Louis BECQUEY / biorseo

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Nathalie BERNARD
d56ef2c7 1 parent 7a0cde71

correction

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Showing 1 changed file with 14 additions and 13 deletions
......@@ -25,29 +25,29 @@ def run_test(cmd, log):
rc = process.poll()
def create_command_E(name, estimator):
#cmd = ("python3 /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/biorseo.py -i " +
cmd = ("python3 /local/local/BiorseoNath/biorseo.py -i " +
"/local/local/BiorseoNath/data/fasta/" +
cmd = ("python3 /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/biorseo.py -i " +
#cmd = ("python3 /local/local/BiorseoNath/biorseo.py -i " +
"//mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/fasta/" +
name + ".fa " +
"-O results/ " +
"--contacts " +
"--patternmatch " +
"--func E --" + estimator + " -v " +
"--biorseo-dir /local/local/BiorseoNath " +
"--modules-path /local/local/BiorseoNath/data/modules/ISAURE/Motifs_derniere_version ")
"--biorseo-dir /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo " +
"--modules-path /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/modules/ISAURE/Motifs_derniere_version ")
return cmd
def create_command_F(name, estimator):
#cmd = ("python3 /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/biorseo.py -i " +
cmd = ("python3 /local/local/BiorseoNath/biorseo.py -i " +
"/local/local/BiorseoNath/data/fasta/" +
cmd = ("python3 /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/biorseo.py -i " +
#cmd = ("python3 /local/local/BiorseoNath/biorseo.py -i " +
"/mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/fasta/" +
name + ".fa " +
"-O results/ " +
"--contacts " +
"--patternmatch " +
"--func F --" + estimator + " -v " +
"--biorseo-dir /local/local/BiorseoNath " +
"--modules-path /local/local/BiorseoNath/data/modules/ISAURE/Motifs_derniere_version ")
"--biorseo-dir /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo " +
"--modules-path /mnt/c/Users/natha/Documents/IBISC/biorseo2/biorseo/data/modules/ISAURE/Motifs_derniere_version ")
return cmd
# ================== Code from Louis Beckey Benchark.py ==============================
......@@ -240,6 +240,7 @@ def set_axis_style(ax, labels):
def visualization_best_mcc(list_struct2d, list_contacts, estimator, function, color, lines_color):
print(estimator + " + " + function + ": ")
np_struct2d = np.array(list_struct2d)
np_contacts = np.array(list_contacts)
......@@ -453,13 +454,13 @@ countF_MFE = 0
countE_MEA = 0
countF_MEA = 0
"""
while seq:
name = name[6:].strip()
print(name)
cmd2 = ("cppsrc/Scripts/deletePdb " + name)
os.system(cmd2)
cmd3 = create_command_E(name, 'MFE')
os.system(cmd3)
......@@ -513,7 +514,7 @@ visualization_best_mcc(list_struct2d_F_MEA, list_contacts_F_MEA, 'MEA', 'F', 'bl
print("countE_MFE: " + str(countE_MFE) + "\n")
print("countF_MFE: " + str(countF_MFE) + "\n")
print("countE_MEA: " + str(countE_MEA) + "\n")
print("countF_MEA: " + str(countF_MEA) + "\n")"""
print("countF_MEA: " + str(countF_MEA) + "\n")
myfile.close()
path_benchmark = "data/modules/ISAURE/Motifs_version_initiale/benchmark.txt"
visualization_all_mcc(path_benchmark,'MEA', 'F')
......