ost.bindings.clustalw Namespace Reference

Functions
def	ClustalW

Function Documentation

def ost.bindings.clustalw.ClustalW	(		seq1,
			seq2 = None,
			clustalw = None,
			keep_files = False,
			nopgap = False,
			clustalw_option_string = False
	)

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 7 of file clustalw.py.