(self) -> [int, int, ...]
Return the ids of all sets contained in this track
"""
return list(self._sets.keys())
def range(self):
""" range(self) -> (int, int)
Returns the lowest and highest base (or mark) numbers as a tuple
"""
lows, highs = [], [] # Holds set of low and high values from sets
if self.start is not None:
lows.append(self.start)
if self.end is not None:
highs.append(self.end)
for set in self._sets.values():
low, high = set.range() # Get each set range
lows.append(low)
highs.append(high)
if lows:
low = min(lows)
else:
low = None
if highs:
high = max(highs)
else:
high = None
return low, high # Return lowest and highest values
def to_string(self, verbose=0):
""" to_string(self, verbose=0) -> ""
o verbose Boolean indicating whether a short or complete
account of the track is required
Returns a formatted string with information about the track
"""
if not verbose: # Return the short description
return "%s" % self # Use __str__ method instead
else: # Return the long description
outstr = ["\n<%s: %s>" % (self.__class__, self.name)]
outstr.append("%d sets" % len(self._sets))
for key in self._sets:
outstr.append("set: %s" % self._sets[key])
return "\n".join(outstr)
def __getitem__(self, key):
""" __getitem__(self, key) -> int
o key The id of a set in the track
Return the set with the passed id
"""
return self._sets[key]
def __str__(self):
""" __str__(self) -> ""
Returns a formatted string with information about the Track
"""
outstr = ["\n<%s: %s>" % (self.__class__, self.name)]
outstr.append("%d sets" % len(self._sets))
return "\n".join(outstr)
################################################################################
# RUN AS SCRIPT
################################################################################
if __name__ == '__main__':
# test code
from Bio import SeqIO
from random import normalvariate
genbank_entry = SeqIO.read('/data/genomes/Bacteria/Nanoarchaeum_equitans/NC_005213.gbk', 'gb')
gdfs1 = FeatureSet(0, 'Nanoarchaeum equitans CDS - CDS')
gdfs2 = FeatureSet(1, 'Nanoarchaeum equitans CDS - gene')
for feature in genbank_entry.features:
if feature.type == 'CDS':
gdfs1.add_feature(feature)
if feature.type == 'gene':
gdfs2.add_feature(feature)
gdt = Track()
gdt.add_set(gdfs1)
gdt.add_set(gdfs2)
graphdata = []
for pos in range(1, len(genbank_entry.seq), 1000):
graphdata.append((pos, normalvariate(0.5, 0.1)))
gdgs = GraphSet(2, 'test data')
gdgs.add_graph(graphdata, 'Test Data')
gdt.add_set(gdgs)
print(gdt.get_ids())
sets = gdt.get_sets()
for set in sets:
print(set)
print(gdt.get_element_limits())
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