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Sourcecode: python-biopython version File versions

def Bio::Clustalw::MultipleAlignCL::__str__ (   self  ) 

Write out the command line as a string.

Definition at line 378 of file __init__.py.

00378                      :
        """Write out the command line as a string."""
        cline = self.command + " " + self.sequence_file

        # general options
        if self.type:
            cline = cline + " -TYPE=%s" % self.type
        if self.is_quick == 1:
            cline = cline + " -INTERACTIVE"
        if self.allow_negative == 1:
            cline = cline + " -NEGATIVE"

        # output options
        if self.output_file:
            cline = cline + " -OUTFILE=%s" % self.output_file
        if self.output_type:
            cline = cline + " -OUTPUT=%s" % self.output_type
        if self.output_order:
            cline = cline + " -OUTORDER=%s" % self.output_order
        if self.change_case:
            cline = cline + " -CASE=%s" % self.change_case
        if self.add_seqnos:
            cline = cline + " -SEQNOS=%s" % self.add_seqnos
        if self.new_tree:
            # clustal does not work if -align is written -ALIGN
            cline = cline + " -NEWTREE=%s -align" % self.new_tree

        # multiple alignment options
        if self.guide_tree:
            cline = cline + " -USETREE=%s" % self.guide_tree
        if self.protein_matrix:
            cline = cline + " -MATRIX=%s" % self.protein_matrix
        if self.dna_matrix:
            cline = cline + " -DNAMATRIX=%s" % self.dna_matrix
        if self.gap_open_pen:
            cline = cline + " -GAPOPEN=%s" % self.gap_open_pen
        if self.gap_ext_pen:
            cline = cline + " -GAPEXT=%s" % self.gap_ext_pen
        if self.is_no_end_pen == 1:
            cline = cline + " -ENDGAPS"
        if self.gap_sep_range:
            cline = cline + " -GAPDIST=%s" % self.gap_sep_range
        if self.is_no_pgap == 1:
            cline = cline + " -NOPGAP"
        if self.is_no_hgap == 1:
            cline = cline + " -NOHGAP"
        if len(self.h_gap_residues) != 0:
            # stick the list of residues together as one big list o' residues
            residue_list = ''
            for residue in self.h_gap_residues:
                residue_list = residue_list + residue
            cline = cline + " -HGAPRESIDUES=%s" % residue_list
        if self.max_div:
            cline = cline + " -MAXDIV=%s" % self.max_div
        if self.trans_weight:
            cline = cline + " -TRANSWEIGHT=%s" % self.trans_weight

        return cline

    def set_output(self, output_file, output_type = None, output_order = None,


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