fatmacankara commited on
Commit
bc51ec4
·
1 Parent(s): 2f5f179

Update code/pdb_featureVector.py

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Files changed (1) hide show
  1. code/pdb_featureVector.py +8 -2
code/pdb_featureVector.py CHANGED
@@ -163,7 +163,7 @@ def pdb(input_set, mode, impute):
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  data.at[i, 'wt_sequence_match'] = 'i'
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  data.at[i, 'whichIsoform'] = whichIsoform
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  break
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- st.write('UNIPROT DF')
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  st.write(data)
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  data.wt_sequence_match = data.wt_sequence_match.astype('str')
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  data.replace({'': 'nan'}, inplace=True)
@@ -441,7 +441,11 @@ def pdb(input_set, mode, impute):
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  aligned_m = final_stage(dfM, annotation_list, Path(path_to_output_files / 'alignment_files'))
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  aligned_nm = final_stage(dfNM, annotation_list, Path(path_to_output_files / 'alignment_files'))
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-
 
 
 
 
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  # When PDB sequence is nan, it is wrongly aligned to the UniProt sequence. Fix them.
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  for i in aligned_m.index:
@@ -483,6 +487,7 @@ def pdb(input_set, mode, impute):
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  yes_pdb_no_match = after_up_pdb_alignment[
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  (after_up_pdb_alignment.pdbID != 'nan') & (after_up_pdb_alignment.mutationPositionOnPDB == 'nan')]
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  no_pdb = no_pdb.copy()
 
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  st.write(pdb_aligned)
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  print('PDB matching is completed...\n')
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  print('SUMMARY')
@@ -1416,6 +1421,7 @@ def pdb(input_set, mode, impute):
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  st.write(chain)
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  st.write(uniprotID)
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  st.write(pdbID)
 
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  st.write('INputs')
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  st.write(uniprotID, pdbSequence, source, chain, pdbID, mode )
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  data.at[i, 'wt_sequence_match'] = 'i'
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  data.at[i, 'whichIsoform'] = whichIsoform
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  break
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+ st.write('MATCHING UNIPTOR')
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  st.write(data)
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  data.wt_sequence_match = data.wt_sequence_match.astype('str')
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  data.replace({'': 'nan'}, inplace=True)
 
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  aligned_m = final_stage(dfM, annotation_list, Path(path_to_output_files / 'alignment_files'))
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  aligned_nm = final_stage(dfNM, annotation_list, Path(path_to_output_files / 'alignment_files'))
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+ st.write('aligned_m')
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+ st.write(aligned_m)
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+ st.write('aligned_nm')
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+ st.write(aligned_nm)
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+
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  # When PDB sequence is nan, it is wrongly aligned to the UniProt sequence. Fix them.
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  for i in aligned_m.index:
 
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  yes_pdb_no_match = after_up_pdb_alignment[
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  (after_up_pdb_alignment.pdbID != 'nan') & (after_up_pdb_alignment.mutationPositionOnPDB == 'nan')]
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  no_pdb = no_pdb.copy()
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+ st.write('-----PDB ALIGNED-----')
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  st.write(pdb_aligned)
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  print('PDB matching is completed...\n')
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  print('SUMMARY')
 
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  st.write(chain)
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  st.write(uniprotID)
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  st.write(pdbID)
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+ st.write(uniprotID)
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  st.write('INputs')
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  st.write(uniprotID, pdbSequence, source, chain, pdbID, mode )
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