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# Application Controller Documentation

Section author: Greg Caporaso, Sandra Smit

## About this document

This document was written by Greg Caporaso and Sandra Smit, the developers of the application controller framework in PyCogent. Since its beginnings, the application controller framework has been further developed and improved by multiple people involved in the PyCogent project, and of course many application controllers have been implemented. Thanks!

The purpose of this document (together with the code in the PyCogent library) is to serve as a guideline for new users who want to implement application controllers. It should also be helpful as a reference document for more experienced coders. To meet the different needs of these people, this document is split up into multiple sections that discuss the framework in different levels of detail. We first provide a summary, then documentation for application controller users, then documentation for application controller developers, and finally a developer’s reference detailing the underlying objects.

Feedback from users of this document will help us to improve it, so please don’t hesitate to contact us: gregcaporaso@gmail.com or sandra_smit at users.sourceforge.net.

## The application controller framework: brief overview

### Summary

An application performs a certain task. It uses parameters to give the user control over the possible settings. In general an application requires some input data and produces some output. To run RNAfold on (i.e. predict an RNA secondary structure for) the sequence in seqs.txt, using some settings for temperature and GU pairs), and to save the output in the file result.txt, the following command would have to be executed:

    RNAfold -T 25 -noGU <seqs.txt >result.txt

Suppose you want to fold the sequences at two different temperatures (25 and 37 degrees Celcius) and investigate the difference between the structures. This would require a lot of manual work (run RNA fold twice, store all the files, use python to read in the files, parse the output, and calculate the difference). This task becomes a lot easier if we can control the application RNAfold from within the python environment. The following example folds two sequences at two different temperatures and reports the symmetric difference between the resulting structures. It works by creating a single application controller, and running it with different settings on the same input. The output is parsed and compared. The code snippet doesn’t leave any files on the system.

    seqs = ['GCCCGGAUAGCUCAGUUAAAAUCCCCGUGUCGGUGGUUCAAUUCCGCCUCCGGGCCCA',\
    'CCCCUGGUGGCCAUAGCGGGGAUUAACCCGGCCUGUGCCGGCAGCGGCACGGGAGGUCGCUGCCAGGGG']
    r = RNAfold(WorkingDir="/tmp")

    r.Parameters['-T'].on(25)
    print "COMMAND AT 25C:", r.BaseCommand
    res = r(seqs)
    fold_25 = just_seqs_parser(res['StdOut'].readlines())
    res.cleanUp()

    r.Parameters['-T'].on(37)
    print "COMMAND AT 37C:", r.BaseCommand
    res = r(seqs)
    fold_37 = just_seqs_parser(res['StdOut'].readlines())
    res.cleanUp()

    for seq_25, struct_25 in fold_25:
        for seq_37, struct_37 in fold_37:
            if seq_25 == seq_37:
                print 'SEQ:', seq_25
                print '25C:', struct_25
                print '37C:', struct_37
                print 'BASE PAIR SIMILARITY: %.3f'%\
                    (compare_pairs(struct_25.toPairs(), struct_37.toPairs()))

Running the script results in the following output:

    COMMAND AT 25C: cd "/tmp/"; RNAfold -d1 -T 25 -S 1.07
    COMMAND AT 37C: cd "/tmp/"; RNAfold -d1 -T 37 -S 1.07
    SEQ: GCCCGGAUAGCUCAGUUAAAAUCCCCGUGUCGGUGGUUCAAUUCCGCCUCCGGGCCCA
    25C: (((((((..((..((((.....(((((...))).))...))))..)).)))))))... (-26.25)
    37C: ((((((.((((...)))).............(((((.......))))).))))))... (-19.6)
    BASE PAIR SIMILARITY: 0.222
    SEQ: CCCCUGGUGGCCAUAGCGGGGAUUAACCCGGCCUGUGCCGGCAGCGGCACGGGAGGUCGCUGCCAGGGG
    25C: (((((((((((.((..((((......)))).(((((((((....)))))))))..)).))))))))))) (-55.52)
    37C: (((((((..((.....((((......)))).(((((((((....))))))))).....))..))))))) (-46.3)
    BASE PAIR SIMILARITY: 0.846

It has tremendous benefits to have the capability to run an application in an integrative fashion from the Python environment, using Python object as input, catching and directly using the output in a downstream analysis. It is timesaving and allows for the full automation of an analysis (prevents manual intervention). This is extremely convenient, for example, if you wish to perform a comparison of a large variety of parameters passed to a single application. Rather than manually running the application many times from the command line, you can script the runs and automatically process the output. A piece of python code that handles this is called an application controller (APPC). The purpose of the application controller framework is to support various application controllers in general. The framework is generic and supports actions that all applications have in common. Each application requires a specific APPC that defines all the variables and methods for that unique application.

At the moment the framework supports only one type of application: the command line application. In the (near) future we want to support web applications as well.

This section addresses the different components of an application and how these components are represented in the framework. The framework is set up in two files: cogent/app/util.py and cogent/app/parameters.py

### Command line applications

Every application requires a base command (such as RNAfold, muscle, or clustalw) and some parameters. These two properties are stored in the high level class Application.

The class CommandlineApplication inherits from Application and has additional features. It deals with the working directory, input, and output. The central method is the __call__ method in which the full command-to-execute is built up and executed. The result of running the application controller is returned to the user.

The util.py file contains one other class: ApplicationError. This class is used to raise exceptions for application controllers.

### Parameters

Most applications allow you to specify a certain set of parameters to control how the program runs. Parameters can control many different features of an application, such as the temperature at which RNA is folded, the number of gaps allowed in an alignment, or the name of an output file. They come in many forms as well, some are simply flags, some always require a value, some can have optional values.

