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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
########################################################################
************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
@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Only out of date jobs (comparing input and output files) will be re-run.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.
.. _decorators.collate_ex:
.. index::
pair: @collate (Advanced Usage); Syntax
pair: @collate, inputs(...); Syntax
pair: @collate, add_inputs(...); Syntax
.. seealso::
* :ref:`Use of add_inputs(...) | inputs(...) <new_manual.inputs>` in the **Ruffus** Manual
.. |coll_input| replace:: `input`
.. _coll_input: `decorators.collate_ex.input`_
.. |coll_extras| replace:: `extras`
.. _coll_extras: `decorators.collate_ex.extras`_
.. |coll_output| replace:: `output`
.. _coll_output: `decorators.collate_ex.output`_
.. |coll_filter| replace:: `filter`
.. _coll_filter: `decorators.collate_ex.filter`_
.. |coll_matching_regex| replace:: `matching_regex`
.. _coll_matching_regex: `decorators.collate_ex.matching_regex`_
.. |coll_matching_formatter| replace:: `matching_formatter`
.. _coll_matching_formatter: `decorators.collate_ex.matching_formatter`_
.. |coll_replace_inputs| replace:: `replace_inputs`
.. _coll_replace_inputs: `decorators.collate_ex.replace_inputs`_
.. |coll_add_inputs| replace:: `add_inputs`
.. _coll_add_inputs: `decorators.collate_ex.add_inputs`_
************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
collate( |coll_input|_, |coll_filter|_, |coll_replace_inputs|_ | |coll_add_inputs|_, |coll_output|_, [|coll_extras|_,...] )
************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
**Purpose:**
Use |coll_filter|_ to identify common sets of |coll_input|_\s which are to be grouped or collated together:
Each set of |coll_input|_\ s which generate identical |coll_output|_ and |coll_extras|_ using the
:ref:`formatter<decorators.formatter>` or :ref:`regex<decorators.regex>` (regular expression)
filters are collated into one job.
This variant of ``@collate`` allows additional inputs or dependencies to be added
dynamically to the task, with optional string substitution.
:ref:`add_inputs<decorators.add_inputs>` nests the the original input parameters in a list before adding additional dependencies.
:ref:`inputs<decorators.inputs>` replaces the original input parameters wholescale.
This is a **many to fewer** operation.
Only out of date jobs (comparing input and output files) will be re-run.
**Example of** :ref:`add_inputs<decorators.add_inputs>`
``regex(r".*(\..+)"), "\1.summary"`` creates a separate summary file for each suffix.
But we also add date of birth data for each species::
animal_files = "tuna.fish", "shark.fish", "dog.mammals", "cat.mammals"
# summarise by file suffix:
@collate(animal_files, regex(r".+\.(.+)$"), add_inputs(r"\1.date_of_birth"), r'\1.summary')
def summarize(infiles, summary_file):
pass
This results in the following equivalent function calls::
summarize([ ["shark.fish", "fish.date_of_birth" ],
["tuna.fish", "fish.date_of_birth" ] ], "fish.summary")
summarize([ ["cat.mammals", "mammals.date_of_birth"],
["dog.mammals", "mammals.date_of_birth"] ], "mammals.summary")
**Example of** :ref:`add_inputs<decorators.inputs>`
using ``inputs(...)`` will summarise only the dates of births for each species group::
animal_files = "tuna.fish", "shark.fish", "dog.mammals", "cat.mammals"
# summarise by file suffix:
@collate(animal_files, regex(r".+\.(.+)$"), inputs(r"\1.date_of_birth"), r'\1.summary')
def summarize(infiles, summary_file):
pass
This results in the following equivalent function calls::
summarize(["fish.date_of_birth" ], "fish.summary")
summarize(["mammals.date_of_birth"], "mammals.summary")
**Parameters:**
.. _decorators.collate_ex.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_ex.filter:
.. _decorators.collate_ex.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_ex.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_ex.add_inputs:
.. _decorators.collate_ex.replace_inputs:
* **add_inputs** = *add_inputs*\ (...) or **replace_inputs** = *inputs*\ (...)
Specifies the resulting |coll_input|_\ (s) to each job.
Positional parameters must be disambiguated by wrapping the values in :ref:`inputs(...)<decorators.inputs>` or an :ref:`add_inputs(...)<decorators.add_inputs>`.
Named parameters can be passed the values directly.
Takes:
#. Task / list of tasks.
File names are taken from the output of the specified task(s)
#. (Nested) list of file name strings.
Strings will be subject to substitution.
File names containing ``*[]?`` will be expanded as a |glob|_.
E.g. ``"a.*" => "a.1", "a.2"``
.. _decorators.collate_ex.output:
* **output** = *output*
Specifies the resulting output file name(s).
.. _decorators.collate_ex.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= [...]``
See :ref:`@collate <decorators.collate>` for more straightforward ways to use collate.
|
