Class AbstractCommandline

Executes the command, waits for it to finish, and returns output.

        Runs the command line tool and waits for it to finish. If it returns
        a non-zero error level, an exception is raised. Otherwise two strings
        are returned containing stdout and stderr.

        The optional stdin argument should be a string of data which will be
        passed to the tool as standard input.

        The optional stdout and stderr argument are treated as a booleans, and
        control if the output should be captured (True, default), or ignored
        by sending it to /dev/null to avoid wasting memory (False). In the
        later case empty string(s) are returned.

        The optional cwd argument is a string giving the working directory
        to run the command from. See Python's subprocess module documentation
        for more details.

        The optional env argument is a dictionary setting the environment
        variables to be used in the new process. By default the current
        process' environment variables are used. See Python's subprocess
        module documentation for more details.

        Default example usage:

        from Bio.Emboss.Applications import WaterCommandline
        water_cmd = WaterCommandline(gapopen=10, gapextend=0.5,
                                     stdout=True, auto=True,
                                     asequence="a.fasta", bsequence="b.fasta")
        print "About to run:
%s" % water_cmd
        std_output, err_output = water_cmd()

        This functionality is similar to subprocess.check_output() added in
        Python 2.7. In general if you require more control over running the
        command, use subprocess directly.

        As of Biopython 1.56, when the program called returns a non-zero error
        level, a custom ApplicationError exception is raised. This includes
        any stdout and stderr strings captured as attributes of the exception
        object, since they may be useful for diagnosing what went wrong.
        

Create a new instance of a command line wrapper object.

Overrides: object.__init__

Return a representation of the command line object for debugging.

e.g.
>>> from Bio.Emboss.Applications import WaterCommandline
>>> cline = WaterCommandline(gapopen=10, gapextend=0.5)
>>> cline.asequence = "asis:ACCCGGGCGCGGT"
>>> cline.bsequence = "asis:ACCCGAGCGCGGT"
>>> cline.outfile = "temp_water.txt"
>>> print cline
water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5
>>> cline
WaterCommandline(cmd='water', outfile='temp_water.txt', asequence='asis:ACCCGGGCGCGGT', bsequence='asis:ACCCGAGCGCGGT', gapopen=10, gapextend=0.5)

Overrides: object.__repr__

Set attribute name to value (PRIVATE).

This code implements a workaround for a user interface issue.
Without this __setattr__ attribute-based assignment of parameters
will silently accept invalid parameters, leading to known instances
of the user assuming that parameters for the application are set,
when they are not.

>>> from Bio.Emboss.Applications import WaterCommandline
>>> cline = WaterCommandline(gapopen=10, gapextend=0.5, stdout=True)
>>> cline.asequence = "a.fasta"
>>> cline.bsequence = "b.fasta"
>>> cline.csequence = "c.fasta"
Traceback (most recent call last):
...
ValueError: Option name csequence was not found.
>>> print cline
water -stdout -asequence=a.fasta -bsequence=b.fasta -gapopen=10 -gapextend=0.5

This workaround uses a whitelist of object attributes, and sets the
object attribute list as normal, for these.  Other attributes are
assumed to be parameters, and passed to the self.set_parameter method
for validation and assignment.

Overrides: object.__setattr__

Make the commandline string with the currently set options.

e.g.
>>> from Bio.Emboss.Applications import WaterCommandline
>>> cline = WaterCommandline(gapopen=10, gapextend=0.5)
>>> cline.asequence = "asis:ACCCGGGCGCGGT"
>>> cline.bsequence = "asis:ACCCGAGCGCGGT"
>>> cline.outfile = "temp_water.txt"
>>> print cline
water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5
>>> str(cline)
'water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5'

Overrides: object.__str__