The application controller framework supports three types of parameters, which will be discussed below. Subclassing to specify new types of parameters or to make certain attributes fixed, is very easy.

The abstract Parameter class defines the basic functionality of a parameter: it initializes all the Parameter attributes and it defines a Parameter ID which is a unique identifier for each parameter. In general a parameter has a prefix (usually a dash) and a name. Some parameters have values. The Parameter object is discussed in more detail in section Designing and implementing a new type of application controller.

There are three subclasses from the class Parameter. FlagParameter is used for parameters that don’t have values (e.g. allow GU pairs or not). ValuedParameters are used for paramaters that specify some value (e.g. the temperature or some input file). MixedParameters are parameters that might or might not have a value (e.g. the -d parameter in RNAfold). All parameters of an application are grouped in a Paramters object. The class Parameters is a special type of dictionary that allows lookups by parameter ID or synonyms.

The parameters.py file contains two more classes. ParameterError is used to raise exceptions in the parameter framework. The class FilePath defines paths on a system, it can print itself in a special way and add other parts of a path.

### Input

Input can be very diverse between applications. Most often it requires a file or some data directly from the command line. Application input is handled by “input handlers”. There are a few generic input handlers in CommandLineApplication object. Specific APPCs can use these methods directly or overwrite them. The methods process the input data for the application. They might for example write a certain Python object to a temporary file, and change some application parameters to use this file.

### Output

All applications produce some form of output. It can be limited to information on “standard output” (stdout) and “standard error” (stderr). Many applications produce additional output files. Most (unfortunately not all) applications report a meaningful exit status that inform the user on whether the execution of the program was succesful. The class CommandLineAppResult handles all aspects of application output: stdout, stderr, exit status, and the additional output files. Access to all the available files is handles by the class ResultPath. More technical aspect of these classes is discussed in section Designing and implementing a new type of application controller.

## Using an application controller

### Summary

1. Create an instance of some app controller
2. Turn parameters on and off
3. Optionally change the working directory
4. Optionally check the base command which is built-up from the above information
5. Set the input handler
6. Possibly redirect StdOut and StdErr
7. Apply the instance to the input data, store the results
8. Use the results as you like
9. Possibly clean up files created by the program and the APPC

### Creating an instance with basic settings (parameters, working directory)

The first step toward running an application is creating an instance of the APPC. Two basic settings are the parameters and the working directory. Below are some examples on how to do this. Note that the working directory must be an absolute path.

All parameters have the methods isOn and isOff to check whether the parameter is active or not. Parameters can be turned on and off (with or without a value) with the on() and off() methods. The values can also be set during initialization of the APPC. When specifying the parameters upon initialization the __init__ parameter params should be a dictionary of parameters that should be turned on, keyed by either the Parameter ID or a synonym. The values in params should be the values to turn the parameters on with for Valued or Mixed Parameters, or None for Flag or Mixed Parameters.

It is useful to check the BaseCommand to see if all the parameters have the correct settings and if the working directory is correct. During debugging it is useful to check whether the command runs on the normal command line.

    Initialization without params, only defaults are on.
    >>> from cogent.app.vienna_package import RNAfold
    >>> r = RNAfold()

    Initialization with params, set new values for this instance
    >>> r = RNAfold(params={'-T':25,'-d':None,'-4':None,'-S':1.2})

    Initialization changing the Working directory (must be absolute path!)
    >>> r = RNAfold(WorkingDir='/tmp')
    >>> print r.BaseCommand
    cd "/tmp/"; RNAfold -d1 -T 37 -S 1.07

    Changing the working directory after initialization (must be absolute path!)
    >>> r = RNAfold()
    >>> r.WorkingDir = '/tmp'
    >>> print r.BaseCommand
    cd "/tmp/"; RNAfold -d1 -T 37 -S 1.07

    Checking the parameters
    >>> r = RNAfold()
    >>> print r.Parameters['-P'].isOn()
    False
    >>> print r.Parameters['-P']
    <BLANKLINE>
    >>> print r.Parameters['-T'].isOn()
    True
    >>> print r.Parameters['-T']
    -T 37

### Other settings on initialization

The input handler could be set (if not, the default is used)

    On initialization
    >>> r = RNAfold(InputHandler="_input_as_string")
    >>> print r.InputHandler
    _input_as_string

    After initialization
    >>> r = RNAfold()
    >>> print r.InputHandler # default
    _input_as_lines
    >>> r.InputHandler = "_input_as_path"
    >>> print r.InputHandler
    _input_as_path

Standard out and standard error can be suppressed. If SuppressStderr or SuppressStdout are set to True, stdout and stderr will be routed to /dev/null. The default is to store these results in a temporary file. Redirecting StdErr might be useful for programs that write a lot of useless information to this filestream.

Some parameters concerning the creation of temporary files can be changed. TmpDir: default is /tmp. TmpNameLen is the length of the filenames, default is 20.

HALT_EXEC is a parameter that can be set to True for debugging purposes. It stops the process right before execution of the system call, it leaves all the input files (incl. temporary) in place. This allows the user to check whether the input is generated correctly. See Section HALT_EXEC is your friend for more details.

### Running the application, using the output, and cleaning up

When calling the instance of the APPC on some data the __call__ method is invoked. The call method has to optional parameters: data (the input data) and remove_tmp (if True the temporary files are removed). The call method returns a CommandLineAppResult object, containing all the application output information.

The output dictionary can be used to access the resulting files. All the information can be incorporated in a downstream analysis. In the example below the aligned sequences in clustalw format are parsed and printed.

