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Fixed some doc typos
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Harrison Deng 2023-04-28 13:46:58 -05:00
parent e942b65ebd
commit adf7473587
3 changed files with 22 additions and 10 deletions
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6
src/bmlsa/aligner.py
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@ -26,11 +26,9 @@ def align_many_to_one_ssw(
:type open_gap_score: int :type open_gap_score: int
:param alignment_mode: The alignment mode to use. Either "local" or "global". :param alignment_mode: The alignment mode to use. Either "local" or "global".
:type alignment_mode: str :type alignment_mode: str
:param substitution_matrix: The name of the substitution matrix available :param substitution_matrix: The name of the substitution matrix available in :mod:`Bio.Align`, defaults to "BLOSUM62"
in :mod:`Bio.Align`, defaults to "BLOSUM62"
:type substitution_matrix: str, optional :type substitution_matrix: str, optional
:yield: Pairs of :obj:`bmlsa.datatypes.QuerySequence` objects where the first is :yield: Pairs of :obj:`bmlsa.datatypes.QuerySequence` objects where the first is the original, and the second is the aligned version
the original, and the second is the aligned version
:rtype: a generator of :obj:`bmlsa.datatypes.QuerySequence` objects :rtype: a generator of :obj:`bmlsa.datatypes.QuerySequence` objects
""" """
# TODO Consider using the built in "scoring" parameter # TODO Consider using the built in "scoring" parameter

17
src/bmlsa/datatypes.py
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@ -11,6 +11,23 @@ class QuerySequence:
end: int = None, end: int = None,
score: int = None, score: int = None,
) -> None: ) -> None:
"""Instantiates a :obj:bmlsa.datatypes.QuerySequence object
:param id: The id of the query sequence
:type id: str
:param sequence: The sequence itself
:type sequence: str
:param name: The name of the sequence, defaults to None
:type name: str, optional
:param description: The description of the sequence, defaults to None
:type description: str, optional
:param start: The start of the sequence, defaults to None
:type start: int, optional
:param end: The end of the sequence, defaults to None
:type end: int, optional
:param score: The alignment score of the sequence, defaults to None
:type score: int, optional
"""
self._description = description self._description = description
self._start = start self._start = start
self._end = end self._end = end

9
src/bmlsa/io.py
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@ -23,14 +23,11 @@ def queries_from_csv(
:type sequence_header: str :type sequence_header: str
:param name_header: The column title for the name of the sequence, defaults to None :param name_header: The column title for the name of the sequence, defaults to None
:type name_header: str, optional :type name_header: str, optional
:param desc_header: The column title for the description of the sequence, :param desc_header: The column title for the description of the sequence, defaults to None
defaults to None
:type desc_header: str, optional :type desc_header: str, optional
:param start_header: The column title for the start position of the sequence, :param start_header: The column title for the start position of the sequence, defaults to None
defaults to None
:type start_header: str, optional :type start_header: str, optional
:param end_header: The column title for the end position of the sequence, :param end_header: The column title for the end position of the sequence, defaults to None
defaults to None
:type end_header: str, optional :type end_header: str, optional
:yield: One :obj:`bmlsa.datatypes.QuerySequence` for each row :yield: One :obj:`bmlsa.datatypes.QuerySequence` for each row
:rtype: A generator that yields objects of :class:`bmlsa.datatypes.QuerySequence` :rtype: A generator that yields objects of :class:`bmlsa.datatypes.QuerySequence`