def test_diagram_via_object_pdf(self):
"""Construct and draw PDF using object approach."""
genbank_entry = self.record
gdd = Diagram('Test Diagram')
gdt1 = Track('CDS features',
greytrack=True,
scale_largetick_interval=1e4,
scale_smalltick_interval=1e3,
greytrack_labels=10,
greytrack_font_color="red",
scale_format="SInt")
gdt2 = Track('gene features',
greytrack=1,
scale_largetick_interval=1e4)
# First add some feature sets:
gdfsA = FeatureSet(name='CDS backgrounds')
gdfsB = FeatureSet(name='gene background')
gdfs1 = FeatureSet(name='CDS features')
gdfs2 = FeatureSet(name='gene features')
gdfs3 = FeatureSet(name='misc_features')
gdfs4 = FeatureSet(name='repeat regions')
prev_gene = None
cds_count = 0
for feature in genbank_entry.features:
if feature.type == 'CDS':
cds_count += 1
if prev_gene:
# Assuming it goes with this CDS!
if cds_count % 2 == 0:
dark, light = colors.peru, colors.tan
else:
dark, light = colors.burlywood, colors.bisque
# Background for CDS,
a = gdfsA.add_feature(SeqFeature(
FeatureLocation(feature.location.start,
feature.location.end,
strand=0)),
color=dark)
# Background for gene,
b = gdfsB.add_feature(SeqFeature(
FeatureLocation(prev_gene.location.start,
prev_gene.location.end,
strand=0)),
color=dark)
# Cross link,
gdd.cross_track_links.append(CrossLink(a, b, light, dark))
prev_gene = None
if feature.type == 'gene':
prev_gene = feature
# Some cross links on the same linear diagram fragment,
f, c = fill_and_border(colors.red)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(2220, 2230)),
color=f,
border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(2200, 2210)),
color=f,
border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c))
f, c = fill_and_border(colors.blue)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(2150, 2200)),
color=f,
border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(2220, 2290)),
color=f,
border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c, flip=True))
f, c = fill_and_border(colors.green)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(2250, 2560)),
color=f,
border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(2300, 2860)),
color=f,
border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c))
# Some cross links where both parts are saddling the linear diagram fragment boundary,
f, c = fill_and_border(colors.red)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(3155, 3250)),
color=f,
border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(3130, 3300)),
color=f,
border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c))
# Nestled within that (drawn on top),
f, c = fill_and_border(colors.blue)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(3160, 3275)),
color=f,
border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(3180, 3225)),
color=f,
border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c, flip=True))
# Some cross links where two features are on either side of the linear diagram fragment boundary,
f, c = fill_and_border(colors.green)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(6450, 6550)),
color=f,
border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(6265, 6365)),
color=f,
border=c)
gdd.cross_track_links.append(CrossLink(a, b, color=f, border=c))
f, c = fill_and_border(colors.gold)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(6265, 6365)),
color=f,
border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(6450, 6550)),
color=f,
border=c)
gdd.cross_track_links.append(CrossLink(a, b, color=f, border=c))
f, c = fill_and_border(colors.red)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(6275, 6375)),
color=f,
border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(6430, 6530)),
color=f,
border=c)
gdd.cross_track_links.append(
CrossLink(a, b, color=f, border=c, flip=True))
f, c = fill_and_border(colors.blue)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(6430, 6530)),
color=f,
border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(6275, 6375)),
color=f,
border=c)
gdd.cross_track_links.append(
CrossLink(a, b, color=f, border=c, flip=True))
cds_count = 0
for feature in genbank_entry.features:
if feature.type == 'CDS':
cds_count += 1
if cds_count % 2 == 0:
gdfs1.add_feature(feature,
color=colors.pink,
sigil="ARROW")
else:
gdfs1.add_feature(feature, color=colors.red, sigil="ARROW")
if feature.type == 'gene':
# Note we set the colour of ALL the genes later on as a test,
gdfs2.add_feature(feature, sigil="ARROW")
if feature.type == 'misc_feature':
gdfs3.add_feature(feature, color=colors.orange)
if feature.type == 'repeat_region':
gdfs4.add_feature(feature, color=colors.purple)
# gdd.cross_track_links = gdd.cross_track_links[:1]
gdfs1.set_all_features('label', 1)
gdfs2.set_all_features('label', 1)
gdfs3.set_all_features('label', 1)
gdfs4.set_all_features('label', 1)
gdfs3.set_all_features('hide', 0)
gdfs4.set_all_features('hide', 0)
# gdfs1.set_all_features('color', colors.red)
gdfs2.set_all_features('color', colors.blue)
gdt1.add_set(gdfsA) # Before CDS so under them!
