Merge branch 'stage_aglae' of ssh://forge.ibisc.univ-evry.fr:6622/lbecquey/RNANet into stage_aglae
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21 additions
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13 deletions
... | @@ -1927,8 +1927,8 @@ def measure_hrna_basepairs_chain(chain, df, thr_idx): | ... | @@ -1927,8 +1927,8 @@ def measure_hrna_basepairs_chain(chain, df, thr_idx): |
1927 | 1927 | ||
1928 | resnum=int(resnum) | 1928 | resnum=int(resnum) |
1929 | try : | 1929 | try : |
1930 | - d=basepair_apex_distance(chain[(' ',resseq, icode_res)], chain[(' ', resnum, icode_pair)]) #calculation of the distance between the tips of the paired nucleotides | 1930 | + d = basepair_apex_distance(chain[(' ',resseq, icode_res)], chain[(' ', resnum, icode_pair)]) # calculation of the distance between the tips of the paired nucleotides |
1931 | - angle=basepair_flat_angle(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)]) | 1931 | + angle = basepair_flat_angle(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)]) |
1932 | if d != 0.0: | 1932 | if d != 0.0: |
1933 | liste_dist.append([chain, type_LW, resseq, resnum, d, angle[0], angle[1], angle[2], angle[3]]) | 1933 | liste_dist.append([chain, type_LW, resseq, resnum, d, angle[0], angle[1], angle[2], angle[3]]) |
1934 | except : | 1934 | except : |
... | @@ -1952,8 +1952,8 @@ def measure_hrna_basepairs_chain(chain, df, thr_idx): | ... | @@ -1952,8 +1952,8 @@ def measure_hrna_basepairs_chain(chain, df, thr_idx): |
1952 | resnum=resnum[:l-1] | 1952 | resnum=resnum[:l-1] |
1953 | resnum=int(resnum) | 1953 | resnum=int(resnum) |
1954 | try : | 1954 | try : |
1955 | - d=basepair_apex_distance(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)]) | 1955 | + d = basepair_apex_distance(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)]) |
1956 | - angle=basepair_flat_angle(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)]) | 1956 | + angle = basepair_flat_angle(chain[(' ', resseq, icode_res)], chain[(' ', resnum, icode_pair)]) |
1957 | if d != 0.0: | 1957 | if d != 0.0: |
1958 | liste_dist.append([chain, type_LW[j], resseq, resnum, d, angle[0], angle[1], angle[2], angle[3]]) | 1958 | liste_dist.append([chain, type_LW[j], resseq, resnum, d, angle[0], angle[1], angle[2], angle[3]]) |
1959 | except: | 1959 | except: |
... | @@ -2043,7 +2043,7 @@ def GMM_histo(data_ori, name_data, toric=False, hist=True, couleur=None, save=Tr | ... | @@ -2043,7 +2043,7 @@ def GMM_histo(data_ori, name_data, toric=False, hist=True, couleur=None, save=Tr |
2043 | else: | 2043 | else: |
2044 | D = obs.ravel() | 2044 | D = obs.ravel() |
2045 | xmin = D.min() | 2045 | xmin = D.min() |
2046 | - xmax = D.max() | 2046 | + xmax = min(10.0, D.max()) |
2047 | x = np.linspace(xmin,xmax,1000) | 2047 | x = np.linspace(xmin,xmax,1000) |
2048 | colors=['red', 'blue', 'gold', 'cyan', 'magenta', 'white', 'black', 'green'] | 2048 | colors=['red', 'blue', 'gold', 'cyan', 'magenta', 'white', 'black', 'green'] |
