Aglaé TABOT

Merge branch 'stage_aglae' of ssh://forge.ibisc.univ-evry.fr:6622/lbecquey/RNANet into stage_aglae

......@@ -1927,8 +1927,8 @@ def measure_hrna_basepairs_chain(chain, df, thr_idx):
resnum=int(resnum)
try :
d=basepair_apex_distance(chain[(' ',resseq, icode_res)], chain[(' ', resnum, icode_pair)]) #calculation of the distance between the tips of the paired nucleotides
angle=basepair_flat_angle(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)])
d = basepair_apex_distance(chain[(' ',resseq, icode_res)], chain[(' ', resnum, icode_pair)]) # calculation of the distance between the tips of the paired nucleotides
angle = basepair_flat_angle(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)])
if d != 0.0:
liste_dist.append([chain, type_LW, resseq, resnum, d, angle[0], angle[1], angle[2], angle[3]])
except :
......@@ -1952,8 +1952,8 @@ def measure_hrna_basepairs_chain(chain, df, thr_idx):
resnum=resnum[:l-1]
resnum=int(resnum)
try :
d=basepair_apex_distance(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)])
angle=basepair_flat_angle(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)])
d = basepair_apex_distance(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)])
angle = basepair_flat_angle(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)])
if d != 0.0:
liste_dist.append([chain, type_LW[j], resseq, resnum, d, angle[0], angle[1], angle[2], angle[3]])
except:
......@@ -2043,7 +2043,7 @@ def GMM_histo(data_ori, name_data, toric=False, hist=True, couleur=None, save=Tr
else:
D = obs.ravel()
xmin = D.min()
xmax = D.max()
xmax = min(10.0, D.max())
x = np.linspace(xmin,xmax,1000)
colors=['red', 'blue', 'gold', 'cyan', 'magenta', 'white', 'black', 'green']
......@@ -2366,8 +2366,8 @@ def gmm_wadley():
p_c4p = list(df["C4'-P"][~ np.isnan(df["C4'-P"])])
c4p_p = list(df["P-C4'"][~ np.isnan(df["P-C4'"])])
os.makedirs(runDir + "/results/figures/Pyle/distances/", exist_ok=True)
os.chdir(runDir + "/results/figures/Pyle/distances/")
os.makedirs(runDir + "/results/figures/GMM/Pyle/distances/", exist_ok=True)
os.chdir(runDir + "/results/figures/GMM/Pyle/distances/")
GMM_histo(p_c1p, "P-C1'")
GMM_histo(c1p_p, "C1'-P")
......@@ -2390,8 +2390,8 @@ def gmm_wadley():
c1p_psuiv_c1psuiv = list(df["C1'-P°-C1'°"][~ np.isnan(df["C1'-P°-C1'°"])])
os.makedirs(runDir + "/results/figures/Pyle/angles/", exist_ok=True)
os.chdir(runDir + "/results/figures/Pyle/angles/")
os.makedirs(runDir + "/results/figures/GMM/Pyle/angles/", exist_ok=True)
os.chdir(runDir + "/results/figures/GMM/Pyle/angles/")
GMM_histo(p_c1p_psuiv, "P-C1'-P°", toric=True)
GMM_histo(c1p_psuiv_c1psuiv, "C1'-P°-C1'°", toric=True)
......@@ -2427,8 +2427,8 @@ def gmm_wadley():
theta_base=[i for i in theta_base if i != None]
os.makedirs(runDir + "/results/figures/Pyle/pseudotorsions/", exist_ok=True)
os.chdir(runDir + "/results/figures/Pyle/pseudotorsions/")
os.makedirs(runDir + "/results/figures/GMM/Pyle/pseudotorsions/", exist_ok=True)
os.chdir(runDir + "/results/figures/GMM/Pyle/pseudotorsions/")
GMM_histo(eta, "Eta", toric=True)
GMM_histo(theta, "Theta", toric=True)
......@@ -2507,8 +2507,8 @@ def gmm_hrna():
c4p_c1p_b1 = list(df["C4'-C1'-B1"][~ np.isnan(df["C4'-C1'-B1"])])
c1p_b1_b2 = list(df["C1'-B1-B2"][~ np.isnan(df["C1'-B1-B2"])])
os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/distances/", exist_ok=True)
os.chdir(runDir + "/results/figures/GMM/HiRE-RNA/distances/")
os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/angles/", exist_ok=True)
os.chdir(runDir + "/results/figures/GMM/HiRE-RNA/angles/")
GMM_histo(lastc4p_p_o5p, "C4'-P-O5'", toric=True)
GMM_histo(lastc1p_lastc4p_p, "C1'-C4'-P", toric=True)
......@@ -2908,12 +2908,20 @@ if __name__ == "__main__":
DO_WADLEY_ANALYSIS = True
os.makedirs(runDir+"/results/geometry/Pyle/distances/", exist_ok=True)
os.makedirs(runDir+"/results/geometry/Pyle/angles/", exist_ok=True)
os.makedirs(runDir+"/results/geometry/Pyle/pseudotorsions/", exist_ok=True)
os.makedirs(runDir+"/results/figures/GMM/Pyle/distances/", exist_ok=True)
os.makedirs(runDir+"/results/figures/GMM/Pyle/angles/", exist_ok=True)
os.makedirs(runDir+"/results/figures/GMM/Pyle/pseudotorsions/", exist_ok=True)
elif opt=='--hire-rna':
DO_HIRE_RNA_MEASURES = True
os.makedirs(runDir + "/results/geometry/HiRE-RNA/distances/", exist_ok=True)
os.makedirs(runDir + "/results/geometry/HiRE-RNA/angles/", exist_ok=True)
os.makedirs(runDir + "/results/geometry/HiRE-RNA/torsions/", exist_ok=True)
os.makedirs(runDir + "/results/geometry/HiRE-RNA/basepairs/", exist_ok=True)
os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/distances/", exist_ok=True)
os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/angles/", exist_ok=True)
os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/torsions/", exist_ok=True)
os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/basepairs/", exist_ok=True)
# Load mappings. famlist will contain only families with structures at this resolution threshold.
......