gdt1.add_set(gdfs1)
gdt2.add_set(gdfsB) # Before genes so under them!
gdt2.add_set(gdfs2)
gdt3 = Track('misc features and repeats',
greytrack=1,
scale_largetick_interval=1e4)
gdt3.add_set(gdfs3)
gdt3.add_set(gdfs4)
# Now add some graph sets:
# Use a fairly large step so we can easily tell the difference
# between the bar and line graphs.
step = len(genbank_entry) // 200
gdgs1 = GraphSet('GC skew')
graphdata1 = apply_to_window(genbank_entry.seq, step, calc_gc_skew,
step)
gdgs1.new_graph(graphdata1,
'GC Skew',
style='bar',
color=colors.violet,
altcolor=colors.purple)
gdt4 = Track('GC Skew (bar)',
height=1.94,
greytrack=1,
scale_largetick_interval=1e4)
gdt4.add_set(gdgs1)
gdgs2 = GraphSet('GC and AT Content')
gdgs2.new_graph(apply_to_window(genbank_entry.seq, step,
calc_gc_content, step),
'GC content',
style='line',
color=colors.lightgreen,
altcolor=colors.darkseagreen)
gdgs2.new_graph(apply_to_window(genbank_entry.seq, step,
calc_at_content, step),
'AT content',
style='line',
color=colors.orange,
altcolor=colors.red)
gdt5 = Track('GC Content(green line), AT Content(red line)',
height=1.94,
greytrack=1,
scale_largetick_interval=1e4)
gdt5.add_set(gdgs2)
gdgs3 = GraphSet('Di-nucleotide count')
step = len(genbank_entry) // 400 # smaller step
gdgs3.new_graph(apply_to_window(genbank_entry.seq, step,
calc_dinucleotide_counts, step),
'Di-nucleotide count',
style='heat',
color=colors.red,
altcolor=colors.orange)
gdt6 = Track('Di-nucleotide count',
height=0.5,
greytrack=False,
scale=False)
gdt6.add_set(gdgs3)
# Add the tracks (from both features and graphs)
# Leave some white space in the middle/bottom
gdd.add_track(gdt4, 3) # GC skew
gdd.add_track(gdt5, 4) # GC and AT content
gdd.add_track(gdt1, 5) # CDS features
gdd.add_track(gdt2, 6) # Gene features
gdd.add_track(gdt3, 7) # Misc features and repeat feature
gdd.add_track(gdt6, 8) # Feature depth
# Finally draw it in both formats, and full view and partial
gdd.draw(format='circular',
orientation='landscape',
tracklines=0,
pagesize='A0')
output_filename = os.path.join('Graphics', 'GD_by_obj_circular.pdf')
gdd.write(output_filename, 'PDF')
gdd.circular = False
gdd.draw(format='circular',
orientation='landscape',
tracklines=0,
pagesize='A0',
start=3000,
end=6300)
output_filename = os.path.join('Graphics',
'GD_by_obj_frag_circular.pdf')
gdd.write(output_filename, 'PDF')
gdd.draw(format='linear',
orientation='landscape',
tracklines=0,
pagesize='A0',
fragments=3)
output_filename = os.path.join('Graphics', 'GD_by_obj_linear.pdf')
gdd.write(output_filename, 'PDF')
gdd.set_all_tracks("greytrack_labels", 2)
gdd.draw(format='linear',
orientation='landscape',
tracklines=0,
pagesize=(30 * cm, 10 * cm),
fragments=1,
start=3000,
end=6300)
output_filename = os.path.join('Graphics', 'GD_by_obj_frag_linear.pdf')
gdd.write(output_filename, 'PDF')
def test_diagram_via_object_pdf(self):
"""Construct and draw PDF using object approach."""
