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.. include:: ../global.inc
.. _decorators.combinations:
.. index::
pair: @combinations; Syntax
.. seealso::
* :ref:`@combinations <new_manual.combinations>` in the **Ruffus** Manual
* :ref:`Decorators <decorators>` for more decorators
.. |input| replace:: `input`
.. _input: `decorators.combinations.input`_
.. |tuple_size| replace:: `tuple_size`
.. _tuple_size: `decorators.combinations.tuple_size`_
.. |filter| replace:: `filter`
.. _filter: `decorators.combinations.filter`_
.. |extras| replace:: `extras`
.. _extras: `decorators.combinations.extras`_
.. |output| replace:: `output`
.. _output: `decorators.combinations.output`_
.. |matching_formatter| replace:: `matching_formatter`
.. _matching_formatter: `decorators.combinations.matching_formatter`_
################################################################################################################################################
@combinations( |input|_, |filter|_, |tuple_size|_, |output|_, [|extras|_,...] )
################################################################################################################################################
**Purpose:**
Generates the **combinations**, between all the elements of a set of |input|_ (e.g. **A B C D**),
i.e. r-length tuples of |input|_ elements with no repeated elements (*not* **A A**)
and where order of the tuples is irrelevant (either **A B** or **B A**, not both).
The effect is analogous to the python `itertools <http://docs.python.org/2/library/itertools.html#itertools.combinations>`__
function of the same name:
.. code-block:: pycon
:emphasize-lines: 2
>>> from itertools import combinations
>>> # combinations('ABCD', 3) --> ABC ABD ACD BCD
>>> [ "".join(a) for a in combinations("ABCD", 3)]
['ABC', 'ABD', 'ACD', 'BCD']
Only out of date tasks (comparing |input|_ and |output|_ files) will be run
|output|_ file names and strings in the extra parameters
are generated by string replacement via the :ref:`formatter()<decorators.formatter>` filter
from the |input|_. This can be, for example, a list of file names or the
|output|_ of up stream tasks.
.
The replacement strings require an extra level of nesting to refer to
parsed components.
#. The first level refers to which *set* in each tuple of |input|_.
#. The second level refers to which |input|_ file in any particular *set* of |input|_.
This will be clear in the following example:
**Example**:
Calculate the **@combinations** of **A,B,C,D** files
If |input|_ is four pairs of file names
.. code-block:: python
:emphasize-lines: 1-6
input_files = [ [ 'A.1_start', 'A.2_start'], # 0
[ 'B.1_start', 'B.2_start'], # 1
[ 'C.1_start', 'C.2_start'], # 2
[ 'D.1_start', 'D.2_start'] ] # 3
The first job of:
.. code-block:: python
@combinations(input_files, formatter(), 3, ...)
Will be
.. <<python
.. code-block:: python
:emphasize-lines: 1-6
# Three file pairs at a time
['A.1_start', 'A.2_start'], # 0
# versus
['B.1_start', 'B.2_start'], # 1
# versus
['C.1_start', 'c.2_start'], # 2
..
python
First level of nesting:
.. code-block:: python
:emphasize-lines: 1-6
['A.1_start', 'A.2_start'] # [0]
['B.1_start', 'B.2_start'] # [1]
['C.1_start', 'C.2_start'] # [2]
Second level of nesting:
.. code-block:: python
:emphasize-lines: 1-6
'A.2_start' # [0][1]
'B.2_start' # [1][1]
'C.2_start' # [2][1]
Parse filename without suffix
.. code-block:: python
:emphasize-lines: 1-6
'A' # {basename[0][1]}
'B' # {basename[1][1]}
'C' # {basename[2][1]}
Python code:
.. code-block:: python
:emphasize-lines: 13,17,20,25,28-30
from ruffus import *
from ruffus.combinatorics import *
# initial file pairs
@originate([ ['A.1_start', 'A.2_start'],
['B.1_start', 'B.2_start'],
['C.1_start', 'C.2_start'],
['D.1_start', 'D.2_start']])
def create_initial_files_ABCD(output_files):
for output_file in output_files:
with open(output_file, "w") as oo: pass
# @combinations
@combinations(create_initial_files_ABCD, # Input
formatter(), # match input files
# tuple of 3 at a time
3,
# Output Replacement string
"{path[0][0]}/"
"{basename[0][1]}_vs_"
"{basename[1][1]}_vs_"
"{basename[2][1]}.combinations",
# Extra parameter: path for 1st set of files, 1st file name
"{path[0][0]}",
# Extra parameter
["{basename[0][0]}", # basename for 1st set of files, 1st file name
"{basename[1][0]}", # 2nd
"{basename[2][0]}", # 3rd
])
def combinations_task(input_file, output_parameter, shared_path, basenames):
print " - ".join(basenames)
#
# Run
#
pipeline_run(verbose=0)
This results in:
.. code-block:: pycon
>>> pipeline_run(verbose=0)
A - B - C
A - B - D
A - C - D
B - C - D
**Parameters:**
.. _decorators.combinations.input:
* **input** = *tasks_or_file_names*
can be a:
#. Task / list of tasks.
File names are taken from the |output|_ of the specified task(s)
#. (Nested) list of file name strings.
File names containing ``*[]?`` will be expanded as a |glob|_.
E.g.:``"a.*" => "a.1", "a.2"``
.. _decorators.combinations.filter:
.. _decorators.combinations.matching_formatter:
* **filter** = *formater(...)*
a :ref:`formatter<decorators.formatter>` indicator object containing optionally
a python `regular expression (re) <http://docs.python.org/library/re.html>`_.
.. _decorators.combinations.tuple_size:
* **tuple_size** = *N*
Select N elements at a time.
.. _decorators.combinations.output:
* **output** = *output*
Specifies the resulting output file name(s) after string substitution
.. _decorators.combinations.extras:
* **extras** = *extras*
Any extra parameters are passed verbatim to the task function
If you are using named parameters, these can be passed as a list, i.e. ``extras= [...]``
Any extra parameters are consumed by the task function and not forwarded further down the pipeline.
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