Add a warning for safer reading of FASTA files using IndexedFastaCustom + bumped GitHub Actions python version to 3.9
#122
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SagiPolaczek
changed the title
IndexedFastaCustomIndexedFastaCustom + bumped GitHub Actions python version to 3.9
mosheraboh
reviewed
Apr 18, 2024
| fasta_file_creation_time = os.path.getctime(self.filename) | ||
| index_file_creation_time = os.path.getctime(self.index_filename) | ||
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| if fasta_file_creation_time > index_file_creation_time + 42: |
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Why the extra 42 seconds?
| @@ -98,6 +99,16 @@ def __init__( | |||
| print(f"index file already found: {index_filename}") | |||
| already_found = True | |||
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| if already_found: | |||
| # Fasta file should be older than it's corresponding index file | |||
| fasta_file_creation_time = os.path.getctime(self.filename) | |||
| index_file_creation_time = os.path.getctime(self.index_filename) | ||
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| if fasta_file_creation_time > index_file_creation_time + 42: | ||
| warnings.warn( |
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Maybe raise an error and suggest deleting the index file to recreate it?
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@SagiPolaczek is it something you want to merge? |
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Issue
A case that the code didn't cover yet:
IndexedFastaCustom(.hdf5files were created)IndexedFastaCustomwithforce_recreate_index=False.Now the offset values are not matching the
.fastafiles content and the user didn't get any notice for that.Suggested (relaxed) fix
.fastafiles is newer than the.hdf5(index) file by a margin bigger than 42 (arbitrary number less than a minute)