genbank_entry = self.record
gdd = Diagram('Test Diagram')
gdt1 = Track('CDS features', greytrack=True,
scale_largetick_interval=1e4,
scale_smalltick_interval=1e3,
greytrack_labels=10,
greytrack_font_color="red",
scale_format = "SInt")
gdt2 = Track('gene features', greytrack=1,
scale_largetick_interval=1e4)
#First add some feature sets:
gdfsA = FeatureSet(name='CDS backgrounds')
gdfsB = FeatureSet(name='gene background')
gdfs1 = FeatureSet(name='CDS features')
gdfs2 = FeatureSet(name='gene features')
gdfs3 = FeatureSet(name='misc_features')
gdfs4 = FeatureSet(name='repeat regions')
prev_gene = None
cds_count = 0
for feature in genbank_entry.features:
if feature.type == 'CDS':
cds_count += 1
if prev_gene:
#Assuming it goes with this CDS!
if cds_count % 2 == 0:
dark, light = colors.peru, colors.tan
else:
dark, light = colors.burlywood, colors.bisque
#Background for CDS,
a = gdfsA.add_feature(SeqFeature(FeatureLocation(feature.location.start, feature.location.end, strand=0)),
color=dark)
#Background for gene,
b = gdfsB.add_feature(SeqFeature(FeatureLocation(prev_gene.location.start, prev_gene.location.end, strand=0)),
color=dark)
#Cross link,
gdd.cross_track_links.append(CrossLink(a, b, light, dark))
prev_gene = None
if feature.type == 'gene':
prev_gene = feature
#Some cross links on the same linear diagram fragment,
f, c = fill_and_border(colors.red)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(2220,2230)), color=f, border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(2200,2210)), color=f, border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c))
f, c = fill_and_border(colors.blue)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(2150,2200)), color=f, border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(2220,2290)), color=f, border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c, flip=True))
f, c = fill_and_border(colors.green)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(2250,2560)), color=f, border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(2300,2860)), color=f, border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c))
#Some cross links where both parts are saddling the linear diagram fragment boundary,
f, c = fill_and_border(colors.red)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(3155,3250)), color=f, border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(3130,3300)), color=f, border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c))
#Nestled within that (drawn on top),
f, c = fill_and_border(colors.blue)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(3160,3275)), color=f, border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(3180,3225)), color=f, border=c)
gdd.cross_track_links.append(CrossLink(a, b, f, c, flip=True))
#Some cross links where two features are on either side of the linear diagram fragment boundary,
f, c = fill_and_border(colors.green)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(6450,6550)), color=f, border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(6265,6365)), color=f, border=c)
gdd.cross_track_links.append(CrossLink(a, b, color=f, border=c))
f, c = fill_and_border(colors.gold)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(6265,6365)), color=f, border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(6450,6550)), color=f, border=c)
gdd.cross_track_links.append(CrossLink(a, b, color=f, border=c))
f, c = fill_and_border(colors.red)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(6275,6375)), color=f, border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(6430,6530)), color=f, border=c)
gdd.cross_track_links.append(CrossLink(a, b, color=f, border=c, flip=True))
f, c = fill_and_border(colors.blue)
a = gdfsA.add_feature(SeqFeature(FeatureLocation(6430,6530)), color=f, border=c)
b = gdfsB.add_feature(SeqFeature(FeatureLocation(6275,6375)), color=f, border=c)
gdd.cross_track_links.append(CrossLink(a, b, color=f, border=c, flip=True))
cds_count = 0
for feature in genbank_entry.features:
if feature.type == 'CDS':
cds_count += 1
if cds_count % 2 == 0:
gdfs1.add_feature(feature, color=colors.pink, sigil="ARROW")
else:
gdfs1.add_feature(feature, color=colors.red, sigil="ARROW")
if feature.type == 'gene':
#Note we set the colour of ALL the genes later on as a test,
gdfs2.add_feature(feature, sigil="ARROW")
if feature.type == 'misc_feature':
gdfs3.add_feature(feature, color=colors.orange)
if feature.type == 'repeat_region':
gdfs4.add_feature(feature, color=colors.purple)
#gdd.cross_track_links = gdd.cross_track_links[:1]
gdfs1.set_all_features('label', 1)
gdfs2.set_all_features('label', 1)
gdfs3.set_all_features('label', 1)
gdfs4.set_all_features('label', 1)
gdfs3.set_all_features('hide', 0)
gdfs4.set_all_features('hide', 0)
#gdfs1.set_all_features('color', colors.red)
gdfs2.set_all_features('color', colors.blue)
gdt1.add_set(gdfsA) # Before CDS so under them!
