def plot_plasmid_features(
plasmid_length: int,
features: List[Dict[str, Any]],
figure_width: int = 5,
palette: Optional[Palette] = None,
) -> Tuple[SubplotBase, Tuple[Any, Any]]:
"""Plots features in a circular dna sequence.
Args:
plasmid_length (int): Number of nucleotide bases of the plasmid sequence
features (List[Dict[str, Any]]): Features as obtained from TeselaGen DNA Sequence object
figure_width (int, optional): Width size of figure. Defaults to 5.
palette (Optional[Palette], optional): A SecretColors color palette. \
Defaults to None, meaning `Palette("material")` will be used.
Returns:
Tuple[AxesSubplot, Tuple[Any, Any]]: Axes and a tuple with Graphic features data
"""
# Define random color palette
if palette is None:
palette = Palette("material")
colors = palette.cycle()
# From 'forward' create a 'strand' field if does not exist
if 'strand' not in features[0]:
features = deepcopy(features)
for feat in features:
feat.update({'strand': 1 * feat['forward']})
# Create feat objects
plot_feats = [
GraphicFeature(
start=feat['start'],
end=feat['end'],
strand=feat['strand'],
label=feat['name'],
color=next(colors),
) for i, feat in enumerate(features)
]
# Make graphic record and plot
record = CircularGraphicRecord(sequence_length=plasmid_length,
features=plot_feats)
ax, _ = record.plot(figure_width=figure_width)
# return ax, (features_levels, labels_data)
return record.plot(ax)
def draw_by_dfv():
from dna_features_viewer import GraphicFeature, CircularGraphicRecord
import matplotlib.pyplot as plt
_feat = lambda name, it: GraphicFeature(it[0], it[1], +1, name)
features = [_feat(name, it) for name, it in zip(names, intervals)]
record = CircularGraphicRecord(phase_1 + phase_2, features)
import ipdb
ipdb.set_trace()
def test_by_hand(tmpdir):
"""Test building a GraphicRecord "by hand" """
features = [
GraphicFeature(start=5,
end=20,
strand=+1,
color="#ffd700",
label="Small feature"),
GraphicFeature(
start=20,
end=500,
strand=+1,
color="#ffcccc",
label="Gene 1 with a very long name",
),
GraphicFeature(start=400,
end=700,
strand=-1,
color="#cffccc",
label="Gene 2"),
GraphicFeature(start=600,
end=900,
strand=+1,
color="#ccccff",
label="Gene 3"),
]
# PLOT AND EXPORT A LINEAR VIEW OF THE CONSTRUCT
record = GraphicRecord(sequence_length=1000, features=features)
record.plot(figure_width=5, with_ruler=False) # lazy, just for coverage
ax, _ = record.plot(figure_width=5)
target_file = os.path.join(str(tmpdir), "by_hand.png")
ax.figure.savefig(target_file)
# PLOT AND EXPORT A CIRCULAR VIEW OF THE CONSTRUCT
circular_rec = CircularGraphicRecord(sequence_length=1000,
features=features)
ax2, _ = circular_rec.plot(figure_width=4)
ax2.figure.tight_layout()
target_file = os.path.join(str(tmpdir), "by_hand_circular.png")
ax2.figure.savefig(target_file, bbox_inches="tight")
print(miR.name)
print(str(mir_seed))
for utr in SeqIO.parse(utr_Database, "fasta"):
pos = 0
for seq in window(str(utr.seq), len(str(mir_seed))):
if (hamming2(str(seq.upper()),
str(mir_seed.back_transcribe().reverse_complement()))
<= nb_max_mismatch):
f1.write(utr.id + "\t" + str(pos) + "\t" +
str(pos + len(str(mir_seed))) + "\t" + miR.id + "\t" +
str(
hamming2(
str(seq.upper()),
str(mir_seed.back_transcribe().
reverse_complement()))) + "\t" + "+" +
"\t" + str(seq.upper()) + "\n")
features.append(
GraphicFeature(start=pos,
end=pos + len(str(mir_seed)),
strand=+1,
color="#ccccff",
label=re.sub(r'mmu-', '', miR.id)))
pos = pos + 1
#print(pos)
f1.close()
record = CircularGraphicRecord(sequence_length=1100, features=features) #
record.plot(figure_width=2)
plt.show()
),
GraphicFeature(
start=20,
end=500,
strand=+1,
color="#ffcccc",
label="Gene 1 with a very long name",
),
GraphicFeature(
start=400, end=700, strand=-1, color="#cffccc", label="Gene 2"
),
GraphicFeature(
start=600, end=900, strand=+1, color="#ccccff", label="Gene 3"
),
]
# PLOT AND EXPORT A LINEAR VIEW OF THE CONSTRUCT
record = GraphicRecord(sequence_length=1000, features=features)
ax, _ = record.plot(figure_width=5)
ax.figure.savefig("graphic_record_defined_by_hand.png")
# PLOT AND EXPORT A CIRCULAR VIEW OF THE CONSTRUCT
circular_rec = CircularGraphicRecord(sequence_length=1000, features=features)
ax2, _ = circular_rec.plot(figure_width=4)
ax2.figure.tight_layout()
ax2.figure.savefig(
"graphic_record_defined_by_hand_circular.png", bbox_inches="tight"
)