Logo Search packages:      
Sourcecode: python-biopython version File versions

Applications.py

00001 """Code to interact with and run various EMBOSS programs.

These classes follow the AbstractCommandline interfaces for running
programs.
"""

from Bio import Application
from Bio.Application import _Option, _Argument

00010 class Primer3Commandline(Application.AbstractCommandline):
    """Commandline object for the Primer3 interface from EMBOSS.
    """
    def __init__(self, cmd = "eprimer3"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = \
          [_Option(["-sequence"], ["input"], None, 1, 
                   "Sequence to choose primers from"),
           _Option(["-outfile"], ["output", "file"], None, 1,
                   "Output file name"),
           _Option(["-task"], ["input"], None, 0),
           _Option(["-numreturn"], ["input"], None, 0),
           _Option(["-includedregion"], ["input"], None, 0),
           _Option(["-target"], ["input"], None, 0),
           _Option(["-excludedregion"], ["input"], None, 0),
           _Option(["-forwardinput"], ["input"], None, 0),
           _Option(["-reverseinput"], ["input"], None, 0),
           _Option(["-gcclamp"], ["input"], None, 0),
           _Option(["-osize"], ["input"], None, 0),
           _Option(["-minsize"], ["input"], None, 0),
           _Option(["-maxsize"], ["input"], None, 0),
           _Option(["-otm"], ["input"], None, 0),
           _Option(["-mintm"], ["input"], None, 0),
           _Option(["-maxtm"], ["input"], None, 0),
           _Option(["-maxdifftm"], ["input"], None, 0),
           _Option(["-ogcpercent"], ["input"], None, 0),
           _Option(["-mingc"], ["input"], None, 0),
           _Option(["-maxgc"], ["input"], None, 0),
           _Option(["-saltconc"], ["input"], None, 0),
           _Option(["-dnaconc"], ["input"], None, 0),
           _Option(["-maxployx"], ["input"], None, 0),
           _Option(["-productosize"], ["input"], None, 0),
           _Option(["-productsizerange"], ["input"], None, 0),
           _Option(["-productotm"], ["input"], None, 0),
           _Option(["-productmintm"], ["input"], None, 0),
           _Option(["-productmaxtm"], ["input"], None, 0),
           _Option(["-oligoexcluderegion"], ["input"], None, 0),
           _Option(["-oligoinput"], ["input"], None, 0),
           _Option(["-oligosize"], ["input"], None, 0),
           _Option(["-oligominsize"], ["input"], None, 0),
           _Option(["-oligomaxsize"], ["input"], None, 0),
           _Option(["-oligotm"], ["input"], None, 0),
           _Option(["-oligomintm"], ["input"], None, 0),
           _Option(["-oligomaxtm"], ["input"], None, 0),
           _Option(["-oligoogcpercent"], ["input"], None, 0),
           _Option(["-oligomingc"], ["input"], None, 0),
           _Option(["-oligomaxgc"], ["input"], None, 0),
           _Option(["-oligosaltconc"], ["input"], None, 0),
           _Option(["-oligodnaconc"], ["input"], None, 0),
           _Option(["-oligoselfany"], ["input"], None, 0),
           _Option(["-oligoselfend"], ["input"], None, 0),
           _Option(["-oligomaxpolyx"], ["input"], None, 0)]

00065 class PrimerSearchCommandline(Application.AbstractCommandline):
    """Commandline object for the primersearch program from EMBOSS.
    """
    def __init__(self, cmd = "primersearch"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = \
         [_Option(["-sequences"], ["input"], None, 1,
                  "Sequence to look for the primer pairs in."),
          _Option(["-primers"], ["input", "file"], None, 1,
                  "File containing the primer pairs to search for."),
          _Option(["-out"], ["output", "file"], None, 1,
                  "Name of the output file."),
          _Option(["-mismatchpercent"], ["input"], None, 1,
                  "Allowed percentage mismatch.")]

00082 class EProtDistCommandline(Application.AbstractCommandline):
    """Commandline object for the eprotdist program from EMBOSS.

