def plot_show_score():
scheme_file = biotite.temp_file("json")
gecli.main(args=[
"--seed", "0", "--show-score", "--smin", "30", "--lmin", "60",
"--lmax", "70", "-f", scheme_file
])
return plt.gcf()
def plot_no_green_scheme_alignment():
scheme_file = biotite.temp_file("json")
gecli.main(args=[
"--seed", "0", "--amin", "0", "--lmin", "50", "--lmax", "80", "-f",
scheme_file
])
return show_alignment(scheme_file)
def plot_main_example_alignment():
scheme_file = biotite.temp_file("json")
gecli.main(args=[
"--seed", "0", "--matrix", "BLOSUM62", "--lmin", "60", "--lmax", "75",
"-f", scheme_file
])
return show_alignment(scheme_file)
def plot_high_contrast_scheme_alignment():
scheme_file = biotite.temp_file("json")
gecli.main(args=[
"--seed", "0", "--contrast", "2000", "--lmin", "60", "--lmax", "75",
"-f", scheme_file
])
return show_alignment(scheme_file)
def plot_constrained_scheme_alignment():
scheme_file = biotite.temp_file("json")
gecli.main(args=[
"--seed", "0", "-c", "A", "70", "0", "0", "-c", "W", "70", "-10",
"-45", "--lmin", "60", "--lmax", "75", "-f", scheme_file
])
return show_alignment(scheme_file)
def plot_high_saturation_scheme_alignment():
scheme_file = biotite.temp_file("json")
gecli.main(args=[
"--seed", "0", "--smin", "30", "--lmin", "55", "--lmax", "75", "-f",
scheme_file
])
return show_alignment(scheme_file)
def plot_show_example():
random.seed(0)
scheme_file = biotite.temp_file("json")
gecli.main(args=[
"--show-example", "--smin", "30", "--lmin", "60", "--lmax", "70", "-f",
scheme_file
])
return plt.gcf()
def plot_pb_scheme_alignment():
random.seed(1)
scheme_file = biotite.temp_file("json")
mat_file = biotite.temp_file("mat")
with open(mat_file, "w") as file:
# PB substitution matrix, adapted from PBxplore
file.write("""
a b c d e f g h i j k l m n o p
a 516 -59 113 -105 -411 -177 -27 -361 47 -103 -644 -259 -599 -372 -124 -83
b -59 541 -146 -210 -155 -310 -97 90 182 -128 -30 29 -745 -242 -165 22
c 113 -146 360 -14 -333 -240 49 -438 -269 -282 -688 -682 -608 -455 -147 6
d -105 -210 -14 221 5 -131 -349 -278 -253 -173 -585 -670 -1573 -1048 -691 -497
e -411 -155 -333 5 520 185 186 138 -378 -70 -112 -514 -1136 -469 -617 -632
f -177 -310 -240 -131 185 459 -99 -45 -445 83 -214 -88 -547 -629 -406 -552
g -27 -97 49 -349 186 -99 665 -99 -89 -118 -409 -138 -124 172 128 254
h -361 90 -438 -278 138 -45 -99 632 -205 316 192 -108 -712 -359 95 -399
i 47 182 -269 -253 -378 -445 -89 -205 696 186 8 15 -709 -269 -169 226
j -103 -128 -282 -173 -70 83 -118 316 186 768 196 5 -398 -340 -117 -104
k -644 -30 -688 -585 -112 -214 -409 192 8 196 568 -65 -270 -231 -471 -382
l -259 29 -682 -670 -514 -88 -138 -108 15 5 -65 533 -131 8 -11 -316
m -599 -745 -608 -1573 -1136 -547 -124 -712 -709 -398 -270 -131 241 -4 -190 -155
n -372 -242 -455 -1048 -469 -629 172 -359 -269 -340 -231 8 -4 703 88 146
o -124 -165 -147 -691 -617 -406 128 95 -169 -117 -471 -11 -190 88 716 58
p -83 22 6 -497 -632 -552 254 -399 226 -104 -382 -316 -155 146 58 609
""")
gecli.main(args=[
"--alphabet", "abcdefghijklmnop", "--matrix", mat_file, "--contrast",
"300", "--lmin", "65", "--lmax", "70", "-f", scheme_file
])
colors = graphics.load_color_scheme(scheme_file)["colors"]
fig = plt.figure(figsize=(8.0, 5.0))
ax = fig.gca()
pb_alphabet = seq.LetterAlphabet("abcdefghijklmnop")
fasta_file = fasta.FastaFile()
fasta_file.read(PB_EXAMPLE_FILE_NAME)
seq_strings = list(fasta_file.values())
sequences = [
seq.GeneralSequence(pb_alphabet, seq_str.replace("-", ""))
for seq_str in seq_strings
]
trace = align.Alignment.trace_from_strings(seq_strings)
alignment = align.Alignment(sequences, trace, score=None)
graphics.plot_alignment_type_based(ax,
alignment,
symbols_per_line=60,
spacing=2,
color_scheme=colors)
fig.tight_layout()
return fig
def plot_no_constraints_scheme_alignment():
scheme_file = biotite.temp_file("json")
gecli.main(args=["--seed", "1", "-f", scheme_file])
return show_alignment(scheme_file)