Additionally CommandLineAppResult contains one public method: cleanUp() which takes no parameters. The method cleanUp() should be used when you want to delete the files that were created by the CommandLineApplication from disk. Note that after cleanUp() you may still have access to your files, but these are not reliable. You will only have access to what has already been loaded into memory (ie. only a fraction of your file typically), so you should only run cleanUp() after you are done accessing you files. Also note that running cleanUp() is not required. If you want the result files to remain on disc you should not run cleanUp() and they will be left in place. This is useful for running an application for later analysis of results.

    >>> from cogent import PROTEIN
    >>> from cogent.app.clustalw import Clustalw
    >>> from cogent.parse.clustal import ClustalParser
    >>> s1 = PROTEIN.Sequence('MHSSIVLATVLFVAIASASKTRELCMKSL')
    >>> s2 = PROTEIN.Sequence('MALAEADDGAVVFGEEQEALVLKSWAVMKKDA')
    >>> s3 = PROTEIN.Sequence('MSTVEGREFSEDQEALVVKSWTVMKLNAGELALKF')

    >>> c = Clustalw(InputHandler="_input_as_seqs")
    >>> result = c([s1,s2,s3])
    >>> print result['ExitStatus']
    0
    >>> aln_txt = result['Align'].readlines()
    >>> for label, seq in ClustalParser(aln_txt): print "%s: %s"%(label, seq)
    2: MALAEADDGAVVFGEEQEALVLKSWAVMKKDA-------
    3: MSTVEGRE----FSEDQEALVVKSWTVMKLNAGELALKF
    1: MHSSIVLAT-VLFVAIASASKTRELCMKSL---------
    >>> result.cleanUp()

## Designing and implementing a new type of application controller

Each specific application that you wish to control through PyCogent requires an application controller, i.e., a subclass of CommandLineApplication. Building the new application controller consists of three steps:

1. Creating the application controller class: Overwrite CommandLineApplication to define your new application controller, and define the class data. (Section Step 1: Creating the application controller class and defining class data.)
2. Input handing: Determine whether the built-in input handlers (in CommandLineApplication) are sufficient. If not, write one or more input handling methods. (Section Step 2: Input handling.)
3. Output handling: Determine whether the program writes any output files to disk. If so, implement the _get_result_paths method. (Section Step 3: Output handling.)

### Step 1: Creating the application controller class and defining class data

All of these class variables are discussed in detail in Sections Application: cogent.app. util.py and Command-LineApplication: cogent.app.util.py. —

The following class data must be overwritten:

_command:
  The command used to run the command (a string).

The following class data can be overwritten:

_parameters:
  A dictionary of Parameter objects. Keys should be the identifiers of the parameters, and values should be the Parameter objects.
_command_delimiter:
  String that specifies the delimiter between the components of a full command, e.g. the command, parameters, and arguments.
_synonyms:
  A dictionary of parameter synonyms. Keys should be the alternative keys to lookup a parameter, and values should be the identifiers used in the _parameters dictionary.
_input_handler:
  The name of the input handler method that should be used by default. The value should be a string (see CommandLineApplication.__call__ for how it’s used).
_working_dir:
  Specifies where the command should be run (string). Default is current working directory.
_suppress_stdout:
  Boolean value that specifies what happens with standard output (stdout) by default.
_suppress_stderr:
  Boolean value that specifies what happens with standard error (stderr) by default.

#### Defining parameters

All parameters should be one of the three built-in types: FlagParamater, ValuedParameter, or MixedParameter. (We don’t know of any types that wouldn’t fit into this framework, but if you come across any, please let us know.) Examples illustrating how to define the three different parameter types can be found in Section Parameters: cogent.app. parameters.py. The _parameters dict is a mapping of parameter identifiers, or Prefix and Name joined by the empty string, to parameter objects. All parameters which can be passed to an application should be defined in the parameters dict. Usually you can get this list by reviewing the application’s documentation. See Section A complete Command-LineApplication subclass example for an example including the definition of the _parameters dict. Note: if for a given ValuedParameter or MixedParameter, the value is intended to be a path to a directory or file, `IsPath=True` must be passed when initializing those parameters. — Defining a new Parameter type — If the application you’re working with uses a type of parameter that is not supported by the framework yet, you might want to write your own subclass. To subclass Parameter, the following methods will need to be implemented: __str__, isOn(), isOff(), on(), off(). These methods cover the two important characteristics of each parameter: knowing how to print itself, based on its status, and knowing how to be turned on or off. It is unlikely that you will need to subclass parameter if working with CommandLineApplication subclasses. If you think you do, please let us know. — Writing constructor functions/wrappers — There might be several reasons, such as to make some attribute of the parameter fixed, to write a wrapper around or constructor function for a parameter. For example to fixate the prefix of the FlagParameter, one might write this:

    >>> from cogent.app.parameters import FlagParameter
    >>> def DashedFlag(name):
    ...   return FlagParameter('-',name)
    ...
    >>> tree = DashedFlag('tree')
    >>> tree
    <cogent.app.parameters.FlagParameter object at ...
    >>> tree.on()
    >>> print tree
    -tree

#### A complete Command-LineApplication subclass example

A subclass of CommandLineApplication might look something like this:

    class RNAfold(CommandLineApplication):
        """Application controller for RNAfold (in the Vienna RNA package)
        """
        _command = 'RNAfold'
        _parameters = {
        '-p':MixedParameter(Prefix='-',Name='p',Delimiter='',Value=False),
        '-C':FlagParameter(Prefix='-',Name='C'),
        '-T':ValuedParameter(Prefix='-',Name='T',Value=37,Delimiter=' '),
        '-4':FlagParameter(Prefix='-',Name=4),
        '-d':MixedParameter(Prefix='-',Name='d',Delimiter='',Value=1),
        '-noLP':FlagParameter(Prefix='-',Name='noLP'),
        '-noGU':FlagParameter(Prefix='-',Name='noGU'),
        '-noCloseGU':FlagParameter(Prefix='-',Name='noCloseGU'),
        '-e':ValuedParameter(Prefix='-',Name='e',Delimiter=' '),
        '-P':ValuedParameter(Prefix='-',Name='P',Delimiter=' '),
        '-nsp':ValuedParameter(Prefix='-',Name='nsp',Delimiter=' '),
        '-S':ValuedParameter(Prefix='-',Name='S',Value=1.07,Delimiter=' ')}
        _synonyms = {'Temperature':'-T','Temp':'-T','Scale':'-S'}
        _input_handler = '_input_as_lines'
        _suppress_stderr = True

If the built-in input handlers are sufficient, and no output to disk is written by the program, this would complete the application controller.

