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nigyta / dfast_core

DDBJ Fast Annotation and Submission Tool
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UnicodeDecodeError: 'ascii' codec can't decode #29

Closed martian-yan closed 4 years ago

martian-yan commented 4 years ago

I meet an Error when the annotation is almost finished, during writing DDBJ files.

Traceback (most recent call last):
  File "/pub28/yan/miniconda2/envs/bioinfo/bin/dfast", line 284, in <module>
    pipeline.execute()
  File "/pub28/yan/miniconda2/envs/bioinfo/opt/dfast-1.2.6/dfc/pipeline.py", line 61, in execute
    self.ddbj.create_submission_file()
  File "/pub28/yan/miniconda2/envs/bioinfo/opt/dfast-1.2.6/dfc/utils/ddbj_submission.py", line 65, in create_submission_file
    create_ddbj_submission_file(self.genome, self.metadata, ann_file, fasta_file, self.verbosity)
  File "/pub28/yan/miniconda2/envs/bioinfo/opt/dfast-1.2.6/dfc/utils/ddbj_submission.py", line 165, in create_ddbj_submission_file
    metadata = Metadata(dict_metadata)
  File "/pub28/yan/miniconda2/envs/bioinfo/opt/dfast-1.2.6/dfc/utils/metadata_util.py", line 118, in __init__
    for line in open(self.__class__.METADATA_DEFINITION_FILE):
  File "/pub28/yan/miniconda2/envs/bioinfo/lib/python3.6/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe7 in position 21: ordinal not in range(128)

I solved this error by manually add encoding="utf-8" to File "/pub28/yan/miniconda2/envs/bioinfo/opt/dfast-1.2.6/dfc/utils/metadata_util.py", line 118, make it:

    for line in open(self.__class__.METADATA_DEFINITION_FILE, decoding="utf-8"):

I'm not sure is it a proper way. Make a note for Arthur and for anyone else meet the same error.

nigyta commented 4 years ago

Thank you for reporting an error. I fixed this in ver1.2.7 by adding encoding="utf-8" option, although this may not work in Py2.7 because encoding option is not available in py2.7