Update code/alphafold_featureVector.py

code/alphafold_featureVector.py

@@ -57,6 +57,7 @@ import shutil
 import streamlit as st
 
 
+            
 def run_freesasa(infile, outfile, include_hetatms=True, outdir=None, force_rerun=False, file_type = 'gzip'):
     if not outdir:
         outdir = ''
@@ -697,6 +698,7 @@ def alphafold(input_set, mode, impute):
                     st.write('Calculated')
                     #calculate_freesasa(uniprotID, mod, existing_free_sasa, alphafold_path, path_to_output_files)
                     if (mutationPositionOnPDB != 'nan'):
+                        st.write('Here1')
                         if (int(mutationPositionOnPDB) <= 1400):
                             try:
                                 coordMut = get_coords(mutationPositionOnPDB, alignments, coords, resnums_for_sasa, mode)[0]
@@ -707,8 +709,30 @@ def alphafold(input_set, mode, impute):
                             coordMut = np.NaN
 
                         sasa_pos = get_coords(mutationPositionOnPDB, alignments, coords, resnums_for_sasa, mode)[2]
-                        sasa_val = sasa('alphafold', 'nan', uniprotID, sasa_pos, uniprot_matched.at[i, 'wt'], mode,
-                                        path_to_output_files, file_type='gzip')
+                        st.write('sasa_pos', sasa_pos)
+                        if sasa_pos != np.NaN:
+                            sasa = 'nan'
+                            for filename in  list(Path(path_to_output_files / 'freesasa_files').glob("*")):
+                                st.write('xdfkjlxdjf', filename)
+                                fname = list(filter(None, str(filename).split('.')))[0].split('/')[-1].split('-')[1].upper()
+            
+                                if uniprotID == fname:
+                                    files = open(filename, 'r')
+                                    file = files.readlines()
+                                    for k in file:
+                                        if str(k.strip()[10:13]) == str(sasa_pos):
+                                            residue = str(k[4:7].strip())
+                                            if wt == threeToOne(residue):
+                                                sasa = str(k[22:28]).strip('\n')
+                                            elif wt != threeToOne(residue):
+                                                sasa = str(k[22:28]).strip('\n') + '*'
+                                            else:
+                                                sasa = 'nan'
+            
+                        else:
+                            sasa = 'nan'
+                        #sasa_val = sasa('alphafold', 'nan', uniprotID, sasa_pos, uniprot_matched.at[i, 'wt'], mode,
+                        #                path_to_output_files, file_type='gzip')
 
                         if sasa_val != None:
                             uniprot_matched.at[i, 'sasa'] = sasa_val
@@ -716,7 +740,7 @@ def alphafold(input_set, mode, impute):
                         coordMut = 'nan'
                         sasa_val = 'nan'
                         uniprot_matched.at[i, 'sasa'] = sasa_val
-
+                    st.write('IDK')
                     domainPositionOnPDB_list = list(
                         range(int(uniprot_matched.at[i, 'domStart']), int(uniprot_matched.at[i, 'domEnd'])))
                     domain_distances = []