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src/b/i/biopython-HEAD/Bio/PopGen/SimCoal/Controller.py   biopython(Download)
import os
import sys
from Bio.Application import AbstractCommandline, _Argument, _Option, _Switch
 
class SimCoalController(object):
    def __init__(self, fastsimcoal_dir = None, cmd = 'fastsimcoal', **kwargs):
        self.parameters = [
            _Option(["-i", "--ifile", "parfile"], "Name of the parameter file",
                    filename=True, equate=False, is_required=False,
                    checker_function=lambda x: isinstance(x, str)),
            _Option(["-n", "--numsims", "numsims"], "Number of simulations to perform",
                    filename=False, equate=False, is_required=True,
                    checker_function=lambda x: isinstance(x, int)),
            _Option(["-t", "--tfile", "tfile"], "Name of template parameter file",
                    filename=True, equate=False, is_required=False,
                    checker_function=lambda x: isinstance(x, str)),
            _Option(["-f", "--dfile", "dfile"], "Name of parameter definition file",
                    filename=True, equate=False, is_required=False,
                    checker_function=lambda x: isinstance(x, str)),

src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_samtools.py   biopython(Download)
from __future__ import print_function
__docformat__ = "epytext en"
from Bio.Application import _Option, _Argument, _Switch
from Bio.Application import AbstractCommandline, _ArgumentList
from Bio.Application import _StaticArgument
                    If @SQ header lines are absent,
                    the '-t' option is required."""),
            _Option(["-t", "t"],
                    """This file is TAB-delimited.
                    Each line must contain the reference name and the
                    filename=True, equate=False,
                    checker_function=lambda x: isinstance(x, str)),
            _Option(["-o", "o"], "Output file",
                    filename=True, equate=False,
                    checker_function=lambda x: isinstance(x, str)),
            _Option(["-f", "f"],
                    equate=False,
                    checker_function=lambda x: isinstance(x, int)),
            _Option(["-F", "F"],
                    "Skip alignments with bits present in INT",
                    equate=False,

src/b/i/biopython-1.63/Bio/Blast/Applications.py   biopython(Download)
from Bio import BiopythonDeprecationWarning
 
from Bio.Application import _Option, AbstractCommandline, _Switch
 
 
    def __init__(self, cmd="fastacmd", **kwargs):
        self.parameters = [
           _Option(["-d", "database"],
                   "The database to retrieve from.",
                   is_required=True,
                   equate=False),
           _Option(["-s", "search_string"],
           _Switch(["--help", "help"],
                    "Print USAGE, DESCRIPTION and ARGUMENTS description;  ignore other arguments."),
           _Option(["-d", "database"],
                   "The database to BLAST against.",
                   is_required=True,
                   equate=False),
           _Option(["-i", "infile"],

src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_bwa.py   biopython(Download)
__docformat__ = "epytext en"
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
from Bio.Application import _StaticArgument
 
                [
                    _StaticArgument("index"),
                    _Option(["-a", "a", "algorithm"],
                            """Algorithm for constructing BWT index.
 
                            checker_function=lambda x: x in ["is", "bwtsw"],
                            equate=False, is_required=True),
                    _Option(["-p", "p", "prefix"],
                            "Prefix of the output database [same as db filename]",
                            equate=False, is_required=False),
                    _Argument(["read_file"], "Read file name",
                              filename=True, is_required=True),
                    _Option(["-n", "n"],
                            "Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]",
                            checker_function=lambda x: isinstance(x, (int, float)),
                            equate=False),
                    _Option(["-o", "o"],

src/b/i/biopython-1.63/Bio/Sequencing/Applications/_bwa.py   biopython(Download)
__docformat__ = "epytext en"
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
from Bio.Application import _StaticArgument
 
                [
                    _StaticArgument("index"),
                    _Option(["-a", "a", "algorithm"],
                            """Algorithm for constructing BWT index.
 
