renamed aa_index folder to aa_index_scripts

scripts/aa_index_scripts/aaindex/data/parse_aaindex.py

@@ -0,0 +1,90 @@
+from collections import defaultdict
+
+import os
+import pickle
+
+DATA_FOLDER = "/home/chmrodrigues/Documents/ppi2/reverse_mutations/data/aaindex"
+
+def main():
+
+    aaindex2_file = os.path.join(DATA_FOLDER,"aaindex2")
+    aaindex3_file = os.path.join(DATA_FOLDER,"aaindex3")
+
+    lines_index2 = ' '.join([item for item in open(aaindex2_file,'r').readlines()])
+    lines_index3 = ' '.join([item for item in open(aaindex3_file,'r').readlines()])
+
+    attrs_index2 = [item for item in lines_index2.split('//\n') if len(item) != 0]
+    attrs_index3 = [item for item in lines_index3.split('//\n') if len(item) != 0]
+    
+    attr_name = str()
+    all_matrices = dict()
+    for line in attrs_index2:
+        attr_elements = line.split('\n')
+
+        attr_name = [item for item in attr_elements if item.strip().startswith("H ")][0].split()[-1]
+        rows_columns_index = [attr_elements.index(item) for item in attr_elements if item.startswith(" M rows =")][0]
+
+        rows = attr_elements[rows_columns_index].split()[3].replace(",","")
+        columns = attr_elements[rows_columns_index].split()[-1]
+
+        attr_dict = dict()
+        for row in rows:
+            attr_dict[row] = dict()
+            for col in columns:
+                attr_dict[row][col] = None
+
+        for i in range(rows_columns_index+1,len(attr_elements)):
+            values = attr_elements[i].split()
+            try:
+                row = rows[i-(rows_columns_index+1)]
+                for idx,value in enumerate(values):
+                    col = columns[idx]
+                    try:
+                        attr_dict[row][col] = float(value)
+                    except ValueError:
+                        attr_dict[row][col] = value
+            except IndexError:
+                pass
+		
+        all_matrices[attr_name] = attr_dict
+    print(len(all_matrices))
+    pickle.dump(all_matrices, open('index2.p','wb'),protocol=2)
+
+    attr_name = str()
+    all_matrices = dict()
+    for line in attrs_index3:
+        attr_elements = line.split('\n')
+
+        attr_name = [item for item in attr_elements if item.strip().startswith("H ")][0].split()[-1]
+        rows_columns_index = [attr_elements.index(item) for item in attr_elements if item.startswith(" M rows =")][0]
+
+        rows = attr_elements[rows_columns_index].split()[3].replace(",","")
+        columns = attr_elements[rows_columns_index].split()[-1]
+
+        attr_dict = dict()
+        for row in rows:
+            attr_dict[row] = dict()
+            for col in columns:
+                attr_dict[row][col] = None
+
+        for i in range(rows_columns_index+1,len(attr_elements)):
+            values = attr_elements[i].split()
+            try:
+                row = rows[i-(rows_columns_index+1)]
+                for idx,value in enumerate(values):
+                    col = columns[idx]
+                    try:
+                        attr_dict[row][col] = float(value)
+                    except ValueError:
+                        attr_dict[row][col] = value
+            except IndexError:
+                pass
+		
+        all_matrices[attr_name] = attr_dict
+    pickle.dump(all_matrices, open('index3.p','wb'),protocol=2)
+    print(len(all_matrices))
+
+    return True
+
+if __name__ == "__main__":
+    main()

