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')
#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')
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')
#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')