    This is an EMBOSS wrapper around protdist from PHYLIP.
    """
    def __init__(self, cmd = "eprotdist"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = \
         [_Option(["-msf"], ["input"], None, 1,
                  "File containing sequences"),
          _Option(["-outfile"], ["output"], None, 1,
                  "Output file name"),
          _Option(["-method"], ["input"], None, 1,
                  "Choose the method to use"),
          _Option(["-categ"], ["input"], None, 0,
                  "Choose the categorie to use"),
          _Option(["-gencode"], ["input"], None, 0,
                  "Which genetic code"),
          _Option(["-prob"], ["input"], None, 0,
                  "Prob change category (1.0=easy)"),
          _Option(["-tranrate"], ["input"], None, 0,
                  "Transition/transversion ratio"),
          _Option(["-freqa"], ["input"], None, 0,
                  "Frequency for A"),
          _Option(["-freqc"], ["input"], None, 0,
                  "Frequency for C"),
          _Option(["-freqg"], ["input"], None, 0,
                  "Frequency for G"),
          _Option(["-freqt"], ["input"], None, 0,
                  "Frequency for T"),
          _Option(["-printdata"], ["input"], None, 0,
                  "Print out the data at start of run"),
          _Option(["-progress"], ["input"], None, 0,
                  "Print indications of progress of run"),
          _Option(["-basefrequency"], ["input"], None, 0,
                  "Use empirical base frequencies")]

00121 class ENeighborCommandline(Application.AbstractCommandline):
    """Commandline object for the eneighbor program from EMBOSS.

    This is an EMBOSS wrapper around neighbor from PHYLIP.
    """
    def __init__(self, cmd = "eneighbor"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = \
         [_Option(["-infile"], ["input"], None, 1,
                  "infile value"),
          _Option(["-outfile"], ["output"], None, 1,
                  "Output file name"),
          _Option(["-trout"], ["input"], None, 1,
                  "Create a tree file"),
          _Option(["-treefile"], ["input"], None, 1,
                  "Tree file name"),
          _Option(["-nj"], ["input"], None, 1,
                  "Neighbor-joining"),
          _Option(["-noog"], ["input"], None, 1,
                  "Outgroup root"),
          _Option(["-outgnum"], ["input"], None, 0,
                  "number of the outgroup"),
          _Option(["-randseed"], ["input"], None, 0,
                  "Random number seed (must be odd)"),
          _Option(["-datasets"], ["input"], None, 0,
                  "How many data sets"),
          _Option(["-drawtree"], ["input"], None, 0,
                  "Draw tree"),
          _Option(["-lt"], ["input"], None, 0,
                  "Lower-triangular data matrix"),
          _Option(["-ut"], ["input"], None, 0,
                  "Upper-triangular data matrix"),
          _Option(["-sr"], ["input"], None, 0,
                  "Subreplicates"),
          _Option(["-random"], ["input"], None, 0,
                  "Randomize input order of species"),
          _Option(["-multsets"], ["input"], None, 0,
                  "Analyze multiple data sets"),
          _Option(["-printdata"], ["input"], None, 0,
                  "Print out the data at start of run"),
          _Option(["-progress"], ["input"], None, 0,
                  "Print indications of progress of run")]

00166 class EProtParsCommandline(Application.AbstractCommandline):
    """Commandline object for the eprotpars program from EMBOSS.

    This is an EMBOSS wrapper around protpars from PHYLIP.
    """
    def __init__(self, cmd = "eprotpars"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = \
         [_Option(["-msf"], ["input", "file"], None, 1,
                  "Sequences file to be read in"),
          _Option(["-outfile"], ["output", "file"], None, 1,
                  "Output file"),
          _Option(["-besttree"], ["input"], None, 0,
                  "Search for the best tree"),
          _Option(["-random"], ["input"], None, 0,
                  "Randomize input order of species"),
          _Option(["-norandom"], ["input"], None, 0,
                  "Do not randomize input order of species"),
          _Option(["-randseed"], ["input"], None, 0,
                  "Random number seed (must be odd)"),
          _Option(["-randtimes"], ["input"], None, 0,
                  "How many times to randomize"),
          _Option(["-og"], ["input"], None, 0,
                  "Use an outgroup root"),
          _Option(["-noog"], ["input"], None, 0,
                  "Do not use an outgroup root"),
          _Option(["-outgnum"], ["input"], None, 0,
                  "Number of the outgroup"),
          _Option(["-thresh"], ["input"], None, 0,
                  "Use Threshold parsimony"),
          _Option(["-valthresh"], ["input"], None, 0,
                  "threshold value"),
          _Option(["-printdata"], ["input"], None, 0,
                  "Print out the data at start of run"),
          _Option(["-progress"], ["input"], None, 0,
                  "Print indications of progress of run"),
          _Option(["-steps"], ["input"], None, 0,
                  "Print out steps in each site"),
          _Option(["-seqatnodes"], ["input"], None, 0,
                  "Print sequences at all nodes of tree"),
          _Option(["-drawtree"], ["input"], None, 0,
                  "Draw tree"),
          _Option(["-trout"], ["input"], None, 0,
                  "Create a tree file"),
          _Option(["-notrout"], ["input"], None, 0,
                  "Do not create a tree file"),
          _Option(["-treefile"], ["output", "file"], None, 0,
                  "Output treefile name")]

00217 class EConsenseCommandline(Application.AbstractCommandline):
    """Commandline object for the econsense program from EMBOSS.