                            checker_function=lambda x: x in ["is", "bwtsw"],
                            equate=False, is_required=True),
                    _Option(["-p", "p", "prefix"],
                            "Prefix of the output database [same as db filename]",
                            equate=False, is_required=False),
                    _Argument(["read_file"], "Read file name",
                              filename=True, is_required=True),
                    _Option(["-n", "n"],
                            "Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]",
                            checker_function=lambda x: isinstance(x, (int, float)),
                            equate=False),
                    _Option(["-o", "o"],

src/b/i/biopython-HEAD/Bio/Align/Applications/_TCoffee.py   biopython(Download)
__docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
from Bio.Application import _Option, _Switch, AbstractCommandline
 
 
    def __init__(self, cmd="t_coffee", **kwargs):
        self.parameters = [
           _Option(["-output", "output"],
                   """Specify the output type.
                   One (or more separated by a comma) of:
                   """,  # TODO - Can we read the PHYLIP output?
                   equate=False),
           _Option(["-infile", "infile"],
                   "Specify the input file.",
                   filename=True,
                   is_required=True,
                   equate=False),
           #Indicates the name of the alignment output by t_coffee. If the
           #default is used, the alignment is named <your sequences>.aln
           _Option(["-outfile", "outfile"],
           _Switch(["-convert", "convert"],
                   "Specify you want to perform a file conversion"),
           _Option(["-type", "type"],
                   "Specify the type of sequence being aligned",
                   checker_function=lambda x: x in self.SEQ_TYPES,

src/b/i/biopython-1.63/Bio/Align/Applications/_TCoffee.py   biopython(Download)
__docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
from Bio.Application import _Option, _Switch, AbstractCommandline
 
 
    def __init__(self, cmd="t_coffee", **kwargs):
        self.parameters = [
           _Option(["-output", "output"],
                   """Specify the output type.
                   One (or more separated by a comma) of:
                   """,  # TODO - Can we read the PHYLIP output?
                   equate=False),
           _Option(["-infile", "infile"],
                   "Specify the input file.",
                   filename=True,
                   is_required=True,
                   equate=False),
           #Indicates the name of the alignment output by t_coffee. If the
           #default is used, the alignment is named <your sequences>.aln
           _Option(["-outfile", "outfile"],
           _Switch(["-convert", "convert"],
                   "Specify you want to perform a file conversion"),
           _Option(["-type", "type"],
                   "Specify the type of sequence being aligned",
                   checker_function=lambda x: x in self.SEQ_TYPES,

src/b/i/biopython-HEAD/Bio/Phylo/Applications/_Phyml.py   biopython(Download)
from Bio._py3k import basestring
 
from Bio.Application import _Option, _Switch, AbstractCommandline
 
 
    def __init__(self, cmd='phyml', **kwargs):
        self.parameters = [
            _Option(['-i', '--input', 'input'],
                """Name of the nucleotide or amino-acid sequence file in PHYLIP
                format.""",
                ),
 
            _Option(['-d', '--datatype', 'datatype'],
                """Data type is 'nt' for nucleotide (default) and 'aa' for
                amino-acid sequences.""",
                ),
 
            _Option(['-n', '--multiple', 'multiple'],
                "Number of data sets to analyse (integer).",
                checker_function=(lambda x:
                ),
 
            _Option(['-b', '--bootstrap', 'bootstrap'],
                """Number of bootstrap replicates, if value is > 0.
 

src/b/i/biopython-1.63/Bio/Phylo/Applications/_Phyml.py   biopython(Download)
from Bio._py3k import basestring
 
from Bio.Application import _Option, _Switch, AbstractCommandline
 
 
    def __init__(self, cmd='phyml', **kwargs):
        self.parameters = [
            _Option(['-i', '--input', 'input'],
                """Name of the nucleotide or amino-acid sequence file in PHYLIP
                format.""",
                ),
 
            _Option(['-d', '--datatype', 'datatype'],
                """Data type is 'nt' for nucleotide (default) and 'aa' for
                amino-acid sequences.""",
                ),
 
            _Option(['-n', '--multiple', 'multiple'],
                "Number of data sets to analyse (integer).",
                checker_function=(lambda x:
                ),
 
            _Option(['-b', '--bootstrap', 'bootstrap'],
                """Number of bootstrap replicates, if value is > 0.
 

src/b/i/biopython-HEAD/Bio/Emboss/Applications.py   biopython(Download)
from __future__ import print_function
 
from Bio.Application import _Option, _Switch, AbstractCommandline
 
 
    def __init__(self, cmd=None, **kwargs):
        assert cmd is not None
        extra_parameters = [
            _Option(["-outfile", "outfile"],
                    "Output filename",
    def __init__(self, cmd="eprimer3", **kwargs):
        self.parameters = [
           _Option(["-sequence", "sequence"],
                   "Sequence to choose primers from.",
                   is_required=True),
           _Option(["-task", "task"],
                   "Tell eprimer3 what task to perform."),
           _Option(["-hybridprobe", "hybridprobe"],

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