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src/b/i/biopython-1.63/Bio/Blast/Applications.py   biopython(Download)
                   equate=False)
          ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
            #Should we raise an error?  The subclass should have set this up!
            self.parameters = extra_parameters
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
    def _validate(self):
            #Should we raise an error?  The subclass should have set this up!
            self.parameters = extra_parameters
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
    def _validate_incompatibilities(self, incompatibles):

src/b/i/biopython-HEAD/Bio/Blast/Applications.py   biopython(Download)
            #Should we raise an error?  The subclass should have set this up!
            self.parameters = extra_parameters
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
    def _validate_incompatibilities(self, incompatibles):

src/b/i/biopython-HEAD/Bio/PopGen/GenePop/Controller.py   biopython(Download)
            _Argument(["GeographicScale"], "Log or Linear"),
        ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
        self.set_parameter("mode", "Mode=Batch")
 

src/b/i/biopython-1.63/Bio/PopGen/GenePop/Controller.py   biopython(Download)
                    "Log or Linear"),
        ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
        self.set_parameter("mode", "Mode=Batch")
 

src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_samtools.py   biopython(Download)
            _Argument(["region"], "Region", is_required=False),
        ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
 
        ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                      filename=True, is_required=True)
        ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
 
        ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                      filename=True, is_required=True)
        ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 

src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_bwa.py   biopython(Download)
                            "Build color-space index. The input fasta should be in nucleotide space.")
                ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                            "When -b is specified, only use the second read in a read pair in mapping.")
                  ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                            equate=False),
                  ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                            equate=False),
                  ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                            equate=False),
                  ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 

src/b/i/biopython-1.63/Bio/Sequencing/Applications/_bwa.py   biopython(Download)
                            "Build color-space index. The input fasta should be in nucleotide space.")
                ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                            "When -b is specified, only use the second read in a read pair in mapping.")
                  ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                            equate=False),
                  ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                            equate=False),
                  ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                            equate=False),
                  ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 

src/b/i/biopython-HEAD/Bio/motifs/applications/_alignace.py   biopython(Download)
                    checker_function=lambda x: isinstance(x, int)),
          ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                        filename=True),
          ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 

src/b/i/biopython-1.63/Bio/motifs/applications/_alignace.py   biopython(Download)
                    checker_function=lambda x: isinstance(x, int)),
          ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 
                        filename=True),
          ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 

src/b/i/biopython-HEAD/Bio/Sequencing/Applications/_Novoalign.py   biopython(Download)
                    equate=False),
            ]
        AbstractCommandline.__init__(self, cmd, **kwargs)
 
 

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