wrapper for deltablast

Applications_with_deltablast.py

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Wrappers for the new NCBI BLAST+ tools (written in C++):

- NcbiblastpCommandline - Protein-Protein BLAST
- NcbideltablastCommandline - Protein-Protein domain enhanced lookup time accelerated blast

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class NcbideltablastCommandline(_NcbiblastMain2SeqCommandline):
    """Create a commandline for the NCBI BLAST+ program deltablast (for proteins).
        
        This is a wrapper for the deltablast command line command included in the NCBI BLAST+ software (not present in the original BLAST)
        
        >>> from Bio.Blast.Applications import NcbideltablastCommandline
        >>> cline = NcbideltablastCommandline(query="rosemary.pro", db="nr",
        ...                               evalue=0.001, remote=True, ungapped=True)
        >>> cline
        NcbideltablastCommandline(cmd='deltablast', query='rosemary.pro', db='nr', evalue=0.001, remote=True, ungapped=True)
        >>> print(cline)
        deltablast -query rosemary.pro -db nr -evalue 0.001 -remote -ungapped
        
        You would typically run the command line with cline() or via the Python
        subprocess module, as described in the Biopython tutorial.
        """
    def __init__(self, cmd="deltablast", **kwargs):
        self.parameters = [
                           #General search options:
                           _Option(["-task", "task"],
                                   "Task to execute (string,  or deltablast).",
                                   checker_function=lambda value : value in ["deltablast"],
                                   equate=False),
                           _Option(["-matrix", "matrix"],
                                   "Scoring matrix name (default BLOSUM62)."),
                           _Option(["-threshold", "threshold"],
                                   "Minimum word score such that the word is added to the "
                                   "BLAST lookup table (float)",
                                   equate=False),
                           _Option(["-comp_based_stats", "comp_based_stats"],
                                   """Use composition-based statistics (string, default 2, i.e. True).
                                       
                                       0, F or f: no composition-based statistics
                                       2, T or t, D or d : Composition-based score adjustment as in
                                       Bioinformatics 21:902-911, 2005, conditioned on sequence properties
                                       
                                       Note that tblastn also supports values of 1 and 3.""",
                                   checker_function=lambda value : value in "0Ft2TtDd",
                                   equate=False),
                           #Query filtering options:
                           _Option(["-seg", "seg"],
                                   """Filter query sequence with SEG (string).
                                       
                                       Format: "yes", "window locut hicut", or "no" to disable.
                                       Default is "12 2.2 2.5""",
                                   equate=False),
                           #Extension options:
                           _Switch(["-ungapped", "ungapped"],
                                   "Perform ungapped alignment only?"),
                           #Miscellaneous options: FIXME: these are probably not valid args
                           _Switch(["-use_sw_tback", "use_sw_tback"],
                                   "Compute locally optimal Smith-Waterman alignments?"),
                           ]
        _NcbiblastMain2SeqCommandline.__init__(self, cmd, **kwargs)

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