Big coordinates not handled

Hi,

I’m testing out your tool to see if it’s suited to my needs e.g. visualize primers in a pretty way.

from dna_features_viewer import GraphicFeature, GraphicRecord
import matplotlib.pyplot as plt

sequence = "TCAAGCTTGCCATCTCTTCATGTTAGGAAACAAAAAGCCCTAGAAGCAGAATTAGATGCTCAGCACTTATCAGAAACTTT"

record = GraphicRecord(sequence=sequence, features=[
    GraphicFeature(start=112173530, end=112173530+20, strand=+1, color="#ffd700",
                   label="Primer1"),
    GraphicFeature(start=112173530+50, end=112173530+70, strand=-1, color="#cffccc",
                   label="Primer2"),
])
zoom_start1, zoom_end1 = 112173530, 112173530+30  # coordinates of the "detail"
zoom_start2, zoom_end2 = 112173530+40, 112173530+80
cropped_record1 = record.crop((zoom_start1, zoom_end1))
cropped_record2 = record.crop((zoom_start2, zoom_end2))

fig, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(14, 3))

# PLOT THE WHOLE SEQUENCE

ax1.set_title("Whole sequence", loc='left', weight='bold')
record.plot(ax=ax1)
ax1.fill_between((zoom_start1, zoom_end1), +80, -80, alpha=0.15)
ax1.fill_between((zoom_start2, zoom_end2), +80, -80, alpha=0.15)

# PLOT THE SEQUENCE DETAILS

cropped_record1.plot(ax=ax2)
cropped_record1.plot_sequence(ax=ax2)
ax2.set_title("Sequence detail", loc='left')

#

cropped_record2.plot(ax=ax3)
cropped_record2.plot_sequence(ax=ax3)
ax3.set_title("Sequence detail", loc='left')

fig.savefig('overview_and_detail.png')

I copied some of your code and replaced some values to suit a real life situation and the program returns ValueError: out-of-bound cropping. Can the tool not handle big coordinates?

[Zulko]

I’m not entirely sure about your scenario but here is some alternative code which (I hope) does the same thing:

from dna_features_viewer import GraphicFeature, GraphicRecord
import matplotlib.pyplot as plt
full_sequence = 120_000_000 * "n"  # replace with the actual sequence.
x = 112173530  # index of the region to plot
primer1 = GraphicFeature(start=x, end=x+20, strand=+1, color="#ffd700", label="Primer1")
primer2 = GraphicFeature(start=x+50, end=x+70, strand=-1, color="#cffccc", label="Primer2")
record = GraphicRecord(sequence = full_sequence, features=[primer1, primer2])
region_record = record.crop((x-20, x+700))
detail_record = record.crop((x-5, x+75))

fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(15, 3), gridspec_kw={"width_ratios": [1, 2]})
region_record.plot(ax=ax1)
detail_record.plot(ax=ax2)
detail_record.plot_sequence(ax2)

I am not sure why the x coordinates are truncated for you but it could be due to Matplotlib’s way of writing the coordinates. Have you noticed that there is a “+1.1217e8” notation under the axis, indicating that you should add 112,170,000 to the x-coordinate.

[Zulko]

Thanks!