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All Samples(27)  |  Call(24)  |  Derive(0)  |  Import(3)

src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_samtools.py   biopython(Download)
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"),
    def __init__(self, cmd="samtools", **kwargs):
        self.program_name = cmd
        self.parameters = [
            _StaticArgument("mpileup"),
            _Switch(["-E", "E"],
    def __init__(self, cmd="samtools", **kwargs):
        self.program_name = cmd
        self.parameters = [
            _StaticArgument("reheader"),
            _Argument(["input_header", "header_sam", "sam_file"],
    def __init__(self, cmd="samtools", **kwargs):
        self.program_name = cmd
        self.parameters = [
            _StaticArgument("cat"),
            _Option(["-h", "h"], "Header SAM file",

src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_bwa.py   biopython(Download)
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
from Bio.Application import _StaticArgument
 
 
    def __init__(self, cmd="bwa", **kwargs):
        self.program_name = cmd
        self.parameters = \
                [
                    _StaticArgument("index"),
    def __init__(self, cmd="bwa", **kwargs):
        self.program_name = cmd
        self.parameters = \
                [
                    _StaticArgument("aln"),
    def __init__(self, cmd="bwa", **kwargs):
        self.program_name = cmd
        self.parameters = \
                [
                    _StaticArgument("samse"),
    def __init__(self, cmd="bwa", **kwargs):
        self.program_name = cmd
        self.parameters = \
                [
                    _StaticArgument("sampe"),

src/b/i/biopython-1.63/Bio/Sequencing/Applications/_bwa.py   biopython(Download)
 
from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
from Bio.Application import _StaticArgument
 
 
    def __init__(self, cmd="bwa", **kwargs):
        self.program_name = cmd
        self.parameters = \
                [
                    _StaticArgument("index"),
    def __init__(self, cmd="bwa", **kwargs):
        self.program_name = cmd
        self.parameters = \
                [
                    _StaticArgument("aln"),
    def __init__(self, cmd="bwa", **kwargs):
        self.program_name = cmd
        self.parameters = \
                [
                    _StaticArgument("samse"),
    def __init__(self, cmd="bwa", **kwargs):
        self.program_name = cmd
        self.parameters = \
                [
                    _StaticArgument("sampe"),