2049 | 2049 | ||
... | @@ -2366,8 +2366,8 @@ def gmm_wadley(): | ... | @@ -2366,8 +2366,8 @@ def gmm_wadley(): |
2366 | p_c4p = list(df["C4'-P"][~ np.isnan(df["C4'-P"])]) | 2366 | p_c4p = list(df["C4'-P"][~ np.isnan(df["C4'-P"])]) |
2367 | c4p_p = list(df["P-C4'"][~ np.isnan(df["P-C4'"])]) | 2367 | c4p_p = list(df["P-C4'"][~ np.isnan(df["P-C4'"])]) |
2368 | 2368 | ||
2369 | - os.makedirs(runDir + "/results/figures/Pyle/distances/", exist_ok=True) | 2369 | + os.makedirs(runDir + "/results/figures/GMM/Pyle/distances/", exist_ok=True) |
2370 | - os.chdir(runDir + "/results/figures/Pyle/distances/") | 2370 | + os.chdir(runDir + "/results/figures/GMM/Pyle/distances/") |
2371 | 2371 | ||
2372 | GMM_histo(p_c1p, "P-C1'") | 2372 | GMM_histo(p_c1p, "P-C1'") |
2373 | GMM_histo(c1p_p, "C1'-P") | 2373 | GMM_histo(c1p_p, "C1'-P") |
... | @@ -2390,8 +2390,8 @@ def gmm_wadley(): | ... | @@ -2390,8 +2390,8 @@ def gmm_wadley(): |
2390 | c1p_psuiv_c1psuiv = list(df["C1'-P°-C1'°"][~ np.isnan(df["C1'-P°-C1'°"])]) | 2390 | c1p_psuiv_c1psuiv = list(df["C1'-P°-C1'°"][~ np.isnan(df["C1'-P°-C1'°"])]) |
2391 | 2391 | ||
2392 | 2392 | ||
2393 | - os.makedirs(runDir + "/results/figures/Pyle/angles/", exist_ok=True) | 2393 | + os.makedirs(runDir + "/results/figures/GMM/Pyle/angles/", exist_ok=True) |
2394 | - os.chdir(runDir + "/results/figures/Pyle/angles/") | 2394 | + os.chdir(runDir + "/results/figures/GMM/Pyle/angles/") |
2395 | 2395 | ||
2396 | GMM_histo(p_c1p_psuiv, "P-C1'-P°", toric=True) | 2396 | GMM_histo(p_c1p_psuiv, "P-C1'-P°", toric=True) |
2397 | GMM_histo(c1p_psuiv_c1psuiv, "C1'-P°-C1'°", toric=True) | 2397 | GMM_histo(c1p_psuiv_c1psuiv, "C1'-P°-C1'°", toric=True) |
... | @@ -2427,8 +2427,8 @@ def gmm_wadley(): | ... | @@ -2427,8 +2427,8 @@ def gmm_wadley(): |
2427 | theta_base=[i for i in theta_base if i != None] | 2427 | theta_base=[i for i in theta_base if i != None] |
2428 | 2428 | ||
2429 | 2429 | ||
2430 | - os.makedirs(runDir + "/results/figures/Pyle/pseudotorsions/", exist_ok=True) | 2430 | + os.makedirs(runDir + "/results/figures/GMM/Pyle/pseudotorsions/", exist_ok=True) |
2431 | - os.chdir(runDir + "/results/figures/Pyle/pseudotorsions/") | 2431 | + os.chdir(runDir + "/results/figures/GMM/Pyle/pseudotorsions/") |
2432 | 2432 | ||
2433 | GMM_histo(eta, "Eta", toric=True) | 2433 | GMM_histo(eta, "Eta", toric=True) |
2434 | GMM_histo(theta, "Theta", toric=True) | 2434 | GMM_histo(theta, "Theta", toric=True) |
... | @@ -2507,8 +2507,8 @@ def gmm_hrna(): | ... | @@ -2507,8 +2507,8 @@ def gmm_hrna(): |
2507 | c4p_c1p_b1 = list(df["C4'-C1'-B1"][~ np.isnan(df["C4'-C1'-B1"])]) | 2507 | c4p_c1p_b1 = list(df["C4'-C1'-B1"][~ np.isnan(df["C4'-C1'-B1"])]) |
2508 | c1p_b1_b2 = list(df["C1'-B1-B2"][~ np.isnan(df["C1'-B1-B2"])]) | 2508 | c1p_b1_b2 = list(df["C1'-B1-B2"][~ np.isnan(df["C1'-B1-B2"])]) |
2509 | 2509 | ||
