def write_schemadelica_plot(self):
"""Write schemadelica plot as SVG and PDF."""
gd_diagram = GenomeDiagram.Diagram("Primer Scheme", track_size=0.15)
primer_feature_set = GenomeDiagram.FeatureSet()
# make the gc track
window = 50
gc_set = GenomeDiagram.GraphSet("GC content")
graphdata1 = self.apply_to_window(self.primary_ref.seq, window,
self.calc_gc)
gc_set.new_graph(
graphdata1,
"GC content",
style="line",
color=colors.violet,
altcolor=colors.purple,
)
gc_track = GenomeDiagram.Track("GC content",
height=1.5,
greytrack=0,
scale_largetick_interval=1e3)
gc_track.add_set(gc_set)
# make the primer track
for r in self.regions:
region = str(r.region_num)
strand = 1 if r.region_num % 2 else -1
fwd_feature = SeqFeature(
FeatureLocation(r.left.start, r.left.end, strand=strand))
rev_feature = SeqFeature(
FeatureLocation(r.right.end, r.right.start, strand=strand))
region_feature = SeqFeature(
FeatureLocation(r.left.start, r.right.start, strand=strand))
primer_color = colors.red
region_color = colors.palevioletred
primer_feature_set.add_feature(
region_feature,
color=region_color,
name=region,
label=True,
label_position="middle",
label_angle=0 if strand == 1 else -180,
)
primer_feature_set.add_feature(fwd_feature,
color=primer_color,
name=region)
primer_feature_set.add_feature(rev_feature,
color=primer_color,
name=region)
primer_track = GenomeDiagram.Track(name="Annotated Features", height=1)
primer_track.add_set(primer_feature_set)
gd_diagram.add_track(primer_track, 2)
gd_diagram.add_track(gc_track, 1)
rows = max(2, int(round(len(self.primary_ref) / 10000.0)))
gd_diagram.draw(
format="linear",
pagesize=(300 * rows, 200 * rows),
fragments=rows,
start=0,
end=len(self.primary_ref),
)
pdf_filepath = self.outpath / f"{self.prefix}.plot.pdf"
svg_filepath = self.outpath / f"{self.prefix}.plot.svg"
logger.info(f"Writing {pdf_filepath}")
logger.info(f"Writing {svg_filepath}")
gd_diagram.write(str(pdf_filepath), "PDF", dpi=300)
gd_diagram.write(str(svg_filepath), "SVG", dpi=300)
def write_schemadelica_plot(self, path='./'):
logger.info('Writing plot')
#print(dir(GenomeDiagram))
gd_diagram = GenomeDiagram.Diagram("Primer Scheme", track_size=0.15)
primer_feature_set = GenomeDiagram.FeatureSet()
#make the gc track
window = 50
gc_set = GenomeDiagram.GraphSet('GC skew')
graphdata1 = self.apply_to_window(self.primary_reference.seq, window,
self.calc_gc_skew)
gc_set.new_graph(graphdata1,
'GC Skew',
style='line',
color=colors.violet,
altcolor=colors.purple)
gc_track = GenomeDiagram.Track('GC Skew',
height=1.5,
greytrack=0,
scale_largetick_interval=1e3)
gc_track.add_set(gc_set)
#make the primer track
for r in self.regions:
region = str(r.region_num)
strand = 1 if r.region_num % 2 else -1
fwd_feature = SeqFeature(
FeatureLocation(r.top_pair.left.start,
r.top_pair.left.end,
strand=strand))
rev_feature = SeqFeature(
FeatureLocation(r.top_pair.right.end,
r.top_pair.right.start,
strand=strand))
region_feature = SeqFeature(
FeatureLocation(r.top_pair.left.start,
r.top_pair.right.start,
strand=strand))
primer_color = colors.red #if strand == 1 else colors.blue
region_color = colors.palevioletred #if strand == 1 else colors.lightblue
primer_feature_set.add_feature(
region_feature,
color=region_color,
name=region,
label=True,
label_position="middle",
label_angle=0 if strand == 1 else -180)
primer_feature_set.add_feature(fwd_feature,
color=primer_color,
name=region)
primer_feature_set.add_feature(rev_feature,
color=primer_color,
name=region)
primer_track = GenomeDiagram.Track(name="Annotated Features", height=1)
primer_track.add_set(primer_feature_set)
gd_diagram.add_track(primer_track, 2)
gd_diagram.add_track(gc_track, 1)
rows = max(2, int(round(len(self.primary_reference) / 10000.0)))
gd_diagram.draw(format='linear',
pagesize=(300 * rows, 200 * rows),
fragments=rows,
start=0,
end=len(self.primary_reference))
pdf_filepath = os.path.join(path, '{}.pdf'.format(self.prefix))
svg_filepath = os.path.join(path, '{}.svg'.format(self.prefix))
gd_diagram.write(pdf_filepath, 'PDF', dpi=300)
gd_diagram.write(svg_filepath, 'SVG', dpi=300)
label_angle=0)
if (len(track_list) == 0 or len(track_list) == 4):
track_for_this_feature = GenomeDiagram.Track(
name=feature.qualifiers.get('gene'),
scale=1,
scale_fontsize=15,
scale_ticks=1,
scale_largeticks=0.5,
scale_largetick_interval=500)
else:
track_for_this_feature = GenomeDiagram.Track(
name=feature.qualifiers.get('gene'))
track_for_this_feature.add_set(gd_feature_set)
track_list.append(track_for_this_feature)
gdgs = GenomeDiagram.GraphSet('GC Content')
seq_string = str(record.seq)
def chunkstring(string, length):
return (string[0 + i:length + i] for i in range(0, len(string), length))
def gdps(str_list):
ret_list = []
i = 50
for strng in str_list:
ret_list.append((i, SeqUtils.GC(strng)))
i = i + 100
return ret_list
SNV_track = GenomeDiagram.Track('SNV',
greytrack=False,
scale=True,
scale_format='SInt',
scale_fontsize=10,
scale_fontangle=90,
scale_largetick_interval=5000,
scale_smalltick_interval=1000,
scale_largeticks=0.5,
scale_smallticks=0.2)
SNV_track.add_set(feature_set_SNV)
#%%
entropy_graph_set = GenomeDiagram.GraphSet('entropy')
entropy_graph = entropy_graph_set.new_graph(alignment_entropy,
name='entropy',
style='line')
entropy_track = GenomeDiagram.Track('entropy')
entropy_track.add_set(entropy_graph_set)
HUMAN_YFV_diagram = GenomeDiagram.Diagram("YFV Human Infections",
pagesize='A4',
orientation='portrait',
x=0.2,
y=0.3,
tracklines=False)
HUMAN_YFV_diagram.add_track(genes_track, 1)
HUMAN_YFV_diagram.add_track(entropy_track, 2)
