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.. include:: ../global.inc
.. _decorators.collate:
.. index::
pair: @collate; Syntax
.. role:: raw-html(raw)
:format: html
:raw-html:`<style> .red {color:red} </style>`
.. role:: red
.. seealso::
* :ref:`@collate <new_manual.collate>` in the **Ruffus** Manual
* :ref:`Decorators <decorators>` for more decorators
.. |input| replace:: `input`
.. _input: `decorators.collate.input`_
.. |extras| replace:: `extras`
.. _extras: `decorators.collate.extras`_
.. |output| replace:: `output`
.. _output: `decorators.collate.output`_
.. |filter| replace:: `filter`
.. _filter: `decorators.collate.filter`_
.. |matching_regex| replace:: `matching_regex`
.. _matching_regex: `decorators.collate.matching_regex`_
.. |matching_formatter| replace:: `matching_formatter`
.. _matching_formatter: `decorators.collate.matching_formatter`_
########################################################################
@collate( |input|_, |filter|_, |output|_, [|extras|_,...] )
########################################################################
**Purpose:**
Use |filter|_ to identify common sets of |input|_\s which are to be grouped or collated together:
Each set of |input|_\ s which generate identical |output|_ and |extras|_ using the
:ref:`formatter<decorators.formatter>` or :ref:`regex<decorators.regex>` (regular expression)
filters are collated into one job.
This is a **many to fewer** operation.
Only out of date jobs (comparing input and output files) will be re-run.
**Example**:
``regex(r".+\.(.+)$")``, ``"\1.summary"`` creates a separate summary file for each suffix::
animal_files = "a.fish", "b.fish", "c.mammals", "d.mammals"
# summarise by file suffix:
@collate(animal_files, regex(r".+\.(.+)$"), r'\1.summary')
def summarize(infiles, summary_file):
pass
#. |output|_ and optional |extras|_ parameters are passed to the functions after string
substitution. Non-string values are passed through unchanged.
#. Each collate job consists of |input|_ files which are aggregated by string substitution
to identical |output|_ and |extras|_
#. | The above example results in two jobs:
| ``["a.fish", "b.fish" -> "fish.summary"]``
| ``["c.mammals", "d.mammals" -> "mammals.summary"]``
**Parameters:**
.. _decorators.collate.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 (as in the example above).
File names containing ``*[]?`` will be expanded as a |glob|_.
E.g.:``"a.*" => "a.1", "a.2"``
.. _decorators.collate.filter:
.. _decorators.collate.matching_regex:
* **filter** = *matching_regex*
is a python regular expression string, which must be wrapped in
a :ref:`regex<decorators.regex>` indicator object
See python `regular expression (re) <http://docs.python.org/library/re.html>`_
documentation for details of regular expression syntax
.. _decorators.collate.matching_formatter:
* **filter** = *matching_formatter*
a :ref:`formatter<decorators.formatter>` indicator object containing optionally
a python `regular expression (re) <http://docs.python.org/library/re.html>`_.
.. _decorators.collate.output:
* **output** = *output*
Specifies the resulting output file name(s) after string substitution
.. _decorators.collate.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.
**Example2**:
Suppose we had the following files::
cows.mammals.animal
horses.mammals.animal
sheep.mammals.animal
snake.reptile.animal
lizard.reptile.animal
crocodile.reptile.animal
pufferfish.fish.animal
and we wanted to end up with three different resulting output::
cow.mammals.animal
horse.mammals.animal
sheep.mammals.animal
-> mammals.results
snake.reptile.animal
lizard.reptile.animal
crocodile.reptile.animal
-> reptile.results
pufferfish.fish.animal
-> fish.results
This is the ``@collate`` code required::
animals = [ "cows.mammals.animal",
"horses.mammals.animal",
"sheep.mammals.animal",
"snake.reptile.animal",
"lizard.reptile.animal",
"crocodile.reptile.animal",
"pufferfish.fish.animal"]
@collate(animals, regex(r"(.+)\.(.+)\.animal"), r"\2.results")
# \1 = species [cow, horse]
# \2 = phylogenetics group [mammals, reptile, fish]
def summarize_animals_into_groups(species_file, result_file):
" ... more code here"
pass
See :ref:`@merge <decorators.merge>` for an alternative way to summarise files.
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