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docs: Database with custom scoring example #10

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7 changes: 7 additions & 0 deletions src/pyopal/lib.pyx
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Expand Up @@ -486,6 +486,13 @@ cdef class Database(BaseDatabase):

Create a new database with the given sequences.

Example:
>>> # creating a database with a custom scoring matrix
>>> from scoring_matrices import ScoringMatrix
>>>
>>> alphabet = ScoringMatrix.from_name("VTML80").alphabet
>>> db = pyopal.Database(["ATGC", "TTCA"], alphabet=alphabet)

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The example uses DNA sequences ("ATGC", "TTCA") with a protein scoring matrix (VTML80). VTML80 is designed for protein sequences, not DNA. Consider using protein sequences in the example to match the scoring matrix, such as sequences containing amino acid codes like "MVLIGWIFSLIFLLFLFGFLGLLLLLIIGIIFGFLGLLI" (from the issue example).

Suggested change
>>> db = pyopal.Database(["ATGC", "TTCA"], alphabet=alphabet)
>>> db = pyopal.Database(["MVLIGWIFSLIF", "LLFLFGFLGLLL"], alphabet=alphabet)

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Comment on lines +493 to +494

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The example demonstrates how to create a Database with a custom alphabet, but doesn't show how to use it with an Aligner to avoid the "database and score matrix have different alphabets" error mentioned in issue #9. Consider extending the example to show the complete workflow of creating both a Database and an Aligner with matching alphabets and performing alignment.

Suggested change
>>> alphabet = ScoringMatrix.from_name("VTML80").alphabet
>>> db = pyopal.Database(["ATGC", "TTCA"], alphabet=alphabet)
>>> scoring = ScoringMatrix.from_name("VTML80")
>>> alphabet = scoring.alphabet
>>> db = pyopal.Database(["ATGC", "TTCA"], alphabet=alphabet)
>>>
>>> # use the same scoring matrix/alphabet when creating the aligner
>>> aligner = pyopal.Aligner(scoring)
>>> result = aligner.align("ATGC", db)

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There is trailing whitespace on this line. Please remove it to maintain code cleanliness.

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"""
super().__init__(alphabet=alphabet)
# reset the collection if `__init__` is called more than once
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