Louis BECQUEY / RNANet

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Louis BECQUEY
95a00b56 1 parent 40cb5b7f

using sqlite instead of text files

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Showing 2 changed files with 20 additions and 15 deletions
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......@@ -17,7 +17,7 @@ from functools import partial
from multiprocessing import Pool
from os import path
from collections import Counter
from RNAnet import read_cpu_number
from RNAnet import read_cpu_number, sql_ask_database
path_to_3D_data = "/nhome/siniac/lbecquey/Data/RNA/3D/"
......@@ -182,17 +182,22 @@ def stats_len(mappings_list, points):
fig = plt.figure(figsize=(10,3))
ax = fig.gca()
ax.hist(lengths, bins=100, stacked=True, log=True, color=cols, label=sorted(mappings_list.keys()))
ax.set_xlabel("Sequence length (nucleotides)")
ax.set_ylabel("Number of 3D chains")
ax.set_xlabel("Sequence length (nucleotides)", fontsize=8)
ax.set_ylabel("Number of 3D chains", fontsize=8)
ax.set_xlim(left=-150)
ax.tick_params(axis='both', which='both', labelsize=8)
fig.tight_layout()
filtered_handles = [mpatches.Patch(color='red'), mpatches.Patch(color='white'),
mpatches.Patch(color='blue'), mpatches.Patch(color='white'),
fig.subplots_adjust(right=0.78)
filtered_handles = [mpatches.Patch(color='red'), mpatches.Patch(color='white'), mpatches.Patch(color='white'), mpatches.Patch(color='white'),
mpatches.Patch(color='blue'), mpatches.Patch(color='white'), mpatches.Patch(color='white'),
mpatches.Patch(color='green'), mpatches.Patch(color='purple'),
mpatches.Patch(color='orange'), mpatches.Patch(color='grey')]
filtered_labels = ['Large Ribosomal Subunits', '(RF02540, RF02541, RF02543)','Small Ribosomal Subunits','(RF01960, RF00177)',
filtered_labels = ['Large Ribosomal Subunits', '(RF02540,', 'RF02541', 'RF02543)',
'Small Ribosomal Subunits','(RF01960,', 'RF00177)',
'5S rRNA (RF00001)', '5.8S rRNA (RF00002)', 'tRNA (RF00005)', 'Other']
ax.legend(filtered_handles, filtered_labels, loc='best', ncol=2)
fig.savefig("results/lengths.png")
ax.legend(filtered_handles, filtered_labels, loc='right',
ncol=1, fontsize='small', bbox_to_anchor=(1.3, 0.55))
fig.savefig("results/figures/lengths.png")
# print("[3]\tComputed sequence length statistics and saved the figure.")
def format_percentage(tot, x):
......@@ -284,7 +289,7 @@ def stats_pairs(mappings_list, points):
ax = total_series.plot(figsize=(5,3), kind='bar', log=True, ylim=(1e4,5000000) )
ax.set_ylabel("Number of observations")
plt.subplots_adjust(bottom=0.2, right=0.99)
plt.savefig("results/pairings.png")
plt.savefig("results/figures/pairings.png")
# print("[5]\tComputed nucleotide statistics and saved CSV and PNG file.")
......@@ -350,7 +355,7 @@ def seq_idty(mappings_list):
fig.tight_layout()
fig.subplots_adjust(wspace=0.1, hspace=0.3)
fig.colorbar(im, ax=axs[-1], shrink=0.8)
fig.savefig(f"results/distances.png")
fig.savefig(f"results/figures/distances.png")
# print("[6]\tComputed identity matrices and saved the figure.")
if __name__ == "__main__":
......@@ -389,12 +394,12 @@ if __name__ == "__main__":
# Define threads for the tasks
#################################################################
threads = [
th.Thread(target=reproduce_wadley_results, args=[rna_points], kwargs={'carbon': 1}),
th.Thread(target=reproduce_wadley_results, args=[rna_points], kwargs={'carbon': 4}),
# th.Thread(target=reproduce_wadley_results, args=[rna_points], kwargs={'carbon': 1}),
# th.Thread(target=reproduce_wadley_results, args=[rna_points], kwargs={'carbon': 4}),
th.Thread(target=partial(stats_len, mappings_list), args=[rna_points]),
th.Thread(target=partial(stats_freq, mappings_list), args=[rna_points]),
th.Thread(target=partial(stats_pairs, mappings_list), args=[rna_points]),
th.Thread(target=seq_idty, args=[mappings_list])
# th.Thread(target=partial(stats_freq, mappings_list), args=[rna_points]),
# th.Thread(target=partial(stats_pairs, mappings_list), args=[rna_points]),
# th.Thread(target=seq_idty, args=[mappings_list])
]
for t in threads:
......