def Visualiser_sekvens(gen):
import warnings
from Bio import BiopythonParserWarning
warnings.simplefilter('ignore', BiopythonParserWarning)
if gen == 'alle':
fil = 'Artemisia%20annua.gb'
graphic_record = ChangeFeatures().translate_record(fil)
ax, _ = graphic_record.plot(figure_width=20)
ax.figure.tight_layout()
elif gen == "aldh1":
sequence = "CTGTGTCTAGATTTACGGTTTTGTTGAGTATGGAGTATTTATCCCTGTGTCTAGATTTACGGTTTGAAGACTCAGGAAACTCTCATTAAGCGATCAACGTAGCATGATCATCAAAAGCATGGTTTTGTAAACTCGACATGTCAATGTACCAGCCGATCCAAGTATCCAAGCAATTGGTTCACCACACCAAAAGAGTTTTACACTTAAAAACAACAATTAATTCTAAATAGTCTATGTAATGAAATATGTTTTGTGTGGGTTAGTTTAGTTCATAGTTGCGCCATAAGTATTTACAGCAA"
record = GraphicRecord(sequence=sequence,
features=[
GraphicFeature(start=0,
end=28,
strand=+1,
color='#ffd700',
label="Promotor"),
GraphicFeature(start=29,
end=299,
strand=+1,
color="#ffcccc",
label="aldh1")
])
ax, _ = record.plot(figure_width=50)
record.plot_sequence(ax)
record.plot_translation(ax, (29, 299), fontdict={'weight': 'bold'})
elif gen == 'CYP71AV1':
sequence = "ATTTTTGGGGGCCCCCCCCCATTTTTTGGGGGGCGCGCGATGAAGTTGGTCATTCGAAATATACTTCCAAAATATGAAGTTGGTCATTCGAAATATACTTCCAAACAACCGAGCTGGTCAGGTAGATTTTGTTTCAGATGAAGATGCAATCCACCGTTGGGGGAGTTTCATGAATAACAATCGCAAATAAGATATATTGTTGATTCTTGATGATGTTTGGTCTGATACCATCATCACCGACCTCCAATTCAGGTCACGTGGATACAAGATCCTCGTGACCTCTGAAACAACCTTTAAGAGATTCGATACATATAAAGTGAGACCTCTCAGTGTTCAAGATGCCATCAATCTGTTATGCTATTCAACACTTTCGGAGCGTGCAAGTCAAGCCACAAATGACATACAGACCTTGTTGACAAGGTGAAATTTCAAATTATTCCAAGATTCATGTTTCATACCTTTATAAGAAAGTAATATCTAAACCATATTAACAAATACTAACAATTAACTTTCAAATGTTTTTGTAGTTAACCAAATGTTGCAAGAAGAATCCGCTCGCCTTAAGTGTCATTGGTGGTCGCCTAAAGGGGACACAAATGGAAAGTTGGCATCATACACTGAAAAAGCTATCTCAAGCCACACACCCTCTTATCGACCTTCCTTTGGATGAGGCAAACAGATTTCATCTCGCAAGAGCTCTCGGTTTACTCAAAGATGATGAACGCAACAGCCCCAGAAGTTCAACCTCGAAATTGACCCGATCTTACCAAGTCA"
record = GraphicRecord(sequence=sequence,
features=[
GraphicFeature(start=1,
end=38,
strand=+1,
color='#cffccc',
label="Promotor"),
GraphicFeature(start=39,
end=774,
strand=+1,
color="#cff77d",
label="CYP71AV1")
])
ax, _ = record.plot(figure_width=100)
record.plot_sequence(ax)
record.plot_translation(ax, (39, 774), fontdict={'weight': 'bold'})
return
def haplotype_blocks_fig(model, ref_seq):
s1, s2 = model.align_alleles()
record = GraphicRecord(sequence=ref_seq,
sequence_length=len(ref_seq),
features=[
GraphicFeature(start=0,
end=len(s1),
strand=+1,
color='#ffcccc'),
GraphicFeature(start=0,
end=len(s2),
strand=+1,
color='#cffccc')
])
ax, _ = record.plot(figure_width=5)
record.plot_sequence(ax)
record.plot_translation(ax, (8, 23), fontdict={'weight': 'bold'})
ax.figure.savefig('haplotypes.png', bbox_inches='tight')
def test_sequence_and_translation_plotting():
from dna_features_viewer import (
GraphicFeature,
GraphicRecord,
CircularGraphicRecord,
)
features = [
GraphicFeature(
start=5, end=10, strand=+1, color="#ffd700", label="bbS-1"
),
GraphicFeature(
start=8, end=15, strand=+1, color="#ffcccc", label="CrC"
),
]
record = GraphicRecord(sequence=7 * "ATGC", features=features)
ax, _ = record.plot(figure_width=5)
record.plot_sequence(ax)
record.plot_translation(ax, (8, 23), fontdict={"weight": "bold"})
from dna_features_viewer import GraphicFeature, GraphicRecord
record = GraphicRecord(sequence="ATGCATGCATGCATGCATGCATGCATGC", features=[
GraphicFeature(start=5, end=10, strand=+1, color='#ffcccc'),
GraphicFeature(start=8, end=15, strand=+1, color='#ccccff')
])
ax, _ = record.plot(figure_width=5)
record.plot_sequence(ax)
record.plot_translation(ax, (8, 23), fontdict={'weight': 'bold'})
ax.figure.savefig('sequence_and_translation.png', bbox_inches='tight')
from dna_features_viewer import GraphicFeature, GraphicRecord
record = GraphicRecord(sequence="ATGCATGCATGCATGCATGCATGCATGC",
features=[
GraphicFeature(start=5,
end=10,
strand=+1,
color='#ffcccc'),
GraphicFeature(start=8,
end=15,
strand=+1,
color='#ccccff')
])
ax, _ = record.plot(figure_width=6)
record.plot_sequence(ax, guides_intensity=0.2)
fontdict = {'weight': 'bold'}
record.plot_translation(ax, (8, 23), fontdict=fontdict, guides_intensity=0.8)
ax.figure.savefig('sequence_and_translation.png', bbox_inches='tight')