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"""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
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)]
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.")]
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")]
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")]
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")]
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")]
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")]
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")]
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.")]
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")
]
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")]
class EInvertedCommandline(Application.AbstractCommandline):
"""Commandline object for the einverted program from EMBOSS.
"""
def __init__(self, cmd = "einverted"):
Application.AbstractCommandline.__init__(self)
self.program_name = cmd
self.parameters = [
_Option(["-sequence"], ["input", "file"], None, 1,
"Sequence"),
_Option(["-gap"], ["input", "file"], None, 1,
"Gap penalty"),
_Option(["-threshold"], ["input"], None, 1,
"Minimum score threshold"),
_Option(["-match"], ["input"], None, 1,
"Match score"),
_Option(["-mismatch"], ["input"], None, 1,
"Mismatch score"),
_Option(["-outfile"], ["output", "file"] , None, 1,
"Output report file name"),
_Option(["-maxrepeat"], ["input"], None, 0,
"Maximum separation between the start and end of repeat"),
]
class PalindromeCommandline(Application.AbstractCommandline):
"""Commandline object for the palindrome program from EMBOSS.
"""
def __init__(self, cmd = "palindrome"):
Application.AbstractCommandline.__init__(self)
self.program_name = cmd
self.parameters = [
_Option(["-sequence"], ["input", "file"], None, 1,
"Sequence"),
_Option(["-minpallen"], ["input"], None, 1,
"Minimum palindrome length"),
_Option(["-maxpallen"], ["input"], None, 1,
"Maximum palindrome length"),
_Option(["-gaplimit"], ["input"], None, 1,
"Maximum gap between repeats"),
_Option(["-nummismatches"], ["input"], None, 1,
"Number of mismatches allowed"),
_Option(["-overlap"], ["input"], None, 1,
"Report overlapping matches"),
_Option(["-outfile"], ["output", "file"] , None, 1,
"Output report file name"),
]
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")]
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