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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
    def __init__(self, cmd="samtools", **kwargs):
        self.program_name = cmd
        self.parameters = [
            _StaticArgument("view"),
            _Switch(["-b", "b"], "Output in the BAM format"),
            _Switch(["-c", "c"],
                    All filter options, such as '-f', '-F' and '-q',
                    are taken into account"""),
            _Switch(["-h", "h"], "Include the header in the output"),
            _Switch(["-u", "u"],
                    """Output uncompressed BAM.

src/b/i/biopython-HEAD/Bio/Align/Applications/_Dialign.py   biopython(Download)
__docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
 
 
    def __init__(self, cmd="dialign2-2", **kwargs):
        self.program_name = cmd
        self.parameters = \
            [
            _Switch(["-afc", "afc"],
                    "Creates additional output file '*.afc' "
                    "containing data of all fragments considered "
                    "for alignment WARNING: this file can be HUGE !"),
            _Switch(["-afc_v", "afc_v"],
                    "Like '-afc' but verbose: fragments are explicitly "
                    "printed. WARNING: this file can be EVEN BIGGER !"),
            _Switch(["-anc", "anc"],
                    "Anchored alignment. Requires a file <seq_file>.anc "
                    "containing anchor points."),
            _Switch(["-cs", "cs"],

src/b/i/biopython-1.63/Bio/Align/Applications/_Dialign.py   biopython(Download)
__docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
 
 
    def __init__(self, cmd="dialign2-2", **kwargs):
        self.program_name = cmd
        self.parameters = \
            [
            _Switch(["-afc", "afc"],
                    "Creates additional output file '*.afc' "
                    "containing data of all fragments considered "
                    "for alignment WARNING: this file can be HUGE !"),
            _Switch(["-afc_v", "afc_v"],
                    "Like '-afc' but verbose: fragments are explicitly "
                    "printed. WARNING: this file can be EVEN BIGGER !"),
            _Switch(["-anc", "anc"],
                    "Anchored alignment. Requires a file <seq_file>.anc "
                    "containing anchor points."),
            _Switch(["-cs", "cs"],

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):
                    filename=False, equate=False, is_required=False,
                    checker_function=lambda x: isinstance(x, int)),
            _Switch(["-g", "--genotypic", "genotypic"], "Generates Arlequin projects with genotypic data"),
            _Switch(["-p", "--phased", "phased"], "Specifies that phase is known in Arlequin output"),
            _Option(["-s", "--dnatosnp", "dnatosnp"],
                    """"Output DNA as SNP data (0: ancestral, 1: derived
                    and specify maximum no. SNPs to output.""",
                    filename=False, equate=False, is_required=False,
                    checker_function=lambda x: isinstance(x, int)),
            _Switch(["-S", "--allsites", "allsites"],
            _Switch(["-S", "--allsites", "allsites"],
                    """Output the whole DNA sequence, including monomorphic sites"""),
            _Switch(["-I", "--inf", "inf"],
                    """Generates DNA mutations according to an
                    infinite sites (IS) mutation model."""),

src/b/i/biopython-HEAD/Bio/Align/Applications/_Clustalw.py   biopython(Download)
 
import os
from Bio.Application import _Option, _Switch, AbstractCommandline
 
 
                    filename=True),
            ################## VERBS (do things) #############################
            _Switch(["-options", "-OPTIONS", "OPTIONS", "options"],
                    "List the command line parameters"),
            _Switch(["-help", "-HELP", "HELP", "help"],
                    "Outline the command line params."),
            _Switch(["-check", "-CHECK", "CHECK", "check"],
                    "Outline the command line params."),
            _Switch(["-fullhelp", "-FULLHELP", "FULLHELP", "fullhelp"],

src/b/i/biopython-1.63/Bio/Align/Applications/_Clustalw.py   biopython(Download)
 
import os
from Bio.Application import _Option, _Switch, AbstractCommandline
 
 
                    filename=True),
            ################## VERBS (do things) #############################
            _Switch(["-options", "-OPTIONS", "OPTIONS", "options"],
                    "List the command line parameters"),
            _Switch(["-help", "-HELP", "HELP", "help"],
                    "Outline the command line params."),
            _Switch(["-check", "-CHECK", "CHECK", "check"],
                    "Outline the command line params."),
            _Switch(["-fullhelp", "-FULLHELP", "FULLHELP", "fullhelp"],

src/b/i/biopython-HEAD/Bio/Blast/Applications.py   biopython(Download)
from __future__ import print_function
 
from Bio.Application import _Option, AbstractCommandline, _Switch
 
 
    def __init__(self, cmd=None, **kwargs):
        assert cmd is not None
        extra_parameters = [
            #Core:
            _Switch(["-h", "h"],
                    "Print USAGE and DESCRIPTION;  ignore other arguments."),
            _Switch(["-help", "help"],
                    "Print USAGE, DESCRIPTION and ARGUMENTS description; "
                    "ignore other arguments."),
            _Switch(["-version", "version"],
                    equate=False),
                    #TODO - Document and test the column options
            _Switch(["-show_gis", "show_gis"],
                    "Show NCBI GIs in deflines?"),
            _Option(["-num_descriptions", "num_descriptions"],

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
 
                            equate=False, is_required=False),
                    _Argument(["infile"], "Input file name", filename=True, is_required=True),
                    _Switch(["-c", "c"],
                            "Build color-space index. The input fasta should be in nucleotide space.")
                ]
                            checker_function=lambda x: isinstance(x, int),
                            equate=False),
                    _Switch(["-c", "c"],
                            "Reverse query but not complement it, which is required for alignment in the color space."),
                    _Switch(["-N", "N"],
                            "Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default."),
                    _Switch(["-I", "I"],

src/b/i/biopython-HEAD/Bio/Align/Applications/_Prank.py   biopython(Download)
__docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
from Bio.Application import _Option, _Switch, AbstractCommandline
 
 
                    "7. Fitch      	17. PAUP/NEXUS",
                    checker_function=lambda x: x in OUTPUT_FORMAT_VALUES),
            _Switch(["-noxml", "noxml"],
                    "Do not output XML files "
                    "(PRANK versions earlier than v.120626)"),
            _Switch(["-notree", "notree"],
                    "Do not output dnd tree files "
                    "(PRANK versions earlier than v.120626)"),
            _Switch(["-showxml", "showxml"],
            _Switch(["-showxml", "showxml"],
                    "Output XML files (PRANK v.120626 and later)"),
            _Switch(["-showtree", "showtree"],
                    "Output dnd tree files (PRANK v.120626 and later)"),
            _Switch(["-shortnames", "shortnames"],

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
 
                            equate=False, is_required=False),
                    _Argument(["infile"], "Input file name", filename=True, is_required=True),
                    _Switch(["-c", "c"],
                            "Build color-space index. The input fasta should be in nucleotide space.")
                ]
                            checker_function=lambda x: isinstance(x, int),
                            equate=False),
                    _Switch(["-c", "c"],
                            "Reverse query but not complement it, which is required for alignment in the color space."),
                    _Switch(["-N", "N"],
                            "Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default."),
                    _Switch(["-I", "I"],

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