Louis BECQUEY / biorseo

Go to a project
Toggle navigation Toggle navigation pinning
Nathalie BERNARD
d56ef2c7 1 parent 7a0cde71

correction

Inline Side-by-side
Showing 1 changed file with 13 additions and 12 deletions
...@@ -25,29 +25,29 @@ def run_test(cmd, log): ...@@ -25,29 +25,29 @@ def run_test(cmd, log):
25 rc = process.poll() 25 rc = process.poll()
26 26
27 def create_command_E(name, estimator): 27 def create_command_E(name, estimator):
28 - #cmd = ("python3 /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/biorseo.py -i " + 28 + cmd = ("python3 /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/biorseo.py -i " +
29 - cmd = ("python3 /local/local/BiorseoNath/biorseo.py -i " + 29 + #cmd = ("python3 /local/local/BiorseoNath/biorseo.py -i " +
30 - "/local/local/BiorseoNath/data/fasta/" + 30 + "//mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/fasta/" +
31 name + ".fa " + 31 name + ".fa " +
32 "-O results/ " + 32 "-O results/ " +
33 "--contacts " + 33 "--contacts " +
34 "--patternmatch " + 34 "--patternmatch " +
35 "--func E --" + estimator + " -v " + 35 "--func E --" + estimator + " -v " +
36 - "--biorseo-dir /local/local/BiorseoNath " + 36 + "--biorseo-dir /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo " +
37 - "--modules-path /local/local/BiorseoNath/data/modules/ISAURE/Motifs_derniere_version ") 37 + "--modules-path /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/modules/ISAURE/Motifs_derniere_version ")
38 return cmd 38 return cmd
39 39
40 def create_command_F(name, estimator): 40 def create_command_F(name, estimator):
41 - #cmd = ("python3 /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/biorseo.py -i " + 41 + cmd = ("python3 /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/biorseo.py -i " +
42 - cmd = ("python3 /local/local/BiorseoNath/biorseo.py -i " + 42 + #cmd = ("python3 /local/local/BiorseoNath/biorseo.py -i " +
43 - "/local/local/BiorseoNath/data/fasta/" + 43 + "/mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/fasta/" +
44 name + ".fa " + 44 name + ".fa " +
45 "-O results/ " + 45 "-O results/ " +
46 "--contacts " + 46 "--contacts " +
47 "--patternmatch " + 47 "--patternmatch " +
48 "--func F --" + estimator + " -v " + 48 "--func F --" + estimator + " -v " +
49 - "--biorseo-dir /local/local/BiorseoNath " + 49 + "--biorseo-dir /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo " +
50 - "--modules-path /local/local/BiorseoNath/data/modules/ISAURE/Motifs_derniere_version ") 50 + "--modules-path /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/modules/ISAURE/Motifs_derniere_version ")
51 return cmd 51 return cmd
52 52
53 # ================== Code from Louis Beckey Benchark.py ============================== 53 # ================== Code from Louis Beckey Benchark.py ==============================
...@@ -240,6 +240,7 @@ def set_axis_style(ax, labels): ...@@ -240,6 +240,7 @@ def set_axis_style(ax, labels):
240 240
241 def visualization_best_mcc(list_struct2d, list_contacts, estimator, function, color, lines_color): 241 def visualization_best_mcc(list_struct2d, list_contacts, estimator, function, color, lines_color):
242 242
243 + print(estimator + " + " + function + ": ")
243 np_struct2d = np.array(list_struct2d) 244 np_struct2d = np.array(list_struct2d)
244 np_contacts = np.array(list_contacts) 245 np_contacts = np.array(list_contacts)
245 246
...@@ -453,12 +454,12 @@ countF_MFE = 0 ...@@ -453,12 +454,12 @@ countF_MFE = 0
453 454
454 countE_MEA = 0 455 countE_MEA = 0
455 countF_MEA = 0 456 countF_MEA = 0
456 -"""
457 while seq: 457 while seq:
458 name = name[6:].strip() 458 name = name[6:].strip()
459 print(name) 459 print(name)
460 460
461 cmd2 = ("cppsrc/Scripts/deletePdb " + name) 461 cmd2 = ("cppsrc/Scripts/deletePdb " + name)
462 + os.system(cmd2)
462 463
463 cmd3 = create_command_E(name, 'MFE') 464 cmd3 = create_command_E(name, 'MFE')
464 os.system(cmd3) 465 os.system(cmd3)
...@@ -513,7 +514,7 @@ visualization_best_mcc(list_struct2d_F_MEA, list_contacts_F_MEA, 'MEA', 'F', 'bl ...@@ -513,7 +514,7 @@ visualization_best_mcc(list_struct2d_F_MEA, list_contacts_F_MEA, 'MEA', 'F', 'bl
513 print("countE_MFE: " + str(countE_MFE) + "\n") 514 print("countE_MFE: " + str(countE_MFE) + "\n")
514 print("countF_MFE: " + str(countF_MFE) + "\n") 515 print("countF_MFE: " + str(countF_MFE) + "\n")
515 print("countE_MEA: " + str(countE_MEA) + "\n") 516 print("countE_MEA: " + str(countE_MEA) + "\n")
516 -print("countF_MEA: " + str(countF_MEA) + "\n")""" 517 +print("countF_MEA: " + str(countF_MEA) + "\n")
517 myfile.close() 518 myfile.close()
518 path_benchmark = "data/modules/ISAURE/Motifs_version_initiale/benchmark.txt" 519 path_benchmark = "data/modules/ISAURE/Motifs_version_initiale/benchmark.txt"
519 visualization_all_mcc(path_benchmark,'MEA', 'F') 520 visualization_all_mcc(path_benchmark,'MEA', 'F')
......