### Step 2: Input handling

Not all applications handle their input in the same way. The input might be specified as a filename on the command line, as a list of values on the command line, or an input file might be specified through parameters. Some input data might also require processing before it is used by the application.

To give the user control over how input is handled without having to overwrite __call__(), small input handling methods can be specified in the application controller. In most cases, the CommandLineApplication input handlers can probably be used (e.g., passing data via stdin or a temp file), but for more complicated input formats, custom input handlers may need to be written for a CommandLineApplication subclass. Every input handling method should take one parameter, data, and return a string that will be appended to the command, e.g. `/path/to/input/file.txt`, if a path is passed to the application. (In this example, you would want to use CommandLineApplication._input_as_path as the input handler.)

By writing multiple input handling methods, multiple types of input can be handled by one application. The user can specify which one they want to use in a certain instance by setting the _input_handler class variable, or the InputHandler initialization variable.

For example, RNAfold takes a list of sequences from stdin. In this case, none of the built-in input handlers provides this functionaloty. The following input handler (from cogent.app.rnafold.Rnafold) writes the sequences (data) to a temporary file and redirects them to stdin.

    def _input_as_lines(self,data):
        """Returns '<temp_filename to redirect input to stdin"""
        return ''.join(['<',super(RNAfold,self)._input_as_lines(data)])

Clustalw requires the input filename be passes via the -infile paramter. This custom input handler from cogent.app.clustalw.Clustalw performs that function. Note that the empty string is returned, as input handlers are required to return a string that should be appended to the command line.

    def _input_as_string(self,data):
        """Makes data the value of a specific parameter
        This method returns the empty string. The parameter will be printed
        automatically once set.
        """
        if data:
            self.Parameters['-infile'].on(data)
        return ''

The default input handler should be set (as a string) via the class variable. See the example in Section A complete Command-LineApplication subclass example.

### Step 3: Output handling

Stdout and the exit status of any program are caught automatically. Stderr is accessible as well, unless suppressed via the _suppress_stderr class variable or the SupressStderr instance varaible. Any other files that are written should be made accessible by specifying their paths in the method _get_result_paths(). If you don’t overwrite this method, it is assumed that the program doesn’t create additional output files, so if it does, they will be written, but won’t be accessible through the CommandLineAppResult object, and won’t be cleaned up upon program termination!

Names and locations of output files may be fixed, but they can also be created on the fly based on things such as input file name, data the application is called on, a combination of values of parameters, or specified filename plus a fixed suffix. Since the generation of output files is so application specific and may be very complex, each application controller should handle its own output.

The _get_result_paths method should take data (as passed to __call__) as an argument. This is necessary to allow access to any possible variable used by the program. The user has access to data, self._input_filename (for an on the fly generated input file), all parameter values, and all public attributes of an Application.

_get_result_paths() should return a dictionary of ResultPath objects. The file streams resulting from a run of the application (in the CommandLineAppResult) will be accessed by the keys in the dictionary. The ResultPath specifies the absolute path of a file and whether the file has been written. This dictionary is used as input for the CommandLineAppResult which will handle opening the files etc.

As an example we show the output handling method of RNAfold. For a more complex example, see RnaView.

    def _get_result_paths(self,data):
            """Specifies the paths of output files generated by the application

            data: the data the instance of the application is called on

            You always get back: StdOut,StdErr, and ExitStatus
            RNAfold can produce two additional output files:
                a secondary structure structure graph. Default name: rna.ps
                a dot plot of the base pairing matrix. Default name: dp.ps
            The default names are used for unnamed sequences. Files are created
                in the current working directory.
            You can make a sequence named by inserting a line '>name' above it in
                your input file (or list of sequences). The ss and dp files for
                named sequences will be written to name_ss.ps and name_dp.ps
            """
            result = {}
            name_counter = 0
            seq_counter = 0
            if not isinstance(data,list):
                #means data is file
                data = open(data).readlines()
            for item in data:
                if item.startswith('>'):
                    name_counter += 1
                    name = item.strip('>\n')
                    result[(name+'_ss')] =\
                        ResultPath(Path=(self.WorkingDir+name+'_ss.ps'))
                    result[(name+'_dp')] =\
                        ResultPath(Path=(self.WorkingDir+name+'_dp.ps'),\
                        IsWritten=self.Parameters['-p'].isOn())
                else:
                    seq_counter += 1

            result['SS'] = ResultPath(Path=self.WorkingDir+'rna.ps',\
                IsWritten=seq_counter - name_counter > 0) #Secondary Structure
            result['DP'] = ResultPath(Path=self.WorkingDir+'dot.ps',
                IsWritten=(self.Parameters['-p'].isOn() and\
                seq_counter - name_counter > 0)) #DotPlot
            return result

### Tips and tricks for creating application controllers

#### HALT_EXEC is your friend

The __init__ method takes a boolean parameter, HALT_EXEC, which is False by default. Setting HALT_EXEC=True will cause __call__ to exit before the system call, print out the complete command that was about to be run, and leave all temporary files in place. This is extremely useful for debugging, because it allows you to run the application directly with the input that was generated by the application controller. You can therefore run the command and look directly at stdout and stderr, debug any temporary files that were created, etc. If the application you are controlling is slow, this can also allow you to debug earlier steps without having to wait for the application to run. HALT_EXEC is your friend.

