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| """ | ||
| try: | ||
| table_id = int(table) | ||
| # TODO: only call int if table is of type int |
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| def reverse_complement(sequence, inplace=False): | ||
| def reverse_complement(sequence: Seq, inplace: bool = False) -> str: |
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| def reverse_complement_rna(sequence, inplace=False): | ||
| def reverse_complement_rna(sequence: Seq, inplace: bool = False) -> str: |
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| def complement(sequence, inplace=False): | ||
| def complement(sequence: Seq, inplace: bool = False) -> str: |
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| def complement_rna(sequence, inplace=False): | ||
| def complement_rna(sequence: Seq, inplace: bool = False) -> str: |
| def translate( | ||
| sequence, table="Standard", stop_symbol="*", to_stop=False, cds=False, gap=None | ||
| ): | ||
| sequence: Seq, |
| def _translate_str( | ||
| sequence, table, stop_symbol="*", to_stop=False, cds=False, pos_stop="X", gap=None | ||
| ): | ||
| sequence: Seq, |
* In some cases a new, temporary variable called `encoded_sequence` was used as that value has a different type. * In 3 places attr-defined had to be ignored as mypy complained about missing methods in SeqRecord. This probably needs to be addressed.
| from Bio import BiopythonWarning | ||
| from Bio.Data import CodonTable | ||
| from Bio.Data import IUPACData | ||
| from Bio.SeqRecord import SeqRecord |
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