gdt1.add_set(gdfs1)
gdt2.add_set(gdfsB) # Before genes so under them!
gdt2.add_set(gdfs2)
gdt3 = Track('misc features and repeats', greytrack=1,
scale_largetick_interval=1e4)
gdt3.add_set(gdfs3)
gdt3.add_set(gdfs4)
#Now add some graph sets:
#Use a fairly large step so we can easily tell the difference
#between the bar and line graphs.
step = len(genbank_entry)//200
gdgs1 = GraphSet('GC skew')
graphdata1 = apply_to_window(genbank_entry.seq, step, calc_gc_skew, step)
gdgs1.new_graph(graphdata1, 'GC Skew', style='bar',
color=colors.violet,
altcolor=colors.purple)
gdt4 = Track(
'GC Skew (bar)',
height=1.94, greytrack=1,
scale_largetick_interval=1e4)
gdt4.add_set(gdgs1)
gdgs2 = GraphSet('GC and AT Content')
gdgs2.new_graph(apply_to_window(genbank_entry.seq, step, calc_gc_content, step),
'GC content', style='line',
color=colors.lightgreen,
altcolor=colors.darkseagreen)
gdgs2.new_graph(apply_to_window(genbank_entry.seq, step, calc_at_content, step),
'AT content', style='line',
color=colors.orange,
altcolor=colors.red)
gdt5 = Track(
'GC Content(green line), AT Content(red line)',
height=1.94, greytrack=1,
scale_largetick_interval=1e4)
gdt5.add_set(gdgs2)
gdgs3 = GraphSet('Di-nucleotide count')
step = len(genbank_entry) // 400 # smaller step
gdgs3.new_graph(apply_to_window(genbank_entry.seq, step, calc_dinucleotide_counts, step),
'Di-nucleotide count', style='heat',
color=colors.red, altcolor=colors.orange)
gdt6 = Track('Di-nucleotide count', height=0.5, greytrack=False, scale=False)
gdt6.add_set(gdgs3)
#Add the tracks (from both features and graphs)
#Leave some white space in the middle/bottom
gdd.add_track(gdt4, 3) # GC skew
gdd.add_track(gdt5, 4) # GC and AT content
gdd.add_track(gdt1, 5) # CDS features
gdd.add_track(gdt2, 6) # Gene features
gdd.add_track(gdt3, 7) # Misc features and repeat feature
gdd.add_track(gdt6, 8) # Feature depth
#Finally draw it in both formats, and full view and partial
gdd.draw(format='circular', orientation='landscape',
tracklines=0, pagesize='A0')
output_filename = os.path.join('Graphics', 'GD_by_obj_circular.pdf')
gdd.write(output_filename, 'PDF')
gdd.circular=False
gdd.draw(format='circular', orientation='landscape',
tracklines=0, pagesize='A0', start=3000, end=6300)
output_filename = os.path.join('Graphics', 'GD_by_obj_frag_circular.pdf')
gdd.write(output_filename, 'PDF')
gdd.draw(format='linear', orientation='landscape',
tracklines=0, pagesize='A0', fragments=3)
output_filename = os.path.join('Graphics', 'GD_by_obj_linear.pdf')
gdd.write(output_filename, 'PDF')
gdd.set_all_tracks("greytrack_labels", 2)
gdd.draw(format='linear', orientation='landscape',
tracklines=0, pagesize=(30*cm,10*cm), fragments=1,
start=3000, end=6300)
output_filename = os.path.join('Graphics', 'GD_by_obj_frag_linear.pdf')
gdd.write(output_filename, 'PDF')
def generateCircleGraph(self, file, windows_to_top_topologies,
topologies_to_colors, window_size, window_offset,
sites_to_informative):
"""
Creates genetic circle graph showing the windows and the areas where each topology appears
Inputs:
i. file --- phylip file inputted in GUI
ii. windows_to_top_topologies --- mapping outputted by windows_to_newick()[0]
iii. topologies_to_colors --- mapping outputted by topology_colors()[0]
iv. window_size --- size inputted in GUI
v. window_offset --- size inputted in GUI
Returns:
A genetic circle graph GenomeAtlas.