2510 | - os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/distances/", exist_ok=True) | 2510 | + os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/angles/", exist_ok=True) |
2511 | - os.chdir(runDir + "/results/figures/GMM/HiRE-RNA/distances/") | 2511 | + os.chdir(runDir + "/results/figures/GMM/HiRE-RNA/angles/") |
2512 | 2512 | ||
2513 | GMM_histo(lastc4p_p_o5p, "C4'-P-O5'", toric=True) | 2513 | GMM_histo(lastc4p_p_o5p, "C4'-P-O5'", toric=True) |
2514 | GMM_histo(lastc1p_lastc4p_p, "C1'-C4'-P", toric=True) | 2514 | GMM_histo(lastc1p_lastc4p_p, "C1'-C4'-P", toric=True) |
... | @@ -2908,12 +2908,20 @@ if __name__ == "__main__": | ... | @@ -2908,12 +2908,20 @@ if __name__ == "__main__": |
2908 | DO_WADLEY_ANALYSIS = True | 2908 | DO_WADLEY_ANALYSIS = True |
2909 | os.makedirs(runDir+"/results/geometry/Pyle/distances/", exist_ok=True) | 2909 | os.makedirs(runDir+"/results/geometry/Pyle/distances/", exist_ok=True) |
2910 | os.makedirs(runDir+"/results/geometry/Pyle/angles/", exist_ok=True) | 2910 | os.makedirs(runDir+"/results/geometry/Pyle/angles/", exist_ok=True) |
2911 | + os.makedirs(runDir+"/results/geometry/Pyle/pseudotorsions/", exist_ok=True) | ||
2912 | + os.makedirs(runDir+"/results/figures/GMM/Pyle/distances/", exist_ok=True) | ||
2913 | + os.makedirs(runDir+"/results/figures/GMM/Pyle/angles/", exist_ok=True) | ||
2914 | + os.makedirs(runDir+"/results/figures/GMM/Pyle/pseudotorsions/", exist_ok=True) | ||
2911 | elif opt=='--hire-rna': | 2915 | elif opt=='--hire-rna': |
2912 | DO_HIRE_RNA_MEASURES = True | 2916 | DO_HIRE_RNA_MEASURES = True |
2913 | os.makedirs(runDir + "/results/geometry/HiRE-RNA/distances/", exist_ok=True) | 2917 | os.makedirs(runDir + "/results/geometry/HiRE-RNA/distances/", exist_ok=True) |
2914 | os.makedirs(runDir + "/results/geometry/HiRE-RNA/angles/", exist_ok=True) | 2918 | os.makedirs(runDir + "/results/geometry/HiRE-RNA/angles/", exist_ok=True) |
2915 | os.makedirs(runDir + "/results/geometry/HiRE-RNA/torsions/", exist_ok=True) | 2919 | os.makedirs(runDir + "/results/geometry/HiRE-RNA/torsions/", exist_ok=True) |
2916 | os.makedirs(runDir + "/results/geometry/HiRE-RNA/basepairs/", exist_ok=True) | 2920 | os.makedirs(runDir + "/results/geometry/HiRE-RNA/basepairs/", exist_ok=True) |
2921 | + os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/distances/", exist_ok=True) | ||
2922 | + os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/angles/", exist_ok=True) | ||
2923 | + os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/torsions/", exist_ok=True) | ||
2924 | + os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/basepairs/", exist_ok=True) | ||
2917 | 2925 | ||
2918 | 2926 | ||
2919 | # Load mappings. famlist will contain only families with structures at this resolution threshold. | 2927 | # Load mappings. famlist will contain only families with structures at this resolution threshold. | ... | ... |
-
mentioned in commit 5a04af0a
-
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