Runs a ClustalW multiple sequence alignment. The results are returned as a
:class:`~ost.seq.AlignmentHandle` instance.
There are two ways to use this function:
- align exactly two sequences:
:param seq1: sequence_one
:type seq1: :class:`~ost.seq.SequenceHandle` or :class:`str`
:param seq2: sequence_two
:type seq2: :class:`~ost.seq.SequenceHandle` or :class:`str`
The two sequences can be specified as two separate function parameters
(`seq1`, `seq2`). The type of both parameters can be either
:class:`~ost.seq.SequenceHandle` or :class:`str`, but must be the same for
both parameters.
- align two or more sequences:
:param seq1: sequence_list
:type seq1: :class:`~ost.seq.SequenceList`
:param seq2: must be :class:`None`
Two or more sequences can be specified by using a
:class:`~ost.seq.SequenceList`. It is then passed as the first function
parameter (`seq1`). The second parameter (`seq2`) must be :class:`None`.
:param clustalw: path to ClustalW executable (used in :func:`~ost.settings.Locate`)
:type clustalw: :class:`str`
:param nopgap: turn residue-specific gaps off
:type nopgap: :class:`bool`
:param clustalw_option_string: additional ClustalW flags (see http://www.clustal.org/download/clustalw_help.txt)
:type clustalw_option_string: :class:`str`
:param keep_files: do not delete temporary files
:type keep_files: :class:`bool`
.. note ::
- In the passed sequences ClustalW will convert lowercase to uppercase, and
change all '.' to '-'. OST will convert and '?' to 'X' before aligning
sequences with ClustalW.
- If a :attr:`sequence name <ost.seq.SequenceHandle.name>` contains spaces,
only the part before the space is considered as sequence name. To avoid
surprises, you should remove spaces from the sequence name.
- Sequence names must be unique (:class:`ValueError` exception raised
otherwise).
ClustalW will accept only IUB/IUPAC amino acid and nucleic acid codes:
======= ======================= ======= ============================
Residue Name Residue Name
======= ======================= ======= ============================
A alanine P proline
B aspartate or asparagine Q glutamine
C cystine R arginine
D aspartate S serine
E glutamate T threonine
F phenylalanine U selenocysteine
G glycine V valine
H histidine W tryptophan
I isoleucine Y tyrosine
K lysine Z glutamate or glutamine
L leucine X any
M methionine \\* translation stop
N asparagine \\- gap of indeterminate length
======= ======================= ======= ============================
Definition at line 6 of file clustalw.py.