"""
############################# Format Data #############################
# get the length of the sequence
with open(file) as f:
length_of_sequences = int(f.readline().split()[1])
f.close()
# accounts for offset
windows_to_top_topologies2 = {}
for window in windows_to_top_topologies:
windows_to_top_topologies2[
window * window_offset] = windows_to_top_topologies[window]
windows_to_top_topologies = windows_to_top_topologies2.items()
# gets windows
windows = []
for window_topology in windows_to_top_topologies:
windows.append(window_topology[0])
for i in range(length_of_sequences):
if i not in windows:
windows_to_top_topologies.append((i, 0))
# maps data to topologies
topologies_to_data = {}
for topology in topologies_to_colors:
topologies_to_data[topology] = []
for topology in topologies_to_colors:
for window in windows_to_top_topologies:
if topology == window[1]:
topologies_to_data[topology].append(tuple([window[0], 1]))
else:
topologies_to_data[topology].append(
tuple([window[0], -0.1]))
# maps data to colors
data_to_colors = {}
for topology in topologies_to_data:
data_to_colors[str(
topologies_to_data[topology])] = topologies_to_colors[topology]
includeOther = False
if 'Other' in topologies_to_data:
includeOther = True
# -1 because top_topologies_to_colors includes 'Other'
number_of_top_topologies = len(topologies_to_colors) - 1
else:
number_of_top_topologies = len(topologies_to_colors)
# removes 'Other' from mapping
if includeOther:
minor_topology_data = topologies_to_data['Other']
del topologies_to_data['Other']
data = topologies_to_data.values()
# separates data into windowed and un-windowed
windowed_data = []
nonwindowed_data = []
for i in range(length_of_sequences):
if i not in windows:
nonwindowed_data.append(tuple([i, 1]))
windowed_data.append(tuple([i, 0]))
else:
for j in range(i, i + window_size):
windowed_data.append((j, 1))
nonwindowed_data.append(tuple([i, 0]))
############################# Build Graph #############################
# name of the figure
name = "../plots/GenomeAtlas"
graphStyle = 'bar'
# create the diagram -- highest level container for everything
diagram = GenomeDiagram.Diagram(name)
diagram.new_track(1,
greytrack=0,
name="Track",
height=2,
hide=0,
scale=1,
scale_color=colors.black,
scale_font='Helvetica',
scale_fontsize=6,
scale_fontangle=45,
scale_ticks=1,
scale_largeticks=0.3,
scale_smallticks=0.1,
scale_largetick_interval=(length_of_sequences / 6),
scale_smalltick_interval=(length_of_sequences / 12),
scale_largetick_labels=1,
scale_smalltick_labels=0)
if includeOther:
diagram \