## Application controller base classes: Developer’s reference

### Command line applications

#### Application: cogent.app. util.py

Application is an abstract class that contains some data used by for all application handlers that could be written. Private class data of Application consists of:

_command:

  The command used to run the command (a string). If the command is in your path (in a directory listed in the environment variable `$PATH`, or found by typing `which` followed by the command) you can provide only the command, e.g. `RNAfold`. If the command is not in your path, you must specify the absolute path it, e.g. `/some/other/bin/rnaview`. The use of absolute paths here is not recommended, because the location of the installation might be different on every machine. Instead, consider setting your `$PATH` environment variable to include the directory where the application is installed.

  For example if you are writing an application controller for `ls` where you might run: — ls -al *.jpg — _command should be set to `ls`.

_parameters:

  A dictionary of Parameter objects. Keys should be the identifiers of the parameters, and values should be the Parameter objects. This dictionary defines which parameters are available to the application. No values are specified, except for occasional default values. The default value for _parameters is the empty dictionary. If the application takes any command line parameters, this must be overwritten. This is almost always the case. See cogent.app.clustalw.Clustalw._parameters for an example of when parameters is overwritten.

      _parameters = {'-T':ValuedParameter('-','T',Delimiter='=')}

_synonyms:

  A dictionary of parameter synonyms. Keys should be the alternative keys to lookup a parameter, and values should be the identifiers used in the _parameters dictionary. It probably a good idea to comment on the available synonyms in the docstring of the application controller, so users that haven’t read the manual know what they can use to control the parameters. The default value for _synonyms is the empty dictionary. See cogent.app.vienna_package.ViennaPackage._synonyms for an example of this being overwritten.

      _synonyms = {'Temperature':'-T', 'Temp':'-T'}

_command_delimiter:

  String that specifies the delimiter between the components of a full command, e.g. the command, parameters, and arguments. The default value is ‘ ‘ (a single space). This delimiter will work for any Unix application, so it is usually not overwritten. (We are interested in hearing about any circumstances where this might be overwritten. Please let us know if you come across any. One example might be if the command being constructed is a URL.)

  In the above ‘ls’ example, a single space (‘ ‘) spearates the command componenets: the base command `ls`, the parameters `-al`, and the argument `*.jpg`.

The only method that is defined by Application is __init__, which takes one optional argument, params. The value of params should be a dictionary of parameters that should be turned on. Keys should be either the Parameter ID or a synonym. The values in params should be the values to turn the parameters on with for Valued or Mixed Parameters, or None for Flag or Mixed Parameters.

Application is never directly instantiated, but is instead inherited (either directly or indirectly) by all application controllers. It is necessary that Application.__init__() be called somewhere during the initialization of your class, but if you are inheriting from a higher level class (such as CommandLineApplication) this should already be handled.

#### Command-LineApplication: cogent.app.util.py

CommandLineApplication is an abstract class for command line application controllers. Several variables are class data to facilitate subclassing CommandLineApplication and to allow definition of defaults for Application Controller subclasses. This class was designed to be easily and minimally subclassed.

CommandLineApplication inherits from Application. CommandLineApplication contains the following additional class data:

_input_handler:
  The name of the input handler method that should be used by default. The value should be a string (see CommandLineApplication.__call__ for how it’s used). The input handling methods are private, so they should start with an underscore. The default value for _input_handler is ‘_input_as_string’. The input handler can be changed on instance level via the InputHandler initialization parameter.
_working_dir:
  Specifies the default working directory (string). The working_dir is where many applications write out their output. Setting this value gives you control over where output is written. The value of _working_dir should be an absolute path. If the value of _working_dir is None (the default) the current working directory will be used. The working directory can be changed at instance level via the WorkingDir initialization parameter.
_suppress_stdout:
  Boolean value that specifies what happens with standard output (stdout) by default. If the value is False (default), stdout is caught and accessible in the result object. If the value is True, stdout is routed to /dev/null and won’t be accessible. Suppression of stdout can also be controlled at instance level via the SuppressStdout initialization parameter.
_suppress_stderr:
  Boolean value that specifies what happens with standard error (stderr) by default. Some programs write a lot to stderr which you might want to ignore. If the value is False (default), stderr is caught and accessible in the result object. If the value is True, stderr is routed to /dev/null and won’t be accessible. Suppression of stderr can also be controlled at instance level via the SuppressStderr initialization parameter.

Class data can be overruled on the instance level by passing alternate data in as parameters to __init__(). These parameters are InputHandler, SupressStderr, and WorkingDir. Note that _working_dir and WorkingDir must always be an absolute path, although no explicit checking is done for this. You will get weird results in many cases if you use relative paths. WorkingDir, InputHandler, and SupressStderr are all public attributes of CommandLineApplication, and can be modified at anytime. You should (obviously) not modify the private versions of these attributes. Note that if WorkingDir does not exist on the system it will be created, and it will not be removed after the program runs.

There is an additional private variable _input_filename. This is set to the string containing the absolute path to an input file when the input file is a python generated temporary file. This should not be accessed from outside of the program, but may be useful at times when subclassing.

CommandLineApplication defines several methods. These include:

    __init__(), __call__(), _input_as_string(), _input_as_multiline_string(),
    _input_as_lines(), _input_as_path(), _input_as_paths(), _absolute(),
     _get_base_command(), _get_WorkingDir(), _set_WorkingDir(), _accept_exit_status(),
     _get_result_paths(), getTmpFilename()

We will go over these in differing depths, because for most cases, these are background methods that should never be called directly, or overwritten.

