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#!/usr/bin/env python
from cogent import DNA
from cogent.core import alignment, alphabet, annotation
from cogent.draw.linear import *
from cogent import LoadTree
from cogent.draw.dendrogram import *
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight",
"Matthew Wakefield"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
interactive = True
if not interactive:
import matplotlib
matplotlib.use('PDF') # or Agg
file_ext = "pdf" # or png
def makeSampleSequence():
seq = DNA.makeSequence('aaaccggttt' * 10)
v = seq.addAnnotation(annotation.Feature, 'exon', 'exon', [(20,35)])
v = seq.addAnnotation(annotation.Feature, 'repeat_unit', 'repeat_unit', [(39,49)])
v = seq.addAnnotation(annotation.Feature, 'repeat_unit', 'rep2', [(49,60)])
return seq
def makeSampleAlignment():
# must be an esier way to make an alignment of annotated sequences!
from cogent.align.align import global_pairwise, make_dna_scoring_dict
DNA = make_dna_scoring_dict(10, -8, -8)
seq1 = makeSampleSequence()[:-2]
seq2 = makeSampleSequence()[2:]
seq1.Name = 'FAKE01'
seq2.Name = 'FAKE02'
names = (seq1.getName(), seq2.getName())
align = global_pairwise(seq1, seq2, DNA, 2, 1)
align.addAnnotation(annotation.Variable, 'redline', 'align', [((0,15),1),((15,30),2),((30,45),3)])
align.addAnnotation(annotation.Variable, 'blueline', 'align', [((0,15),1.5),((15,30),2.5),((30,45),3.5)])
return align
seq = makeSampleSequence()
a = seq.addAnnotation(annotation.Variable, 'blueline', 'seq', [((0,15),1),((15,30),2),((30,45),3)])
v = seq.addAnnotation(annotation.Feature, 'gene', 'gene', [(0,15),(20,35),(40,55)])
b = v.addAnnotation(annotation.Variable, 'redline', 'feat', [((0,15),1.5),((15,30),2.5),((30,45),3.5)])
align = makeSampleAlignment()
def fig(msg, seq_display, **kw):
if interactive:
seq_display.showFigure(title=msg, top=.5, **kw)
else:
fname = 'draw_test_%s.%s' % (msg.replace(' ', '_'), file_ext)
seq_display.makeFigure(**kw).savefig(fname)
def test_seqs():
seqd = Display(seq)
fig('sequence wrapped at 50',
seqd, rowlen=50)
small = FontProperties(size=7, stretch='extra-condensed')
fig('squashed sequence',
seqd.copy(seq_font=small, colour_sequences=True))
fig('seq display slice from 10 to 50',
seqd[10:50])
alignd = Display(align, colour_sequences=True, min_feature_height=10)
fig('coloured text alignment',
alignd)
fig('coloured dot alignment',
alignd.copy(show_text=False))
fig('alignment with lines only',
alignd.copy(show_text=False, colour_sequences=False))
# LEGEND
def test_legend():
from cogent.draw.legend import Legend
fig('Feature Legend', Legend())
# DOTPLOT
def test_dotplot():
from cogent.draw.dotplot import Display2D
fig('2d', Display2D(seq, seq[:40]))
#fig('reversed', Display(seq[50:10]), 500)
# no good because seqs slice like lists: ie len==0
# complement() probably doesn't know about annotations either.
# TREES
def test_trees():
treestring = "((A:.1,B:.22)ab:.3,((C:.4,D:.5)cd:.55,E:.6)cde:.7,F:.2)"
for edge in 'ABCDEF':
treestring = treestring.replace(edge, edge+edge.lower()*10)
t = LoadTree(treestring=treestring)
for klass in [
UnrootedDendrogram,
SquareDendrogram,
ContemporaneousDendrogram,
ShelvedDendrogram,
# StraightDendrogram,
# ContemporaneousStraightDendrogram
]:
fig(klass.__name__, klass(t), shade_param="length",
show_params=["length"])
def callback(edge):
return ["blue", "red"][edge.Name.startswith("A")]
fig("Highlight edge A", UnrootedDendrogram(t), edge_color_callback=callback)
if __name__ == '__main__':
test_seqs()
test_legend()
test_dotplot()
test_trees()
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