    This is an EMBOSS wrapper around consense from PHYLIP.
    """
    def __init__(self, cmd = "econsense"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = \
         [_Option(["-infile"], ["input", "file"], None, 1,
                  "file to read in (New Hampshire standard form)"),
          _Option(["-outfile"], ["output", "file"], None, 1,
                  "Output file name"),
          _Option(["-notrout"], ["input"], None, 0,
                  "Do not create a tree file"),
          _Option(["-trout"], ["input"], None, 0,
                  "Create a tree file"),
          _Option(["-treefile"], ["output", "file"], None, 0,
                  "tree file name"),
          _Option(["-noog"], ["input"], None, 0,
                  "Do not use an outgroup"),
          _Option(["-og"], ["input"], None, 0,
                  "Use an outgroup"),
          _Option(["-outgnum"], ["input"], None, 0,
                  "number of the outgroup"),
          _Option(["-nodrawtree"], ["input"], None, 0,
                  "Do not draw a tree"),
          _Option(["-drawtree"], ["input"], None, 0,
                  "Draw tree"),
          _Option(["-root"], ["input"], None, 0,
                  "Trees to be treated as Rooted"),
          _Option(["-progress"], ["input"], None, 0,
                  "Print indications of the progress of run"),
          _Option(["-noprintsets"], ["input"], None, 0,
                  "Do not print out the sets of species"),
          _Option(["-printsets"], ["input"], None, 0,
                  "Print out the sets of species")]

00256 class ESeqBootCommandline(Application.AbstractCommandline):
    """Commandline object for the eseqboot program from EMBOSS.

    This is an EMBOSS wrapper around seqboot from PHYLIP.
    """
    def __init__(self, cmd = "eseqboot"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = \
         [_Option(["-datafile"], ["input", "file"], None, 1,
                  "Input file"),
          _Option(["-outfile"], ["output", "file"], None, 1,
                  "Output file name"),
          _Option(["-randseed"], ["input"], None, 1,
                  "Random number seed (must be odd)"),
          _Option(["-method"], ["input"], None, 1,
                  "Choose the method"),
          _Option(["-test"], ["input"], None, 1,
                  "Choose test"),
          _Option(["-reps"], ["input"], None, 1,
                  "How many replicates"),
          _Option(["-inter"], ["input"], None, 0,
                  "Interleaved input"),
          _Option(["-enzymes"], ["input"], None, 0,
                  "Present in input file"),
          _Option(["-all"], ["input"], None, 0,
                  "All alleles present at each locus"),
          _Option(["-printdata"], ["input"], None, 0,
                  "Print out the data at start of run"),
          _Option(["-progress"], ["input"], None, 0,
                  "Print indications of progress of run")]

00289 class WaterCommandline(Application.AbstractCommandline):
    """Commandline object for the water program from EMBOSS.
    """
    def __init__(self, cmd = "water"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = \
         [_Option(["-asequence"], ["input", "file"], None, 1,
                  "First sequence to align"),
         _Option(["-bsequence"], ["input", "file"], None, 1,
                  "Second sequence to align"),
         _Option(["-gapopen"], ["input"], None, 1,
                 "Gap open penalty"),
         _Option(["-gapextend"], ["input"], None, 1,
                 "Gap extension penalty"),
         _Option(["-outfile"], ["output", "file"], None, 1,
                 "Output file for the alignment"),
         _Option(["-datafile"], ["input", "file"], None, 0,
                 "Matrix file"),
         _Option(["-similarity"], ["input"], None, 0,
                 "Display percent identity and similarity"),
         _Option(["-nosimilarity"], ["input"], None, 0,
                 "Do not display percent identity and similarity"),
         _Option(["-aformat"], ["input"], None, 0,
                 "Display output in a different specified output format")]

