Chapter 9: Python Code for Preparing directories for output with @mkdir()

See also

• Manual Table of Contents
• mkdir() syntax
• formatter() syntax
• regex() syntax
• Back to Chapter 9: Preparing directories for output with @mkdir()

Code for formatter() Zoo example

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


# create directories for each clade
@mkdir(    create_initial_files,                                       # Input

           formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!

           "{subpath[0][1]}/{clade[0]}")                               # new_directory
#   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 "%40s -> %90s" % (input_file, output_file)
        # this works now
        open(output_file, "w")


pipeline_run(verbose=0)

Code for regex() Zoo example

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


# create directories for each clade
@mkdir(    create_initial_files,                                       # Input

           regex(r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"), # Only animals: ignore plants!
           r"\g<clade>")                                             # new_directory
#   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 "%40s -> %90s" % (input_file, output_file)
    # this works now
    open(output_file, "w")


pipeline_run(verbose=0)