.new_track(2, name="Minor Topologies", height=1.0, hide=0, greytrack=0, greytrack_labels=2,
greytrack_font_size=8, grey_track_font_color=colors.black, scale=1, scale_ticks=0,
axis_labels=0) \
.new_set('graph') \
.new_graph(minor_topology_data, style=graphStyle,
colour=colors.HexColor(data_to_colors[str(minor_topology_data)]),
altcolour=colors.transparent, linewidth=1)
for i in range(number_of_top_topologies):
# create tracks -- and add them to the diagram
if i == 0:
diagram \
.new_track(i + 3, name="Track" + str(i + 1), height=1.0, hide=0, greytrack=0,
greytrack_labels=2, greytrack_font_size=8, grey_track_font_color=colors.black,
scale=1, scale_ticks=0, axis_labels=0) \
.new_set('graph') \
.new_graph(data[i], style=graphStyle, colour=colors.HexColor(data_to_colors[str(data[i])]),
altcolour=colors.transparent, linewidth=1)
else:
diagram \
.new_track(i + 3, name="Track" + str(i + 1), height=1.0, hide=0, greytrack=0,
greytrack_labels=2, greytrack_font_size=8, grey_track_font_color=colors.black,
scale=0) \
.new_set('graph') \
.new_graph(data[i], style=graphStyle, colour=colors.HexColor(data_to_colors[str(data[i])]),
altcolour=colors.transparent, linewidth=1)
# outer ring shit
graph_set = GraphSet('graph')
graph_set.new_graph(nonwindowed_data,
style=graphStyle,
color=colors.HexColor('#cccccc'),
altcolour=colors.transparent)
graph_set.new_graph(windowed_data,
style=graphStyle,
color=colors.HexColor('#2f377c'),
altcolour=colors.transparent)
# diagram \
# .new_track(i + 5, name="Track" + str(i + 2), height=2, hide=0, greytrack=0, greytrack_labels=2,
# greytrack_font_size=8, grey_track_font_color=colors.black, scale=0) \
# .add_set(graph_set)
############################################
diagram \
.new_track(i + 4, name="Track" + str(i + 1), height=1.0, hide=0, greytrack=0,
greytrack_labels=2, greytrack_font_size=8, grey_track_font_color=colors.black,
scale=0) \
.new_set('graph') \
.new_graph(sites_to_informative.items(), style='line', colour=colors.coral,
altcolour=colors.transparent, linewidth=0.01)
###########################################################
diagram.draw(format="circular",
pagesize='A5',
orientation='landscape',
x=0.0,
y=0.0,
track_size=1.88,
tracklines=0,
circular=0,
circle_core=0.3,
start=0,
end=length_of_sequences - 1)
# save the file
# diagram.write("../plots/GenomeAtlas.eps", "EPS")
# diagram.write("plots/GenomeAtlas.svg", "SVG")
diagram.write("plots/GenomeAtlas.pdf", "PDF")
diagram.write("plots/GenomeAtlas.png", "PNG")
self.emit(QtCore.SIGNAL('CIRCLE_GRAPH_COMPLETE'))
def test_diagram_via_object_pdf(self):
"""Construct and draw PDF using object approach."""