00316 class FuzznucCommandline(Application.AbstractCommandline):
    """Commandline object for the fuzznuc program from EMBOSS.
    """
    def __init__(self, cmd = "fuzznuc"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = [
         _Option(["-sequence"], ["input"], None, 1,
                 "Sequence database USA"),
         _Option(["-pattern"], ["input"], None, 1,
                 "Search pattern, using standard IUPAC one-letter codes"),
         _Option(["-mismatch"], ["input"], None, 1,
                 "Number of mismatches"),
         _Option(["-outfile"], ["output", "file"], None, 1,
                 "Output report file name"),
         _Option(["-complement"], ["input"], None, 0,
                 "Search complementary strand"),
         _Option(["-rformat"], ["input"], None, 0,
                 "Specify the report format to output in.")]

00337 class Est2GenomeCommandline(Application.AbstractCommandline):
    """Commandline object for the est2genome program from EMBOSS.
    """
    def __init__(self, cmd = "est2genome"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = [
         _Option(["-est"], ["input"], None, 1,
                 "EST sequence(s)"),
         _Option(["-genome"], ["input"], None, 1,
                 "Genomic sequence"),
         _Option(["-outfile"], ["output", "file"], None, 1,
                 "Output file name"),
         _Option(["-match"], ["input"], None, 0, 
                 "Score for matching two bases"),
         _Option(["-mismatch"], ["input"], None, 0,
                 "Cost for mismatching two bases"),
         _Option(["-gappenalty"], ["input"], None, 0,
                 "Cost for deleting a single base in either sequence, " + \
                 "excluding introns"),
         _Option(["-intronpenalty"], ["input"], None, 0,
                 "Cost for an intron, independent of length."),
         _Option(["-splicepenalty"], ["input"], None, 0,
                 "Cost for an intron, independent of length " + \
                 "and starting/ending on donor-acceptor sites"),
         _Option(["-minscore"], ["input"], None, 0,
                 "Exclude alignments with scores below this threshold score."),
         _Option(["-reverse"], ["input"], None, 0,
                 "Reverse the orientation of the EST sequence"),
         _Option(["-splice"], ["input"], None, 0,
                 "Use donor and acceptor splice sites."),
         _Option(["-mode"], ["input"], None, 0,
                 "This determines the comparion mode. 'both', 'forward' " + \
                 "'reverse'"),
         _Option(["-best"], ["input"], None, 0,
                 "You can print out all comparisons instead of just the best"),
         _Option(["-space"], ["input"], None, 0,
                 "for linear-space recursion."),
         _Option(["-shuffle"], ["input"], None, 0,
                 "Shuffle"),
         _Option(["-seed"], ["input"], None, 0,
                 "Random number seed"),
         _Option(["-align"], ["input"], None, 0,
                 "Show the alignment."),
         _Option(["-width"], ["input"], None, 0,
                 "Alignment width")
        ]

00386 class ETandemCommandline(Application.AbstractCommandline):
    """Commandline object for the etandem program from EMBOSS.
    """
    def __init__(self, cmd = "etandem"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = [
         _Option(["-sequence"], ["input", "file"], None, 1,
                 "Sequence"),
         _Option(["-minrepeat"], ["input"], None, 1,
                 "Minimum repeat size"),
         _Option(["-maxrepeat"], ["input"], None, 1,
                 "Maximum repeat size"),
         _Option(["-outfile"], ["output", "file"] , None, 1,
                 "Output report file name"),
         _Option(["-threshold"], ["input"], None, 0,
                 "Threshold score"),
         _Option(["-mismatch"], ["input"], None, 0,
                   "Allow N as a mismatch"),
         _Option(["-uniform"], ["input"], None, 0,
                   "Allow uniform consensus"),
         _Option(["-rformat"], ["output"], None, 0,
                 "Output report format")]

00411 class TranalignCommandline(Application.AbstractCommandline):
    """Commandline object for the tranalign program from EMBOSS.
    """
    def __init__(self, cmd = "tranalign"):
        Application.AbstractCommandline.__init__(self)
        self.program_name = cmd

        self.parameters = [
         _Option(["-asequence"], ["input", "file"], None, 1,
                 "Nucleotide sequences to be aligned."),
         _Option(["-bsequence"], ["input", "file"], None, 1,
                 "Protein sequence alignment"),
         _Option(["-outseq"], ["output", "file"], None, 1,
                 "Output sequence file."),
         _Option(["-table"], ["input"], None, 0,
                 "Code to use")]

Generated by  Doxygen 1.6.0   Back to index