def vis_pegRNA2(df,genome_fasta=None,**kwargs):
"""Given one instance of easy-prime prediction (rawX format), generate DNA visualization
Input
--------
the data frame contains 4 rows: RTT, PBS, sgRNA, ngRNA
"""
pegRNA_id = df.index.tolist()[0]
variant_id = pegRNA_id.split("_")[0]
chr = df['CHROM'][0]
start = df['start'].min()
start -= start%10
start -= 1
end = df['end'].max()
end -= end%10
end += 10
variant_pos = df.POS.min()
ref = df.REF[0]
alt = df.ALT[0]
predicted_efficiency = df.predicted_efficiency[0]*100
pos = variant_pos-start
sequence = get_fasta_single(chr,start,end,genome_fasta).upper()
fig,ax = plt.subplots()
feature_list = []
for s,r in df.iterrows():
r_start = r.start-start
r_end = r_start+(r.end-r.start)
r_strand = get_strand(r.strand)
gf = GraphicFeature(start=r_start, end=r_end, strand=r_strand,
color=my_colors[r.type],label=r.type)
feature_list.append(gf)
record = GraphicRecord(sequence=sequence, features=feature_list)
# ax, _ = record.plot(figure_width=int(len(sequence)/5))
record.plot(ax=ax,figure_width=int(len(sequence)/5))
return 0
record.plot_sequence(ax)
ax.fill_between((pos-1.5, pos-0.5), +1000, -1000, alpha=0.5,color=my_colors['variant'])
locs, labels = plt.xticks()
new_labels = []
flag = True
for i in locs:
if flag:
new_labels.append("%s %s"%(chr,int(start+i+1)))
flag=False
else:
new_labels.append(int(start+i+1))
plt.xticks(locs,new_labels)
plt.title("ID: %s, CHR: %s, POS: %s, REF: %s, ALT: %s \n Predicted efficiency: %.1f"%(variant_id,chr,variant_pos,ref,alt,predicted_efficiency)+"%")
my_stringIObytes = io.BytesIO()
ax.figure.savefig(my_stringIObytes, format='png',bbox_inches='tight')
my_stringIObytes.seek(0)
img_string = base64.b64encode(my_stringIObytes.read())
return "data:image/png;base64,%s"%(img_string.decode("utf-8"))
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')
def probe_graph(file_name, path):
#file_name = "results_riftl_test.txt"
#file_name = sys.argv[1]
f = open(file_name, "r")
probes = []
for line in f:
print(line)
line_info = line.split(':')
#print(line)
#print(line_info)
if (line_info[0] == "Sequence"):
sequence = line_info[1]
elif (line_info[0] == "Initiator"):
initiator1 = line_info[1].upper()
initiator2 = line_info[2].upper()
elif (line_info[0] == "Probes"):
probes.append(line_info[1].upper())
probes.append(line_info[3].upper())
probes.append(line_info[2])
probes.append(line_info[4])
elif (line_info[0] == "Name"):
name = line_info[1].rstrip()
file_write = path + "/" + name + "_Probe_Set" ".txt"
w = open(file_write, "w+")
"""print(sequence)
print(initiator1)
print(initiator2)
print(probe1)
print(probe2)
print(start)"""
x = 1
print(probes)
print(name)
for a in range(0, len(probes), 4):
gstart = 28
gend = 3
probe1 = probes[a]
probe2 = probes[a + 1]
probe1 = Seq(probe1)
probe1 = probe1.complement()
probe2 = Seq(probe2)
probe2 = probe2.complement()
probe1 = str(probe1)
probe2 = str(probe2)
start = probes[a + 2]
end = probes[a + 3]
start = int(start)
start -= 4
if start <= 0:
gend = 0 - start - 1
gstart = gend + 25
start = 0
end = int(end)
subseq = sequence[start:end]
subseq = subseq.upper()
record = GraphicRecord(
sequence=subseq,
features=[
GraphicFeature(start=gstart,
end=gend,
strand=+1,
color='#ffcccc',
label=probe1),
GraphicFeature(start=gstart + 28,
end=gstart + 2,
strand=+1,
color='#ccccff',
label=probe2),
GraphicFeature(start=gstart,
end=gstart,
strand=-1,
color='m',
label="space"),
GraphicFeature(start=gstart + 1,
end=gstart + 1,
strand=-1,
color='m',
label="space"),
GraphicFeature(start=gstart,
end=(gstart - len(initiator1)),
strand=-1,
color='y',
label=initiator1),
GraphicFeature(start=gstart + 2,
end=(gstart + 2 + len(initiator1)),
strand=+1,
color='y',
label=initiator2)
])
ax, _ = record.plot(figure_width=10)
record.plot_sequence(ax)
total1 = initiator1 + "TT" + probe1[::-1]
total2 = probe2[::-1] + "TT" + initiator2
w.write("PROBE SET" + str(x) + "\n")
w.write("Probe1:" + total1 + "\n")
w.write("Probe2:" + total2 + "\n")
#print(total2)
tosave = path + "/" + name + "Plots for Probes" + str(x)
x += 1
ax.figure.savefig(tosave, bbox_inches='tight')
#break
w.close()
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')
def show_crispr_grna_results(
sequence: str,
guides: List[dict],
indexes: Optional[List[int]] = None,
scoreField: str = "onTargetScore",
):
"""Shows guide rnas results for CRISPR.
Args:
sequence (str): A string containing the complete organism sequence
guides (dict): A table on 'records' format that contains guides info.\
The required fields are `start` (int), `end` (ind), indicating the limits of the guide in sequence's index.
indexes(list): Indexes (start and end) of the targeted sequence within the complete sequence. \
If not set, the targeting sequence is not shown.
scoreField (str): Select which score from GRNA tool show in the chart. \
Available scores are "onTargetScore" (default) and "offTargetScore"
"""
targeting_seq_feat = []
# Show main targeted sequence if index are set. If not, we calculate indexes to limit plot range at the `crop`
# instruction.
if indexes is not None:
targeting_seq_feat = [
GraphicFeature(
start=indexes[0],
end=indexes[1],
color="#cffccc",
label="Sequence",
strand=+1,
),
]
else:
# TODO(diegovalenzuelaiturra): Check behavior is the same when using generators instead of lists.
# indexes = [min([x['start'] for x in guides]), max([x['end'] for x in guides])]
indexes = [
min(x['start'] for x in guides),
max(x['end'] for x in guides)
]
# Plot records
record = GraphicRecord(
sequence=sequence,
features=targeting_seq_feat + [
GraphicFeature(
start=x['start'],
end=x['end'] + 1,
color="#ffcccc",
label=f"{scoreField}: {x[scoreField]}",
strand=+1 if x['forward'] else -1,
) for x in guides
],
)
# Limit plot range
record = record.crop((indexes[0] - 10, indexes[1] + 11)) # crop
# Plot and set to show sequence
ax, _ = record.plot(figure_width=20)
record.plot_sequence(ax)