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.. include:: ../../global.inc
.. include:: manual_chapter_numbers.inc
.. _new_manual.output_file_names.code:
############################################################################################################################################################################################################
|new_manual.output_file_names.chapter_num|: Python Code for Specifying output file names with :ref:`formatter() <decorators.formatter>` and :ref:`regex() <decorators.regex>`
############################################################################################################################################################################################################
.. seealso::
* :ref:`Manual Table of Contents <new_manual.table_of_contents>`
* :ref:`suffix() <decorators.suffix>` syntax
* :ref:`formatter() <decorators.formatter>` syntax
* :ref:`regex() <decorators.regex>` syntax
* Back to |new_manual.output_file_names.chapter_num|: :ref:`Specifying output file names <new_manual.output_file_names>`
************************************************************************
Example Code for :ref:`suffix() <decorators.suffix>`
************************************************************************
.. code-block:: python
from ruffus import *
#---------------------------------------------------------------
# create initial files
#
@originate([ ['job1.a.start', 'job1.b.start'],
['job2.a.start', 'job2.b.start'],
['job3.a.start', 'job3.b.start'] ])
def create_initial_file_pairs(output_files):
# create both files as necessary
for output_file in output_files:
with open(output_file, "w") as oo: pass
#---------------------------------------------------------------
#
# suffix
#
@transform(create_initial_file_pairs, # name of previous task(s) (or list of files, or a glob)
suffix(".start"), # matching suffix of the "input file"
[".output.a.1", 45, ".output.b.1"]) # resulting suffix
def first_task(input_files, output_parameters):
print " input_parameters = ", input_files
print " output_parameters = ", output_parameters
#
# Run
#
pipeline_run([first_task])
************************************************************************
Example Code for :ref:`formatter() <decorators.formatter>`
************************************************************************
.. code-block:: python
from ruffus import *
# create initial files
@originate([ ['job1.a.start', 'job1.b.start'],
['job2.a.start', 'job2.b.start'],
['job3.a.start', 'job3.c.start'] ])
def create_initial_file_pairs(output_files):
# create both files as necessary
for output_file in output_files:
with open(output_file, "w") as oo: pass
#---------------------------------------------------------------
#
# formatter
#
# first task
@transform(create_initial_file_pairs, # Input
formatter(".+/job(?P<JOBNUMBER>\d+).a.start", # Extract job number
".+/job[123].b.start"), # Match only "b" files
["{path[0]}/jobs{JOBNUMBER[0]}.output.a.1", # Replacement list
"{path[1]}/jobs{JOBNUMBER[0]}.output.b.1", 45])
def first_task(input_files, output_parameters):
print "input_parameters = ", input_files
print "output_parameters = ", output_parameters
#
# Run
#
pipeline_run(verbose=0)
****************************************************************************************************************
Example Code for :ref:`formatter() <decorators.formatter>` with replacements in *extra* arguments
****************************************************************************************************************
.. code-block:: python
from ruffus import *
# create initial files
@originate([ ['job1.a.start', 'job1.b.start'],
['job2.a.start', 'job2.b.start'],
['job3.a.start', 'job3.c.start'] ])
def create_initial_file_pairs(output_files):
for output_file in output_files:
with open(output_file, "w") as oo: pass
#---------------------------------------------------------------
#
# print job number as an extra argument
#
# first task
@transform(create_initial_file_pairs, # Input
formatter(".+/job(?P<JOBNUMBER>\d+).a.start", # Extract job number
".+/job[123].b.start"), # Match only "b" files
["{path[0]}/jobs{JOBNUMBER[0]}.output.a.1", # Replacement list
"{path[1]}/jobs{JOBNUMBER[0]}.output.b.1"],
"{JOBNUMBER[0]}"
def first_task(input_files, output_parameters, job_number):
print job_number, ":", input_files
pipeline_run(verbose=0)
****************************************************************************************************************
Example Code for :ref:`formatter() <decorators.formatter>` in Zoos
****************************************************************************************************************
.. code-block:: python
from ruffus import *
# Make directories
@mkdir(["tiger", "lion", "dog", "crocodile", "rose"])
@originate(
# List of animals and plants
[ "tiger/mammals.wild.animals",
"lion/mammals.wild.animals",
"lion/mammals.handreared.animals",
"dog/mammals.tame.animals",
"dog/mammals.wild.animals",
"crocodile/reptiles.wild.animals",
"rose/flowering.handreared.plants"])
def create_initial_files(output_file):
with open(output_file, "w") as oo: pass
# Put different animals in different directories depending on their clade
@transform(create_initial_files, # Input
formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"), # Only animals: ignore plants!
"{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food", # Replacement
"{subpath[0][1]}/{clade[0]}", # new_directory
"{subdir[0][0]}", # animal_name
"{tame[0]}") # tameness
def feed(input_file, output_file, new_directory, animal_name, tameness):
print "Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}".format(**locals())
pipeline_run(verbose=0)
Results in:
::
>>> pipeline_run(verbose=0)
Food for the wild crocodile = ./reptiles/wild.crocodile.food will be placed in ./reptiles
Food for the tame dog = ./mammals/tame.dog.food will be placed in ./mammals
Food for the wild dog = ./mammals/wild.dog.food will be placed in ./mammals
Food for the handreared lion = ./mammals/handreared.lion.food will be placed in ./mammals
Food for the wild lion = ./mammals/wild.lion.food will be placed in ./mammals
Food for the wild tiger = ./mammals/wild.tiger.food will be placed in ./mammals
****************************************************************************************************************
Example Code for :ref:`regex() <decorators.regex>` in zoos
****************************************************************************************************************
.. code-block:: python
from ruffus import *
# Make directories
@mkdir(["tiger", "lion", "dog", "crocodile", "rose"])
@originate(
# List of animals and plants
[ "tiger/mammals.wild.animals",
"lion/mammals.wild.animals",
"lion/mammals.handreared.animals",
"dog/mammals.tame.animals",
"dog/mammals.wild.animals",
"crocodile/reptiles.wild.animals",
"rose/flowering.handreared.plants"])
def create_initial_files(output_file):
with open(output_file, "w") as oo: pass
# Put different animals in different directories depending on their clade
@transform(create_initial_files, # Input
regex(r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"), # Only animals: ignore plants!
r"\1/\g<clade>/\g<tame>.\2.food", # Replacement
r"\1/\g<clade>", # new_directory
r"\2", # animal_name
"\g<tame>") # tameness
def feed(input_file, output_file, new_directory, animal_name, tameness):
print "Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}".format(**locals())
pipeline_run(verbose=0)
Results in:
::
>>> pipeline_run(verbose=0)
Food for the wild crocodile = reptiles/wild.crocodile.food will be placed in reptiles
Food for the tame dog = mammals/tame.dog.food will be placed in mammals
Food for the wild dog = mammals/wild.dog.food will be placed in mammals
Food for the handreared lion = mammals/handreared.lion.food will be placed in mammals
Food for the wild lion = mammals/wild.lion.food will be placed in mammals
Food for the wild tiger = mammals/wild.tiger.food will be placed in mammals
|
