Upload 19 files

code/add_sasa.py

@@ -8,7 +8,8 @@ import os
 from pathlib import Path
 import gzip
 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:
@@ -25,7 +26,6 @@ def run_freesasa(infile, outfile, include_hetatms=True, outdir=None, force_rerun
                                        stderr=subprocess.PIPE,
                                        shell=True)
             out, err = command.communicate()
-
     elif file_type == 'gzip':
         with gzip.open(infile, 'rb') as f_in:
             with open('file_temp.pdb', 'wb') as f_out:
@@ -43,8 +43,6 @@ def run_freesasa(infile, outfile, include_hetatms=True, outdir=None, force_rerun
                                        stderr=subprocess.PIPE,
                                        shell=True)
             out, err = command.communicate()
-
-
     return outfile
 
 def calculate_freesasa(ID, model_num, existing_free_sasa, path_to_input,path_to_output_files, file_type = 'gzip'):
@@ -128,4 +126,4 @@ def sasa(source, pdbID, uniprotID, sasa_pos, wt, mode, path_to_output_files,file
                 return sasa
         else:
             sasa = 'nan'
-            return sasa 
+            return sasa

code/add_sequence.py

@@ -41,4 +41,4 @@ def get_isoforms(protein_id):
     except:
         AttributeError
         isoforms = {}
-        return isoforms
+        return isoforms

code/alphafold_featureVector.py

@@ -339,7 +339,6 @@ def alphafold(input_set, mode, impute):
 
                 if get_alignments_3D(uniprotID, mod, pdb_path, pdbSequence, 'nan', 'nan', 'nan', mode, Path(path_to_output_files / '3D_alignment'),
                                      'gzip') != None:
-
                     alignments, coords, resnums_for_sasa = get_alignments_3D(uniprotID, mod, pdb_path, pdbSequence, 'nan',
                                                                             'nan', 'nan', mode, Path(path_to_output_files / '3D_alignment'),
                                                                             'gzip')
@@ -413,11 +412,12 @@ def alphafold(input_set, mode, impute):
                         mod)] = list_dist_of_annots  # Getting minimum of all possible models
                 #                uniprot_matched.at[i, annotation_type] = minimum_position
                 else:
-                    print('Model File Not Found')
 
+                    print('Model File Not Found')
                     uniprot_matched.at[i, 'sasa'] = np.NaN
 
 
+
         if len(all_domain_distances) != 0:
             uniprot_matched.at[i, 'domaindistance3D'] = min(all_domain_distances)
         else:

code/alphafold_model.py

@@ -25,8 +25,11 @@ def which_model(position):
 def modelCount(path_to_models):
     count_list = []
     for file in list(path_to_models.glob("*")):
-        protein_id = str(file).split('-')[1]
-        count_list.append(protein_id)
+        try:
+            protein_id = str(file).split('-')[1]
+            count_list.append(protein_id)
+        except:
+            IndexError
     count_dict = Counter(count_list)
     count_dict = {';'.join(sorted(k for k in count_dict.keys() if count_dict[k] == v)): v for v in
                   set(count_dict.values())}

code/manage_files.py

@@ -7,7 +7,8 @@ def manage_files(mode):
         swiss_model_path = path_to_input_files / 'INDEX.json'
         fisher_path = path_to_input_files / 'significant_domains.txt'
         path_to_interfaces = path_to_input_files / 'H_sapiens_interfacesHQ.txt'
-        
+
+        os.makedirs('out_files', exist_ok=True)
         path_to_output_files = Path('out_files/pdb')
         os.makedirs(path_to_output_files / 'pdb_structures/', exist_ok=True)
         os.makedirs(path_to_output_files / 'alignment_files/', exist_ok=True)
@@ -33,6 +34,7 @@ def manage_files(mode):
         # Unzip before using
         alphafold_path = Path(path_to_input_files/'alphafold_structures')
 
+        os.makedirs('out_files', exist_ok=True)
         path_to_output_files = Path('out_files/alphafold')
         os.makedirs(path_to_output_files, exist_ok=True)
         os.makedirs(path_to_output_files / 'freesasa_files', exist_ok=True)