__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

__str__ ( self )

Write out the command line as a string.

set_dna_matrix ( self,  dna_matrix )

Set the type of DNA matrix to use.

The dna_matrix can either be one of the defined types (iub or clustalw) or a file with the matrix to use.

set_guide_tree ( self,  tree_file )

Provide a file to use as the guide tree for alignment.

Raises: o IOError - If the tree_file doesn't exist.

set_new_guide_tree ( self,  tree_file )

Set the name of the guide tree file generated in the alignment.

set_output (
        self,
        output_file,
        output_type=None,
        output_order=None,
        change_case=None,
        add_seqnos=None,
        )

Set the output parameters for the command line.

set_protein_matrix ( self,  protein_matrix )

Set the type of protein matrix to use.

Protein matrix can be either one of the defined types (blosum, pam, gonnet or id) or a file with your own defined matrix.

set_type ( self,  residue_type )

Set the type of residues within the file.

Clustal tries to guess whether the info is protein or DNA based on the number of GATCs, but this can be wrong if you have a messed up protein or DNA you are working with, so this allows you to set it explicitly.