def get_structures(shape_out, dot, start, end, species, tx, validate, title,
savefn):
out_dict = read_icshape_out(shape_out, pureID=0)
dot_dict = read_dots(dot)
fa_dict = read_fa(fa=None, species=species, pureID=0)
# shape_null_index = read_validate(validate=validate, start=start, end=end)
VARNA = "/Users/gongjing/Downloads/VARNAv3-93-src.jar"
shape = out_dict[tx]['reactivity_ls'][start:end]
dot = dot_dict[tx]['dotbracket'][start:end]
seq = fa_dict[tx][start:end]
shape = ['-1' if i == 'NULL' else '1' for i in shape]
shape_null_index = [[n + 1, n + 1] for n, i in enumerate(shape)
if i == '-1']
visual_cmd = Visual.Plot_RNAStructure_Shape(
seq,
dot,
shape,
mode='heatmap',
title=title,
VARNAProg=VARNA,
highlight_region=shape_null_index,
correctT=True)
visual_cmd = visual_cmd.replace('outline=#FFFFFF',
'outline=#000000').replace(
'fill=00FF00',
'fill=#E6E6E6') # #000000,#9E9E9E
visual_cmd += ' -o {}'.format(savefn)
print(visual_cmd)
ShapeFn = "test_shape.out" shape = General.load_shape(ShapeFn, rem_tVersion=False, min_RPKM=None) dotFn = "test_structure.dot" dot = General.load_dot(dotFn, rem_tVersion=False)[] seqFn = "test_seq.fasta" fasta = General.load_fasta(seqFn, rem_tVersion=False) sequence = fasta['ENST00000558492.1'] dotBracket = dot['ENST00000558492.1'][1] shape_list = shape['ENST00000558492.1'] ##################### # Plot_RNAStructure_Shape(sequence, dot, shape_list, mode='label', correctT=True, highlight_region=[], title="", wait=True, VARNAProg=VARNAProg) ##################### print Visual.Plot_RNAStructure_Shape(sequence, dotBracket, shape_list, mode='fill') print Visual.Plot_RNAStructure_Shape(sequence, dotBracket, shape_list, mode='label') print Visual.Plot_RNAStructure_Shape(sequence, dotBracket, shape_list, mode='heatmap') ##################### # Plot_RNAStructure_Base(sequence, dot, mode='fill', correctT=True, highlight_region=[], title="", wait=True, VARNAProg=VARNAProg) ##################### print Visual.Plot_RNAStructure_Base(sequence, dotBracket, mode='fill') print Visual.Plot_RNAStructure_Base(sequence, dotBracket, mode='label') ##################### # Plot_RNAStructure_highlight(sequence, dot, hg_base_list=[], mode='fill', correctT=True, highlight_region=[], title="", wait=True, VARNAProg=VARNAProg): ##################### print Visual.Plot_RNAStructure_highlight(sequence, dotBracket, hg_base_list=range(20,90), mode='fill')
color = "#12c634"
else:
color = "#ed0c0c"
highlight_region.append([bp[0] - start + 1, bp[0] - start + 1, color])
highlight_region.append([bp[1] - start + 1, bp[1] - start + 1, color])
subbpprob = [(d[0] - start + 1, d[1] - start + 1, d[2]) for d in bpprob
if start <= d[0] < d[1] <= end]
title = f"{start}-{end}"
cmd = Visual.Plot_RNAStructure_Shape(sequence[start - 1:end],
dot[start - 1:end],
shape[start - 1:end],
mode='fill',
highlight_region=highlight_region,
bpprob=subbpprob,
bpprob_mode='both',
title=title,
bpwarning=False,
period=100,
first_base_pos=start,
peroid_color='#ff5722')
#cmd = manual_period(cmd, end-start+1, start, 100)
print(cmd, file=OUT)
start = end + 1
i += 1
OUT.close()
####################
### Frame-Shift Element
####################
shape_list=shape3,
si=-0.4,
sm=1.5,
md=300,
return_pfs=True)
maxexpect_dot3 = Structure.maxExpect(input_pfs_file=pfs3, delete_pfs=True)[0]
clean_dot3 = SARS2.remove_lowporb_bp(prob3,
maxexpect_dot3,
minprob=0.6,
minDist=150)
bp_prob3 = SARS2.collect_bpprob(prob3, clean_dot3)
auc3 = General.calc_AUC_v2(clean_dot3, shape3)
cmd3 = Visual.Plot_RNAStructure_Shape(seq3,
clean_dot3,
shape3,
mode='label',
bpprob=bp_prob3,
bpprob_cutofflist=[0.6, 0.8, 0.95],
bpprob_mode='both',
title=f"5UTR AUC={auc5:.3}")
prob5, pfs5 = Structure.partition(seq5,
shape_list=shape5,
si=-0.4,
sm=1.5,
md=300,
return_pfs=True)
maxexpect_dot5 = Structure.maxExpect(input_pfs_file=pfs5, delete_pfs=True)[0]
clean_dot5 = SARS2.remove_lowporb_bp(prob5,
maxexpect_dot5,
minprob=0.6,
minDist=150)