scripts/aa_index_scripts/aaindex/get_scores.py

@@ -0,0 +1,161 @@
+"""
+    RSA <= 0.2 Buried (Inaccessible)
+    RSA > 0.2 Exposed (Accessible)
+
+    SST = [H,I,G] - Helix
+    SST = [B,E] - Beta
+    SST = [T] - Turn
+    SST = [S,-] - Coil
+"""
+from Bio.PDB import PDBParser, DSSP
+import pickle
+import os
+import sys
+import warnings
+
+warnings.filterwarnings("ignore")
+
+CURRENT_FOLDER = '/home/local/BHRI/sportelli/Desktop/Important_Code/structural/aaindex'
+DATA_FOLDER = os.path.join(CURRENT_FOLDER,'data')
+
+RSA_SST_DEPENDENT = {
+    'exposed_helix' : 'KOSJ950101',
+    'exposed_beta' : 'KOSJ950102',
+    'exposed_turn' : 'KOSJ950103',
+    'exposed_coil' : 'KOSJ950104',
+    'buried_helix' : 'KOSJ950105',
+    'buried_beta' : 'KOSJ950106',
+    'buried_turn' : 'KOSJ950107',
+    'buried_coil' : 'KOSJ950108',
+}
+
+SST_DEPENDENT = {
+    'helix' : 'KOSJ950109',
+    'beta' : 'KOSJ950110',
+    'turn' : 'KOSJ950111',
+    'coil' : 'KOSJ950112',
+}
+
+RSA_DEPENDENT1 = {
+    'exposed' : 'KOSJ950113',
+    'buried' : 'KOSJ950114',
+}
+
+RSA_DEPENDENT2 = {
+    'exposed' : 'OVEJ920104',
+    'buried' : 'OVEJ920105',
+}
+
+def get_environment(pdb_file, chain, position, insertion_code=' '):
+    parser = PDBParser()
+    structure = parser.get_structure(pdb_file, pdb_file)
+    model = structure[0]
+
+    dssp = DSSP(model, pdb_file)
+    dssp_key = [item for item in dssp.keys() if item[0] == chain and item[1][1] == int(position) and item[1][2] == insertion_code]
+
+    dssp_key = dssp_key[0]
+    sst = dssp[dssp_key][2]
+    rsa = float(dssp[dssp_key][3])
+
+    return{'sst':sst, 'rsa':rsa}
+
+def main():
+    """
+        READ IMPUT
+    """
+    pdb_file = sys.argv[1]
+    chain_id = sys.argv[2]
+    mutation_code = sys.argv[3]
+
+    aa_from = mutation_code[0]
+    aa_to = mutation_code[-1]
+    position = mutation_code[1:-1]
+    insertion_code = ' '
+    if not position[-1].isdigit():
+        insertion_code = position[-1]
+        position = position[:-1]
+
+    """
+        READ DATABASES
+        index2 - Amino acid substitution indexes
+        index3 - Statistical protein contact potentials
+    """
+    index2 = pickle.load(open('{}/aaindex2.p'.format(DATA_FOLDER),'rb'))
+    index3 = pickle.load(open('{}/aaindex3.p'.format(DATA_FOLDER),'rb'))
+
+    """
+        LOOP THROUGH TABLES AND EXTRACT VALUES
+    """
+    results_index2 = dict()
+    results_index3 = dict()
+    for key in index2.keys():
+        if index2[key][aa_from][aa_to] != None:
+            results_index2[key] = index2[key][aa_from][aa_to]
+        else:
+            results_index2[key] = index2[key][aa_to][aa_from]
+
+    for key in index3.keys():
+        if index3[key][aa_from][aa_to] != None:
+            results_index3[key] = index3[key][aa_from][aa_to]
+        else:
+            results_index3[key] = index3[key][aa_to][aa_from]
+
+    """
+        GET ENVIRONMENT CHARACTERISTICS
+    """
+    environment = get_environment(pdb_file, chain_id, position, insertion_code)
+
+    buried = 'buried'
+    sst = str()
+    if environment['rsa'] <= 0.2:
+        buried = 'exposed'
+
+    if environment['sst'] in ['H','I','G']:
+        sst = 'helix'
+    elif environment['sst'] in ['B','E']:
+        sst = 'beta'
+    elif environment['sst'] in ['T']:
+        sst = 'turn'
+    else:
+        sst = 'coil'
+
+    results_index2['KOSJ950100_RSA_SST'] = results_index2[RSA_SST_DEPENDENT['{}_{}'.format(buried,sst)]]
+    results_index2['KOSJ950100_SST'] = results_index2[SST_DEPENDENT[sst]]
+    results_index2['KOSJ950110_RSA'] = results_index2[RSA_DEPENDENT1[buried]]
+    results_index2['OVEJ920100_RSA'] = results_index2[RSA_DEPENDENT2[buried]]
+
+    for value in RSA_SST_DEPENDENT.values():
+        results_index2.pop(value)
+    for value in SST_DEPENDENT.values():
+        results_index2.pop(value)
+    for value in RSA_DEPENDENT1.values():
+        results_index2.pop(value)
+    for value in RSA_DEPENDENT2.values():
+        results_index2.pop(value)
+
+    """
+        PRINT RESULTS
+    """
+    output_dict = dict()
+    output_dict.update(results_index2)
+    output_dict.update(results_index3)
+
+    keys = list(output_dict.keys())
+    keys.sort()
+    values = [str(output_dict[item]) for item in keys]
+
+    # print(",".join(keys))
+    print(",".join(values))
+
+    return True
+
+
+if __name__ == "__main__":
+
+    if len(sys.argv) != 4:
+        print("Error on parsing argument list")
+        print("Please provide a one letter code for wild-type and mutant residues")
+        print("Eg.: python get_scores.py pdb_file chain_id mutation_code")
+        sys.exit(1)
+    main()