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Package Bio :: Package Application :: Class AbstractCommandline
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Class AbstractCommandline

source code

object --+
         |
        AbstractCommandline
Known Subclasses:
Generic interface for constructing command line strings.

This class shouldn't be called directly; it should be subclassed to
provide an implementation for a specific application.

For a usage example we'll show one of the EMBOSS wrappers.  You can set
options when creating the wrapper object using keyword arguments - or later
using their corresponding properties:

>>> from Bio.Emboss.Applications import WaterCommandline
>>> cline = WaterCommandline(gapopen=10, gapextend=0.5)
>>> cline
WaterCommandline(cmd='water', gapopen=10, gapextend=0.5)

You can instead manipulate the parameters via their properties, e.g.

>>> cline.gapopen
10
>>> cline.gapopen = 20
>>> cline
WaterCommandline(cmd='water', gapopen=20, gapextend=0.5)

You can clear a parameter you have already added by 'deleting' the
corresponding property:

>>> del cline.gapopen
>>> cline.gapopen
>>> cline
WaterCommandline(cmd='water', gapextend=0.5)

Once you have set the parameters you need, turn the object into a string:

>>> str(cline)
Traceback (most recent call last):
...
ValueError: You must either set outfile (output filename), or enable filter or stdout (output to stdout).

In this case the wrapper knows certain arguments are required to construct
a valid command line for the tool.  For a complete example,

>>> 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)

You would typically run the command line via a standard Python operating
system call (e.g. using the subprocess module).
Instance Methods [hide private]
 
__init__(self, cmd, **kwargs)
Create a new instance of a command line wrapper object.		 source code
 
_validate(self)
Make sure the required parameters have been set (PRIVATE).		 source code
 
__str__(self)
Make the commandline string with the currently set options.		 source code
 
__repr__(self)
Return a representation of the command line object for debugging.		 source code
 
_get_parameter(self, name)
Get a commandline option value.		 source code
 
_clear_parameter(self, name)
Reset or clear a commandline option value.		 source code
 
set_parameter(self, name, value=None)
Set a commandline option for a program.		 source code
 
_check_value(self, value, name, check_function)
Check whether the given value is valid.		 source code
 
__setattr__(self, name, value)
Set attribute name to value (PRIVATE).		 source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd, **kwargs)
(Constructor)

source code  
Create a new instance of a command line wrapper object.
Overrides: object.__init__

_validate(self)

source code  
Make sure the required parameters have been set (PRIVATE).

No return value - it either works or raises a ValueError.

This is a separate method (called from __str__) so that subclasses may
override it.

__str__(self)
(Informal representation operator)

source code  
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__

__repr__(self)
(Representation operator)

source code  
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__

_check_value(self, value, name, check_function)

source code  
Check whether the given value is valid.

No return value - it either works or raises a ValueError.

This uses the passed function 'check_function', which can either
return a [0, 1] (bad, good) value or raise an error. Either way
this function will raise an error if the value is not valid, or
finish silently otherwise.

__setattr__(self, name, value)

source code  
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__

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