__init__():
  Initializes the object, taking as parameters params (see Application), InputHandler, WorkingDir, SupressStderr (discussed above). This method must be called by subclasses in their __init__() if they have one. For most purposes, you will never need to overwrite this method.
__call__():
  This is the method that does most of the work in the CommandLineApplication. Most of a users interaction with CommandLineApplications will be through this method, which takes data as a parameter. data is the data that should be passed as input to the application when it is called, default is None. Note that before data is appended to the command the InputHandler function is called on it. If data=None, no data is passed into the function, and the input handler will not be called. You should at all costs avoid overwriting __call__() as a lot is going on here.
_input_as_string():
  The default input handler. This acts on one parameter, data, that is passed in. It type casts data to a string, and returns the string.
_input_as_lines():
  An alternate input handler. In this case, data is a a sequence of lines to be written in a temporary file. This allows you interact with programs which only takes files as input, when you have created a data file on the fly. The return value of this function is a string representing the absolute path to the filename, which will be created with in self.WorkingDir.
_input_as_multiline_string():
  Input handler, similar to _input_as_lines, except data is a single string which should be written to a temporary file. The temporary file’s path is passed as input to the application as input.
_input_as_path():
  Another alternate input handler. This is similar to _input_as_string, but casts the input to a FilePath object rather than a string. If the input is a path, this input handler should be used.
_input_as_paths():
  Yet another alternate input handler. This is similar to _input_as_path, but operates on a list of paths.
_absolute():
  Converts a filename to an absolute path if it is not already. The path that is appended is self.WorkingDir. The result is a FilePath object.
_get_base_command():
  Appends the necessary parameters to self._command and returns the full command as a string (without input and output).
_get_WorkingDir() and _set_WorkingDir():
  accessor methods for the WorkingDir attribute.
_accept_exit_status():
  This function takes a string containing the return value of the application that was run. It is meant to be overwritten when necessary. It’s purpose is to analyze the exit_status of the application being run to determine if an ApplicationError should be raised. By default, no ApplicationError is raised regardless of the exit_status. In a subclass this is handy because you can customize what exit statuses are acceptable to you, and which are not, or you can not define the function in your subclass and accept all exit statuses.
_get_result_paths():
  This method is used to initialize the CommandLineAppResult class (see Section CommandLine-AppResult: cogent.app.util.py). This method should be overwritten if the application creates output other than stdout and stderr. A dict should be returned with ResultPath objects keyed by the names that you’d like to access their data by in the CommandLineAppResult object. When building the ResultPath objects, you will need to construct the names of all of the files that are being created. For this reason, you will need access to all of the data that the application has access to in the case of dynamic filenames. In order to construct these file name you have access to the Parameters object, data (which is passed in to the function) in the case where, for example, the output filename is specified as input to the program. The name of the input filename, when generated as a temporary file is available as self._input_filename, for cases where the output file name is based on the name of the input filename. This, in addition to system calls if necessary, should provide all of the information needed to build the names and paths of output files.
getTmpFilename():
  Generates a random filename using `TmpLenName` random alphanumeric (upper and lowercase) characters. The result will be an absolute path (presuming that `TmpDir` is absolute, which it should be), and the filename will begin with `prefix`, end with `suffix`, and be in `tmp_dir` or `TmpDir`. The `tmp_dir` parameter overrides the class/object-level default. Note that this function does not actually created the file, just the filename. The result is a `FilePath` object.

Two module level functions are also implemented:

    get_tmp_filename, guess_input_handler

get_tmp_filename:
  A module level implementation of `CommandLineApplication.getTmpFilename().`
guess_input_handler:
  This is a module-level function intended to pick the right input_handler in case the input is a set of sequences. It will return one of four input handlers: — _input_as_multiline_string, _input_as_path, _input_as_seqs, _input_as_lines.

### Parameters

#### Parameter: cogent.app. parameters.py

The class Parameter is an abstract class. Every Parameter object has six attributes: Prefix, Name, Value, Delimiter, Quote, and IsPath. All attributes may have any value, as long as it can be type casted into a string.

The Prefix of a parameter specifies the character that precedes the name of the parameter. It is mandatory to specify a prefix for a parameter, although it may be the empty string. For example: ‘-‘ is the prefix in ‘-T=37’, and ‘*’ is the prefix in ‘*d’. Note that some characters may have to be escaped (e.g. backslash).

Name is the second mandatory attribute of Parameter. The combination of the prefix and name of a parameter should form a unique combination that identifies the parameter. This ID is a public property of Parameter and will function later on as the key in the dictionary of parameters.

The attribute Value specifies the value of a parameter. It will be clear that not all parameters, such as flags, require a value. Therefore this field is optional in the __init__ method. For example, the value in ‘-T=37’ is 37, the value in ‘-d1’ is 1.

The Delimiter specifies what separates the name from the value when a parameter is printed. For example: ‘=’ in ‘T=37’ or ‘ ‘ (single space) in ‘#r 14’.

The Quote is an optional attribute that determines which characters will surround the value when the parameter is printed. Be alert on escaping quotes, since most quote-values will have a special meaning in python. At the moment only symmetrical quotes are supported, such as ” ‘ ” (single quote) in ” -p=’a’ “. Asymmetrical quotes are not possible, e.g. ‘d=[4]’. Is this something that should get supported?

IsPath should be set to true if the Value of the Parameter object is intended to be a path to a directory or file. Paths require special handling when printing, and Value is therefore cast to a cogent.app.parameters.FilePath object. IsPath is only used by ValuedParameter and MixedParameter objects, and has no effect on FlagParameters.

Every type of parameter prints itself differently. A flag will only print a combination of its prefix and name; another parameter may include everything. Therefore, the __str__ has to be specified in each specific subclass of Parameter. Whether a parameter is printed is determined by its value. This is also subclass specific and will be explained in the following sections.

