nestly is a collection of functions designed to ease running software with combinatorial choices of parameters.
It can easily do so for "cartesian products" of parameter choices, but can do much more-- arbitrary "backwards-looking" dependencies can be used.
The vision here is that we take a fixed set of parameters and generate a single type of output for each defined combination, which can then be combined in some way for comparison and retrieval. We would like to set things up tidily with nested directories for output reflecting nested parameter choices.
The full documentation is available on ReadTheDocs.
The easiest way is with pip:
$ pip install nestly
Or, for the latest commit from master:
$ pip install git+git://github.com/fhcrc/nestly.git@master
Python 2.7 is required.
Imagine you'd like to try all possible combinations of the following:
| Option | Choices |
| strategy | approximate, exhaustive |
| run_count | 10, 100, 1000 |
| input file | any file matching inputs/file* |
For this we can write a little make_nest.py. The guts are:
nest = Nest()
nest.add('strategy', ('exhaustive', 'approximate'))
nest.add('run_count', [10**i for i in xrange(3)])
nest.add('input_file', glob.glob(os.path.join(input_dir, 'file*')),
label_func=os.path.basename)
nest.build('runs')
Running make_nest.py, you get a directory tree like:
runs
├── approximate
│ ├── 10
│ │ ├── file1
│ │ │ └── control.json
│ │ ├── file2
│ │ └── control.json
│ ├── 100
│ │ ├── file1
│ │ │ └── control.json
│ │ ├── file2
│ │ └── control.json
│ └── 1000
│ ├── file1
│ │ └── control.json
│ ├── file2
│ └── control.json
└── exhaustive
├── 10
│ ├── file1
│ │ └── control.json
│ ├── file2
│ └── control.json
├── 100
│ ├── file1
│ │ └── control.json
│ ├── file2
│ └── control.json
└── 1000
├── file1
│ └── control.json
├── file2
└── control.json
With the final control.json reading, for example:
{
"input_file": "/Users/cmccoy/Development/nestly/examples/basic_nest/inputs/file3",
"run_count": "1000",
"strategy": "exhaustive"
}
The control files created then serve as inputs to nestrun for template substition, for example:
nestrun --save-cmd-file command.sh \
--template='my_command -s {strategy} --count={run_count} {input_file}' \
$(find runs -name "control.json")
This command runs my_command in all of the tip directories with the appropriate values for the parameters.
This was a "cartesian product" example. The "meal" example in the repository exhibits a setup with more complex dependencies between the nests.
nestrun takes a template and a list of control.json files with variables to
substitute. By default, substitution is performed using the Python built-in
str.format method. See the Python Formatter documentation for details on syntax,
and examples/jsonrun/do_nestrun.sh for an example.
There is also a nestly.scons module to integrate nestly with the make replacement SCons.
Run:
python setup.py test
The mock library is required, but will be downloaded if missing.
McCoy CO, Gallagher A, Hoffman NG, Matsen FA (2013) nestly--a framework for running software with nested parameter choices and aggregating results. Bioinformatics 29: 387-388. pubmed
nestly source code is freely available under the MIT License.