genbank_entry = self.record
gdd = Diagram('Test Diagram')
#First add some feature sets:
gdfs1 = FeatureSet(name='CDS features')
gdfs2 = FeatureSet(name='gene features')
gdfs3 = FeatureSet(name='misc_features')
gdfs4 = FeatureSet(name='repeat regions')
cds_count = 0
for feature in genbank_entry.features:
if feature.type == 'CDS':
cds_count += 1
if cds_count % 2 == 0:
gdfs1.add_feature(feature, color=colors.pink)
else:
gdfs1.add_feature(feature, color=colors.red)
if feature.type == 'gene':
gdfs2.add_feature(feature)
if feature.type == 'misc_feature':
gdfs3.add_feature(feature, color=colors.orange)
if feature.type == 'repeat_region':
gdfs4.add_feature(feature, color=colors.purple)
gdfs1.set_all_features('label', 1)
gdfs2.set_all_features('label', 1)
gdfs3.set_all_features('label', 1)
gdfs4.set_all_features('label', 1)
gdfs3.set_all_features('hide', 0)
gdfs4.set_all_features('hide', 0)
#gdfs1.set_all_features('color', colors.red)
gdfs2.set_all_features('color', colors.blue)
gdt1 = Track('CDS features', greytrack=True,
scale_largetick_interval=1e4,
scale_smalltick_interval=1e3,
greytrack_labels=10,
greytrack_font_color="red",
scale_format = "SInt")
gdt1.add_set(gdfs1)
gdt2 = Track('gene features', greytrack=1,
scale_largetick_interval=1e4)
gdt2.add_set(gdfs2)
gdt3 = Track('misc features and repeats', greytrack=1,
scale_largetick_interval=1e4)
gdt3.add_set(gdfs3)
gdt3.add_set(gdfs4)
#Now add some graph sets:
#Use a fairly large step so we can easily tell the difference
#between the bar and line graphs.
step = len(genbank_entry)/200
gdgs1 = GraphSet('GC skew')
graphdata1 = apply_to_window(genbank_entry.seq, step, calc_gc_skew, step)
gdgs1.new_graph(graphdata1, 'GC Skew', style='bar',
color=colors.violet,
altcolor=colors.purple)
gdt4 = Track(\
'GC Skew (bar)',
height=1.94, greytrack=1,
scale_largetick_interval=1e4)
gdt4.add_set(gdgs1)
gdgs2 = GraphSet('GC and AT Content')
gdgs2.new_graph(apply_to_window(genbank_entry.seq, step, calc_gc_content, step),
'GC content', style='line',
color=colors.lightgreen,
altcolor=colors.darkseagreen)
gdgs2.new_graph(apply_to_window(genbank_entry.seq, step, calc_at_content, step),
'AT content', style='line',
color=colors.orange,
altcolor=colors.red)
gdt5 = Track(\
'GC Content(green line), AT Content(red line)',
height=1.94, greytrack=1,
scale_largetick_interval=1e4)
gdt5.add_set(gdgs2)
gdgs3 = GraphSet('Di-nucleotide count')
step = len(genbank_entry)/400 #smaller step
gdgs3.new_graph(apply_to_window(genbank_entry.seq, step, calc_dinucleotide_counts, step),
'Di-nucleotide count', style='heat',
color=colors.red, altcolor=colors.orange)
gdt6 = Track('Di-nucleotide count', height=0.5, greytrack=False, scale=False)
gdt6.add_set(gdgs3)
#Add the tracks (from both features and graphs)
#Leave some white space in the middle
gdd.add_track(gdt4, 3) # GC skew
gdd.add_track(gdt5, 4) # GC and AT content
gdd.add_track(gdt1, 5) # CDS features
gdd.add_track(gdt2, 6) # Gene features
gdd.add_track(gdt3, 7) # Misc features and repeat feature
gdd.add_track(gdt6, 8) # Feature depth
#Finally draw it in both formats,
gdd.draw(format='circular', orientation='landscape',
tracklines=0, pagesize='A0', circular=True)
output_filename = os.path.join('Graphics', 'GD_by_obj_circular.pdf')
gdd.write(output_filename, 'PDF')
gdd.draw(format='linear', orientation='landscape',
tracklines=0, pagesize='A0', fragments=3)
output_filename = os.path.join('Graphics', 'GD_by_obj_linear.pdf')
gdd.write(output_filename, 'PDF')
def test_diagram_via_object_pdf(self):
"""Construct and draw PDF using object approach."""