#### FlagParameter: cogent.app. parameters.py

FlagParameter inherits from Parameter. A flag can’t have a value, it is just on or off. For example: if ‘-tree’ is set, a dendrogram is calculated; if ‘-tree’ is not set, the tree is not calculated. Since a flag can never have a value, we can easily use the value to specify whether the flag will be printed or not. If Value=True, the parameter will print itself; if Value=False, it won’t.

A FlagParameter can be initialized with three things. Prefix, Name (mandatory), and Value (optional). The default for Value is False to indicate that the parameter is off (i.e. not printed) by default. The only thing that counts for a flag is whether its value evaluates to True or to False.

If a FlagParameter has to print itself, it checks first whether it is on or off (Value=True or Value=False). If it is off, it will return the empty string. If it is on it will return the combination of its prefix and name.

The methods isOn() and isOff() will return True or False depending on the Value of the FlagParameter. These methods can be used to see whether the parameter will be printed on the command line or not. With the methods on() and off() the parameter can be turned on or off. These methods don’t take a value, because a flag can’t have a value. Internally, they’ll set parameter.Value to True or False.

    >>> from cogent.app.parameters import FlagParameter
    >>> tree = FlagParameter(Prefix='-',Name='tree')
    >>> tree.isOn()
    False
    >>> print tree
    <BLANKLINE>
    >>> tree.on()
    >>> print tree
    -tree

#### ValuedParameter: cogent.app. parameters.py

ValuedParameter also inherits from Parameter. In addition to setting all attributes of the parameter during initialization, a default value is set. This is a private property of a ValuedParameter and will be set to the value with which the parameter.Value is initialized. The Default value is available for inspection through parameter.Default. The default value should not be changed by the user. With the method reset() the Value of the parameter will be reset to the default value.

Like in FlagParameter, the value is used to control whether the parameter will print itself or not. If the Value is None, the parameter is off and __str__ will return the empty string. If the Value is anything else, the parameter will be printed in full glory: prefix, name, value and optionally delimiter and quotes. If IsPath is True, the value will be wrapped in double quotes when printed allowing for spaces in paths.

The methods isOn() and isOff() can be used to check whether the parameter will be printed or not. If parameter.Value is not None, the parameter is on and will be printed. If parameter.Value is None the parameter is off and won’t be printed. By using the method on(value) the Value of the parameter is set to the specified value. If you accidentally try to turn the parameter on with the value None, an error will be raised. Calling off() will set the Value of the parameter to None.

    >>> from cogent.app.parameters import ValuedParameter
    >>> temp = ValuedParameter(Prefix='-',Name='T',Delimiter="=")
    >>> temp.isOn()
    False
    >>> print temp
    <BLANKLINE>
    >>> temp.on(37)
    >>> print temp
    -T=37
    >>> temp_def = ValuedParameter(Prefix='-',Name='T',Value=100,Delimiter="=")
    >>> temp_def.Default
    100
    >>> print temp_def
    -T=100
    >>> temp_def.on(15)
    >>> print temp_def
    -T=15
    >>> temp_def.reset()
    >>> print temp_def
    -T=100

#### MixedParameter: cogent.app. parameters.py

MixedParameter is a subclass of ValuedParameter, because they share many features. A MixedParameter is a parameter that has an optional value; sometimes it behaves like a FlagParameter, sometimes like a ValuedParameter. An example is: ‘-d[0mid1mid2]’.

During initialization the Default value is set like in ValuedParameter. The method reset() is available to reset the parameter value to the default.

This type of Parameter has the most complicated control over ‘on’ or ‘off’. If the Value is False, the parameter is off. If the Value is None, the parameter is on, but behaves like a flag (only prefix and name will be printed), if the Value is anything else, the parameter is on and behaves like a ValuedParameter.

The methods isOn() and isOff() have the same functionality as in the other parameter types. When using on(val=None) it is optional to specify the value. If a MixedParameter is turned on without a value it will behave like flag. When turned on with a value, it will behave like a ValuedParameter. The method off() sets the Value to False, which indicates that the parameter should not be printed.

    >>> from cogent.app.parameters import MixedParameter
    >>> d = MixedParameter(Prefix='-',Name='d',Delimiter='')
    >>> d.isOff()
    True
    >>> d.on()
    >>> print d
    -d
    >>> d.on(2)
    >>> print d
    -d2

#### FilePath: cogent.app. parameters.py

The FilePath object inherits from string, and should be used to wrap all strings that represent paths. Examples inlcude:

    my_file.txt
    /path/to/my/file.txt
    /path/to/my/dir/

Wrapping paths in a FilePath object wraps the path in quotes when it should be, for example when passed to a system call, and doesn’t wrap it in quotes when it shouldn’t be, for example when performing operations on strings. The following example illustrates how this fails with a simple string, but performs as it should with a FilePath. In this example, p1 and p2 are simple strings, and p3, p4, p5, and p6 are FilePath objects. Since the example path contains spaces, a system call would not generate the desired result if the path is not wrapped in quotes. The FilePath object will wrap it in quotes when it is cast to a string, but will not wrap it in quotes when performing other string operations. The string object, on the other hand, does not differentiate, and joining p1 and p2 results in quotes placed in the middle of the string.

