The FASTA file is not encoded in UTF-8 #5
Description
The error is generated "The FASTA file is not encoded in UTF-8."
We have confirmed the encoding of FASTA file using file -i and it looks as expected. Any information is greatly appreciated.
The detailed error message in provided below:
[XXXX@XXX Riboformer]$ python data_processing.py -d marmoset -r Old3_2534_fixed -t Old3_1418_fixed
Loading ribosome densities.
Finish reading the ribosome footprints.
Loading genome sequences.
Traceback (most recent call last):
File “/rshare1/ZETTAI_path_WA_slash_home_KARA/home/XXXX/XXXX/Riboformer-main/Riboformer/data_processing.py”, line 283, in
main()
File “/rshare1/ZETTAI_path_WA_slash_home_KARA/home/XXXX/XXXX/Riboformer-main/Riboformer/data_processing.py”, line 237, in main
for record in SeqIO.parse(datapath + fasta_file[0], “fasta”):
File “/home/XXXX/miniconda3/envs/riboformer/lib/python3.9/site-packages/Bio/SeqIO/Interfaces.py”, line 74, in next
return next(self.records)
File “/home/XXXX/miniconda3/envs/riboformer/lib/python3.9/site-packages/Bio/SeqIO/FastaIO.py”, line 198, in iterate
for title, sequence in SimpleFastaParser(handle):
File “/home/XXXX/miniconda3/envs/riboformer/lib/python3.9/site-packages/Bio/SeqIO/FastaIO.py”, line 47, in SimpleFastaParser
for line in handle:
File “/home/XXXX/miniconda3/envs/riboformer/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 0xb0 in position 37: invalid start byte
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