genbank_entry = self.record
gdd = Diagram('Test Diagram')
#First add some feature sets:
gdfs1 = FeatureSet(name='CDS features')
gdfs2 = FeatureSet(name='gene features')
gdfs3 = FeatureSet(name='misc_features')
gdfs4 = FeatureSet(name='repeat regions')
cds_count = 0
for feature in genbank_entry.features:
if feature.type == 'CDS':
cds_count += 1
if cds_count % 2 == 0:
gdfs1.add_feature(feature, color=colors.pink)
else:
gdfs1.add_feature(feature, color=colors.red)
if feature.type == 'gene':
gdfs2.add_feature(feature)
if feature.type == 'misc_feature':
gdfs3.add_feature(feature, color=colors.orange)
if feature.type == 'repeat_region':
gdfs4.add_feature(feature, color=colors.purple)
gdfs1.set_all_features('label', 1)
gdfs2.set_all_features('label', 1)
gdfs3.set_all_features('label', 1)
gdfs4.set_all_features('label', 1)
gdfs3.set_all_features('hide', 0)
gdfs4.set_all_features('hide', 0)
#gdfs1.set_all_features('color', colors.red)
gdfs2.set_all_features('color', colors.blue)
gdt1 = Track('CDS features',
greytrack=True,
scale_largetick_interval=1e4,
scale_smalltick_interval=1e3,
greytrack_labels=10,
greytrack_font_color="red",
scale_format="SInt")
gdt1.add_set(gdfs1)
gdt2 = Track('gene features',
greytrack=1,
scale_largetick_interval=1e4)
gdt2.add_set(gdfs2)
gdt3 = Track('misc features and repeats',
greytrack=1,
scale_largetick_interval=1e4)
gdt3.add_set(gdfs3)
gdt3.add_set(gdfs4)
#Now add some graph sets:
#Use a fairly large step so we can easily tell the difference
#between the bar and line graphs.
step = len(genbank_entry) // 200
gdgs1 = GraphSet('GC skew')
graphdata1 = apply_to_window(genbank_entry.seq, step, calc_gc_skew,
step)
gdgs1.new_graph(graphdata1,
'GC Skew',
style='bar',
color=colors.violet,
altcolor=colors.purple)
gdt4 = Track(\
'GC Skew (bar)',
height=1.94, greytrack=1,
scale_largetick_interval=1e4)
gdt4.add_set(gdgs1)
gdgs2 = GraphSet('GC and AT Content')
gdgs2.new_graph(apply_to_window(genbank_entry.seq, step,
calc_gc_content, step),
'GC content',
style='line',
color=colors.lightgreen,
altcolor=colors.darkseagreen)
gdgs2.new_graph(apply_to_window(genbank_entry.seq, step,
calc_at_content, step),
'AT content',
style='line',
color=colors.orange,
altcolor=colors.red)
gdt5 = Track(\
'GC Content(green line), AT Content(red line)',
height=1.94, greytrack=1,
scale_largetick_interval=1e4)
gdt5.add_set(gdgs2)
gdgs3 = GraphSet('Di-nucleotide count')
step = len(genbank_entry) // 400 #smaller step
gdgs3.new_graph(apply_to_window(genbank_entry.seq, step,
calc_dinucleotide_counts, step),
'Di-nucleotide count',
style='heat',
color=colors.red,
altcolor=colors.orange)
gdt6 = Track('Di-nucleotide count',
height=0.5,
greytrack=False,
scale=False)
gdt6.add_set(gdgs3)
#Add the tracks (from both features and graphs)
#Leave some white space in the middle
gdd.add_track(gdt4, 3) # GC skew
gdd.add_track(gdt5, 4) # GC and AT content
gdd.add_track(gdt1, 5) # CDS features
gdd.add_track(gdt2, 6) # Gene features
gdd.add_track(gdt3, 7) # Misc features and repeat feature
gdd.add_track(gdt6, 8) # Feature depth
#Finally draw it in both formats,
gdd.draw(format='circular',
orientation='landscape',
tracklines=0,
pagesize='A0',
circular=True)
output_filename = os.path.join('Graphics', 'GD_by_obj_circular.pdf')
gdd.write(output_filename, 'PDF')
gdd.draw(format='linear',
orientation='landscape',
tracklines=0,
pagesize='A0',
fragments=3)
output_filename = os.path.join('Graphics', 'GD_by_obj_linear.pdf')
gdd.write(output_filename, 'PDF')