    >>> p1 = '"/path to/"'
    >>> p2 = '"my_file.txt"'
    >>> print str(p1 + p2)
    "/path to/""my_file.txt"
    >>> from cogent.app.parameters import FilePath
    >>> p3 = FilePath("/path to/")
    >>> p4 = FilePath("my_file.txt")
    >>> print str(p3+p4)
    "/path to/my_file.txt"
    >>> p5 = FilePath("/path to/")
    >>> p6 = FilePath("my_file.txt")
    >>> print str(p5+p6)
    "/path to/my_file.txt"

The FilePath object is used by MixedParameter and ValuedParameter when their IsPath attribute is set to True. This causes the Value attribute to be cast to a FilePath object, and it is wrapped in quotes when used in a system call. The _input_as_path input handler also casts the input to a FilePath object. In general, if you are working with a string in an application controller that represents a path to a file or directory, for example in a custom input handler, that string should be cast to a FilePath object. Failure to do this will result in errors if users pass a path that contains spaces.

#### Parameters: cogent.app. parameters.py

For most applications multiple parameters can be set. An application controller should have a set of known parameters with optional default values. All parameters of an application are organized in a dictionary where keys are parameter identifiers (combination of prefix and name) and values are Parameter objects.

Sometimes it might be hard to remember what the identifiers of the parameters in a specific application are. Lets look at an example. Suppose the user knows that the temperature can be set in three applications. In application A with ‘-T’, in application B with ‘*temp’, and in application C with ‘–t’. It is very likely that he/she doesn’t remember what parameter is used in which application. If every application controller has an synonyms dictionary which maps ‘temp’ to the identifier of the application specific parameter, the user can always lookup the temperature with parameters[‘temp’].

To support the lookup of parameters by synonyms, the class Parameters is not a simple dictionary, but a MappedDict (in cogent.util.misc). A MappedDict is a dictionary that can apply some function to a lookup value, before it looks it up in the dictionary. This function is called a mask. In the Parameters object the mask allows users to look up parameters in the dictionary by synonyms.

The Parameters object uses the private function _find_synonym() internally to determine by what key the parameter will be looked up. If the key, given by the user, appears in the synonyms dictionary the key to use for the parameters dictionary is looked up. Otherwise, it is assumed that the user used an existing key in the parameters dictionary.

    >>> from cogent.app.parameters import FlagParameter
    >>> a = FlagParameter('-','a')
    >>> from cogent.app.parameters import  ValuedParameter
    >>> b = ValuedParameter('-','T',Value=37,Delimiter='=')
    >>> from cogent.app.parameters import MixedParameter
    >>> c = MixedParameter('-','d',Value=0)
    >>> params = {'-a':a,'-T':b,'-d':c}
    >>> synonyms = {'temp':'-T','distance':'-d'}
    >>> from cogent.app.parameters import Parameters
    >>> p = Parameters(params,synonyms)
    >>> p['-a'].isOn()
    False
    >>> print p['temp']
    -T=37
    >>> p['distance'].on(2)
    >>> print p['-d']
    -d2

### Input

CommandLineApplication subclasses are called using the __call__ method with a single variable, data. This is the value passed to the application on the command line. The value of data will differ based on the application you are interfacing. Controlling for this without having to overwrite __call__ for every CommandLineApplication is the purpose of the _input_handlers discussed in Section Command-LineApplication: cogent.app.util.py.

Some examples of data that might be passed to CommandLineApplications are strings, via the _input_as_string input handler, a list of lines that should be written to file and then passed to the application, via the _input_as_lines input handler, or a path to a file or directory, via the _input_as_path input handler. To define the input handler that should be used, the class data _input_handler should be set. If one of the default input handlers is not applicable for a new CommandLineApplication, you will need to write a custom input handler. See `cogent.app.raxml.Raxml._input_as_seqs` for an example of a custom input handler.

For a discussion of the predefined input handlers, see Section Command-LineApplication: cogent.app.util.py. For a discussion on defining custom input handlers, see Section Step 2: Input handling.

### Output

#### ResultPath: cogent.app.util.py

The ResultPath object is intended to hold the important information pertaining to output files created by an application, namely the path to where the file can be found, and whether the file was written or not. ResultPath is a very simple container class. It has no methods aside from __init__().

To initialize a ResultPath object you must specify the path to the output file by setting the Path parameter. This must be a string, and it is highly recommended that this be an absolute path, though relative paths will also work in many cases. You can also optionally specify a boolean value specifying whether the file has been written or not by setting the IsWritten parameter. This is True by default.

    >>> from cogent.app.util import ResultPath
    >>> rp = ResultPath(Path='/tmp/my_output.txt',IsWritten=True)
    >>> rp.Path
    '/tmp/my_output.txt'
    >>> rp.IsWritten
    True
    >>> rp
    <cogent.app.util.ResultPath object at ...

#### CommandLine-AppResult: cogent.app.util.py

The CommandLineApp result object is a dictionary, and a container class for the results from a run of a CommandLineApplication. CommandLineAppResult has three default items in it:

StdOut:
  The stdout from the application, a file object
StdErr:
  The stderr from the application, a file object (or None when suppressing stderr, more on this in CommandLineApplication)
ExitStatus:
  The exit status of the application, and int that is returned by the CommandLineApplication, usually indicating the success or failure of the run of the application.

The __init__() method takes several required parameters:

out:
  a file handle which will be assigned to ‘StdOut’ in the CommandLineAppResult
err:
  a file handle or None which will be assigned to ‘StdErr’ in the CommandLineAppResult
exit_status:
  an int or None which will be assigned to ‘ExitStatus’ in the CommandLineAppResult
result_paths:
  a dictionary of ResultPath objects keyed by the name by which you want to access the output. For each item in result_paths, an entry will be created in the CommandLineAppResult and if ResultPath.IsWritten is True, the file specified by ResultPath.Path will be opened. If the file can not be opened (due to not being found at the specified path, or inadequate read access) an ApplicationError will be raised.

Note that as a user, you will never instantiate a CommandLineAppResult, it is taken care of upon calling the CommandLineApplication. You may at times however be responsible for creating the result_paths dict, but more on this in CommandLineApplication.

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