Add manual seq type #478
Add manual seq type #478
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| @@ -16,7 +16,7 @@ | |||
| "get_alignment", "set_alignment"] | |||
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| def get_sequence(fasta_file, header=None): | |||
| def get_sequence(fasta_file, seq_type=None, header=None): | |||
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I think for backwards compatibility reasons the new parameter should be the last parameter in the list, e.g. in case someone uses the header as positional argument in their code. Although Biotite is still in 0.xversion, where compatibility is not strictly required, I would prefer the more compatible way, if there is no clear advantage of the other option.
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I placed the arguments based on gut feeling. However, I agree that compatibility should take priority here.
| seq_str = process_protein_sequence(seq_str) | ||
| # Return the converted sequence | ||
| return seq_type(seq_str) | ||
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| # Biotite alphabets for nucleotide and proteins |
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This part of the comment is also obsolete with the code changes.
| # Biotite alphabets for nucleotide and proteins |
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I went over the comments and removed all remainders of the previous implementation. I also added/moved a comment describing the purpose of each lambda function.
tests/sequence/test_fasta.py
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| assert seq.NucleotideSequence("ACGCTACGT") == fasta.get_sequence( | ||
| file, seq.NucleotideSequence | ||
| ) |
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I also refactored the test by splitting it into three functionally different tests:
- Ambiguous Sequences (i.e. nucleotide sequences which can also be loaded as amino acid sequences)
- Protein Sequences (should fail when loaded as nucleotide sequences)
- Invalid Sequences (should fail in all cases)
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I think we can ignore the error in |
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Thank you for your review! I applied all suggestions. From my side, the PR is ready to be merged. |
This PR implements the
seq_typeparameter as described in #477.