diff --git a/src/bmlsa/aligner.py b/src/bmlsa/aligner.py index 060a085..294077a 100644 --- a/src/bmlsa/aligner.py +++ b/src/bmlsa/aligner.py @@ -26,11 +26,9 @@ def align_many_to_one_ssw( :type open_gap_score: int :param alignment_mode: The alignment mode to use. Either "local" or "global". :type alignment_mode: str - :param substitution_matrix: The name of the substitution matrix available - in :mod:`Bio.Align`, defaults to "BLOSUM62" + :param substitution_matrix: The name of the substitution matrix available in :mod:`Bio.Align`, defaults to "BLOSUM62" :type substitution_matrix: str, optional - :yield: Pairs of :obj:`bmlsa.datatypes.QuerySequence` objects where the first is - the original, and the second is the aligned version + :yield: Pairs of :obj:`bmlsa.datatypes.QuerySequence` objects where the first is the original, and the second is the aligned version :rtype: a generator of :obj:`bmlsa.datatypes.QuerySequence` objects """ # TODO Consider using the built in "scoring" parameter diff --git a/src/bmlsa/datatypes.py b/src/bmlsa/datatypes.py index ad178af..caf7cdf 100644 --- a/src/bmlsa/datatypes.py +++ b/src/bmlsa/datatypes.py @@ -11,6 +11,23 @@ class QuerySequence: end: int = None, score: int = 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._start = start self._end = end diff --git a/src/bmlsa/io.py b/src/bmlsa/io.py index 4561b59..8e47dd7 100644 --- a/src/bmlsa/io.py +++ b/src/bmlsa/io.py @@ -23,14 +23,11 @@ def queries_from_csv( :type sequence_header: str :param name_header: The column title for the name of the sequence, defaults to None :type name_header: str, optional - :param desc_header: The column title for the description of the sequence, - defaults to None + :param desc_header: The column title for the description of the sequence, defaults to None :type desc_header: str, optional - :param start_header: The column title for the start position of the sequence, - defaults to None + :param start_header: The column title for the start position of the sequence, defaults to None :type start_header: str, optional - :param end_header: The column title for the end position of the sequence, - defaults to None + :param end_header: The column title for the end position of the sequence, defaults to None :type end_header: str, optional :yield: One :obj:`bmlsa.datatypes.QuerySequence` for each row :rtype: A generator that yields objects of :class:`bmlsa.datatypes.QuerySequence`