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Sourcecode: python-biopython version File versions

def Bio::Clustalw::MultipleAlignCL::__init__ (   self,
  sequence_file,
  command = 'clustalw' 
)

Initialize some general parameters that can be set as attributes.

Arguments:
o sequence_file - The file to read the sequences for alignment from.
o command - The command used to run clustalw. This defaults to
just 'clustalw' (ie. assumes you have it on your path somewhere).

General attributes that can be set:
o is_quick - if set as 1, will use a fast algorithm to create
the alignment guide tree.
o allow_negative - allow negative values in the alignment matrix.

Multiple alignment attributes that can be set as attributes:
o gap_open_pen - Gap opening penalty
o gap_ext_pen - Gap extension penalty
o is_no_end_pen - A flag as to whether or not there should be a gap
separation penalty for the ends.
o gap_sep_range - The gap separation penalty range.
o is_no_pgap - A flag to turn off residue specific gaps
o is_no_hgap - A flag to turn off hydrophilic gaps
o h_gap_residues - A list of residues to count a hydrophilic
o max_div - A percent identity to use for delay (? - I don't undertand
this!)
o trans_weight - The weight to use for transitions

Definition at line 317 of file __init__.py.

00317                                                            :
        """Initialize some general parameters that can be set as attributes.

        Arguments:
        o sequence_file - The file to read the sequences for alignment from.
        o command - The command used to run clustalw. This defaults to
        just 'clustalw' (ie. assumes you have it on your path somewhere).
        
        General attributes that can be set:
        o is_quick - if set as 1, will use a fast algorithm to create
        the alignment guide tree.
        o allow_negative - allow negative values in the alignment matrix.

        Multiple alignment attributes that can be set as attributes:
        o gap_open_pen - Gap opening penalty
        o gap_ext_pen - Gap extension penalty
        o is_no_end_pen - A flag as to whether or not there should be a gap
        separation penalty for the ends.
        o gap_sep_range - The gap separation penalty range.
        o is_no_pgap - A flag to turn off residue specific gaps
        o is_no_hgap - A flag to turn off hydrophilic gaps
        o h_gap_residues - A list of residues to count a hydrophilic
        o max_div - A percent identity to use for delay (? - I don't undertand
        this!)
        o trans_weight - The weight to use for transitions
        """
        self.sequence_file = sequence_file
        self.command = command
        
        self.is_quick = None
        self.allow_negative = None

        self.gap_open_pen = None
        self.gap_ext_pen = None
        self.is_no_end_pen = None
        self.gap_sep_range = None
        self.is_no_pgap = None
        self.is_no_hgap = None
        self.h_gap_residues = []
        self.max_div = None
        self.trans_weight = None

        # other attributes that should be set via various functions
        # 1. output parameters
        self.output_file = None
        self.output_type = None
        self.output_order = None
        self.change_case = None
        self.add_seqnos = None

        # 2. a guide tree to use
        self.guide_tree = None
        self.new_tree = None

        # 3. matrices
        self.protein_matrix = None
        self.dna_matrix = None

        # 4. type of residues
        self.type = None

    def __str__(self):


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