def DrawMutatedStats(options, mutated_freqs, mutation_pos, log, min_mult):
hist_name1 = os.path.join(options.output_dir, "mutated_seq_freqs.png")
freq_hist_settings = drawing_utils.GetGraphicalSettings(
xlabel="Mutated sequence frequency (>" + str(min_mult) + ")",
ylabel="# sequences",
output_filename=hist_name1)
drawing_utils.DrawHistogram(mutated_freqs, freq_hist_settings)
if os.path.exists(hist_name1):
log.info(
"* Histogram of distribution of mutated sequence frequencies was written to "
+ hist_name1)
else:
log.info(
"ERROR: Histogram of distribution of mutated sequence frequencies was not found"
)
sys.exit(1)
hist_name2 = os.path.join(options.output_dir, "shm_positions.png")
pos_hist_settings = drawing_utils.GetGraphicalSettings(
xlabel="Relative SHM position",
ylabel="# SHMs",
output_filename=hist_name2)
drawing_utils.DrawMutationHistogram(mutation_pos, pos_hist_settings,
options.chain_type)
if os.path.exists(hist_name2):
log.info(
"* Histogram of distribution of SHM positions was written to " +
hist_name2)
else:
log.info(
"ERROR: Histogram of distribution of SHM positions was not found")
sys.exit(1)
def DrawBaseStats(options, base_lens, base_freqs, log, min_mult):
hist_name1 = os.path.join(options.output_dir, "base_seq_lens.png")
len_hist_settings = drawing_utils.GetGraphicalSettings(
xlabel="Sequence length",
ylabel="# sequences",
output_filename=hist_name1)
drawing_utils.DrawHistogram(base_lens, len_hist_settings)
if os.path.exists(hist_name1):
log.info(
"* Histogram of distribution of base sequence lengths was written to "
+ hist_name1)
else:
log.info(
"ERROR: Histogram of distribution of base sequence lengths was not found"
)
sys.exit(1)
hist_name2 = os.path.join(options.output_dir, "base_seq_freqs.png")
freq_hist_settings = drawing_utils.GetGraphicalSettings(
xlabel="Base sequence frequency (>" + str(min_mult) + ")",
ylabel="# sequences",
output_filename=hist_name2)
drawing_utils.DrawHistogram(base_freqs, freq_hist_settings)
if os.path.exists(hist_name2):
log.info(
"* Histogram of distribution of base sequence frequencies was written to "
+ hist_name2)
else:
log.info(
"ERROR: Histogram of distribution of base sequence frequencies was not found"
)
sys.exit(1)
fname = sys.argv[1] #'opt_kmers_tau_4_k_35.txt'
lines = open(fname, 'r').readlines()
rel_pos = list()
for l in lines:
splits = l.strip().split()
length = int(splits[1])
for i in range(2, len(splits)):
rel_pos.append(float(splits[i]) / length)
#print rel_pos
figure_fname = fname.split('.')[0] + '.pdf'
settings = drawing_utils.GetGraphicalSettings(
xlabel="Representative k-mer positions",
ylabel="# k-mers",
title="",
output_filename=figure_fname,
bins=100,
label="",
histtype="bar",
xlog_scale=False,
ylog_scale=False,
draw_legend=False,
colors="",
legend_loc='upper right',
show_xaxis=True,
show_yaxis=True,
xmin_shift=0,
xmax_shift=0,
ymin_shift=0,
ymax_shift=0)
drawing_utils.DrawMutationHistogram(rel_pos, settings)