RachaelMurray
commented
1 year ago Fixed: I was trying to parse a hidden .DS_Store file alongside the pdb structures. I followed https://dev.to/vonhyou/remove-dsstore-file-from-git-repo-2g57 to remove the .DS_Store files and prevent them being written again.
Hi there, I'm using caretta-cli to align all .pdb files in a folder but I get an error message after the files are parsed. I can see that cleaned pdb files are created for all my input pdb but the alignment fails to run. Here is the error message I get:
File "/Users/s1427471/anaconda3/envs/snakes/bin/caretta-cli", line 127, in
app()
File "/Users/s1427471/anaconda3/envs/snakes/bin/caretta-cli", line 108, in align multiple_alignment.align_from_structure_files(
File "/Users/s1427471/anaconda3/envs/snakes/lib/python3.9/site-packages/caretta/multiple_alignment.py", line 476, in align_from_structure_files pdb_files = helper.parse_protein_files_and_clean(input_files, output_files.cleaned_pdb_folder)
File "/Users/s1427471/anaconda3/envs/snakes/lib/python3.9/site-packages/caretta/helper.py", line 169, in parse_protein_files_and_clean protein = parse_structure_file(str(protein_file)).select("protein")
File "/Users/s1427471/anaconda3/envs/snakes/lib/python3.9/site-packages/geometricus/protein_utility.py", line 82, in parse_structure_file protein = pd.parsePDBStream(f)
File "/Users/s1427471/anaconda3/envs/snakes/lib/python3.9/site-packages/prody/proteins/pdbfile.py", line 313, in parsePDBStream lines = stream.readlines()
File "/Users/s1427471/anaconda3/envs/snakes/lib/python3.9/codecs.py", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 3131: invalid start byte
I'm using macOS. Any ideas how to fix this would be much appreciated :)