def test_logo_plot_noref(self):
sc_des = {"sequence": "B"}
# Start test
df = ri.parse_rosetta_file(self.silent1, sc_des)
fig, _ = rp.logo_plot(df, "B", refseq=False, line_break=50)
plt.tight_layout()
return fig
def test_sse_logo(self):
custom = {
'E': '#0000FF', 'H': '#00FF00', 'L': '#FF0000'
}
ff = os.path.join(self.dirpath, 'input_3ssepred.minisilent.gz')
df = ri.parse_rosetta_file(ff, {'structure': 'A'})
fs = df.structure_bits('A')
fig, axs = rp.logo_plot(fs, "A", refseq=False, line_break=50, font_size=10, hight_prop=2,
colors=custom)
return fig
def test_color_scheme_custom( self ):
custom = {
'A': '#e6194b', 'C': '#3cb44b', 'D': '#ffe119', 'E': '#ffe119',
'F': '#f58231', 'G': '#911eb4', 'H': '#46f0f0', 'I': '#f032e6',
'K': '#d2f53c', 'L': '#d2f53c', 'M': '#008080', 'N': '#e6beff',
'P': '#aa6e28', 'Q': '#fffac8', 'R': '#800000', 'S': '#aaffc3',
'T': '#808000', 'V': '#ffd8b1', 'W': '#000080', 'Y': '#808080'
}
df = rc.DesignFrame(pd.read_csv(os.path.join(self.dirpath, 'logo_plot_sequence.csv'),
header=None).rename(columns={0: 'sequence_A'}))
fig, axs = rp.logo_plot(df, "A", refseq=False, line_break=50, font_size=10, hight_prop=2,
colors=custom)
return fig
def test_logo_plot(self):
refseq = "GSISDIRKDAEVRMDKAVEAFKNKLDKFKAAVRKVFPTEERIDMRPEIWIAQELRRIGDE" \
"FNAYRDANDKAAALGKDKEINWFDISQSLWDVQKLTDAAIKKIEAALADMEAWLTQ"
sc_des = {"sequence": "B"}
# Start test
df = ri.parse_rosetta_file(self.silent1, sc_des)
df.add_reference_sequence("B", refseq)
fig, _ = rp.logo_plot(df, "B", refseq=True, line_break=50)
plt.tight_layout()
return fig
def main(options):
if options.ifasta is None:
infile = options.ifile if options.ifile is not None else options.ifiles
defs = {"sequence": options.seqID}
df = parse_rosetta_file(infile, defs, multi=options.ifiles is not None)
else:
df = read_fasta(options.ifasta)
if options.ffile is not None:
refseq = read_fasta(options.ffile).get_sequence("A").values[0]
df.add_reference_sequence(options.seqID, refseq)
# Alignment file
alif = options.ofile + ".clw"
write_clustalw(df, options.seqID, alif)
# Mutation list file
if options.ffile is not None:
mutf = options.ofile + "_mutants.clw"
write_mutant_alignments(df, options.seqID, mutf)
# Logo Plot
logof = options.ofile + "_logo" + "." + options.iformat
lfig, _ = logo_plot(df,
options.seqID,
refseq=options.ffile is not None,
line_break=50,
font_size=int(options.ifont))
plt.tight_layout()
plt.savefig(logof)
# Alignment plot
afig = None
if options.ffile is not None:
alimgf = options.ofile + "_ali" + "." + options.iformat
chunks = len(df.get_sequence(options.seqID).values[0])
chunks = int(math.ceil(float(chunks) / 50))
high_correct = math.ceil(df.shape[0] / 7.0)
afig = plt.figure(figsize=(chunks * high_correct * 10, 10))
grid = (chunks, 1)
ax = []
for i in range(chunks):
ax.append(plt.subplot2grid(grid, (i, 0), fig=afig))
plot_alignment(df, options.seqID, ax, line_break=50, matrix=None)
plt.savefig(alimgf)
return lfig, afig
def test_color_scheme_charge( self ):
df = rc.DesignFrame(pd.read_csv(os.path.join(self.dirpath, 'logo_plot_sequence.csv'),
header=None).rename(columns={0: 'sequence_A'}))
fig, axs = rp.logo_plot(df, "A", refseq=False, line_break=50, font_size=10, hight_prop=2,
colors="CHARGE")
return fig
def test_color_scheme_hydrophobicity( self ):
df = rc.DesignFrame(pd.read_csv(os.path.join(self.dirpath, 'logo_plot_sequence.csv'),
header=None).rename(columns={0: 'sequence_A'}))
fig, axs = rp.logo_plot(df, "A", refseq=False, font_size=10, hight_prop=2,
colors='HYDROPHOBICITY')
return fig