Chapter 17: Python Code for @combinations, @permutations and all versus all @product

See also

• Manual Table of Contents
• @combinations_with_replacement
• @combinations
• @permutations
• @product
• Back to Chapter 17: Preparing directories for output with @combinatorics()

Example code for @product

from ruffus import *
from ruffus.combinatorics import *

#   Three sets of initial files
@originate([ 'a.start', 'b.start'])
def create_initial_files_ab(output_file):
    with open(output_file, "w") as oo: pass

@originate([ 'p.start', 'q.start'])
def create_initial_files_pq(output_file):
    with open(output_file, "w") as oo: pass

@originate([ ['x.1_start', 'x.2_start'],
             ['y.1_start', 'y.2_start'] ])
def create_initial_files_xy(output_file):
    with open(output_file, "w") as oo: pass

#   @product
@product(   create_initial_files_ab,        # Input
            formatter("(.start)$"),         # match input file set # 1

            create_initial_files_pq,        # Input
            formatter("(.start)$"),         # match input file set # 2

            create_initial_files_xy,        # Input
            formatter("(.start)$"),         # match input file set # 3

            "{path[0][0]}/"                 # Output Replacement string
            "{basename[0][0]}_vs_"          #
            "{basename[1][0]}_vs_"          #
            "{basename[2][0]}.product",     #

            "{path[0][0]}",                 # Extra parameter: path for 1st set of files, 1st file name

            ["{basename[0][0]}",            # Extra parameter: basename for 1st set of files, 1st file name
             "{basename[1][0]}",            #                               2nd
             "{basename[2][0]}",            #                               3rd
             ])
def product_task(input_file, output_parameter, shared_path, basenames):
    print "# basenames      = ", " ".join(basenames)
    print "input_parameter  = ", input_file
    print "output_parameter = ", output_parameter, "\n"


#
#       Run
#
pipeline_run(verbose=0)

This results in:

>>> pipeline_run(verbose=0)

# basenames      =  a p x
input_parameter  =  ('a.start', 'p.start', 'x.start')
output_parameter =  /home/lg/temp/a_vs_p_vs_x.product

# basenames      =  a p y
input_parameter  =  ('a.start', 'p.start', 'y.start')
output_parameter =  /home/lg/temp/a_vs_p_vs_y.product

# basenames      =  a q x
input_parameter  =  ('a.start', 'q.start', 'x.start')
output_parameter =  /home/lg/temp/a_vs_q_vs_x.product

# basenames      =  a q y
input_parameter  =  ('a.start', 'q.start', 'y.start')
output_parameter =  /home/lg/temp/a_vs_q_vs_y.product

# basenames      =  b p x
input_parameter  =  ('b.start', 'p.start', 'x.start')
output_parameter =  /home/lg/temp/b_vs_p_vs_x.product

# basenames      =  b p y
input_parameter  =  ('b.start', 'p.start', 'y.start')
output_parameter =  /home/lg/temp/b_vs_p_vs_y.product

# basenames      =  b q x
input_parameter  =  ('b.start', 'q.start', 'x.start')
output_parameter =  /home/lg/temp/b_vs_q_vs_x.product

# basenames      =  b q y
input_parameter  =  ('b.start', 'q.start', 'y.start')
output_parameter =  /home/lg/temp/b_vs_q_vs_y.product

Example code for @permutations

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

#   @permutations
@permutations(create_initial_files_ABCD,      # Input
              formatter(),                    # match input files

              # tuple of 2 at a time
              2,

              # Output Replacement string
              "{path[0][0]}/"
              "{basename[0][1]}_vs_"
              "{basename[1][1]}.permutations",

              # 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
               ])
def permutations_task(input_file, output_parameter, shared_path, basenames):
    print " - ".join(basenames)


#
#       Run
#
pipeline_run(verbose=0)

This results in:

>>> pipeline_run(verbose=0)

A - B
A - C
A - D
B - A
B - C
B - D
C - A
C - B
C - D
D - A
D - B
D - C

Example code for @combinations

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:

>>> pipeline_run(verbose=0)
A - B - C
A - B - D
A - C - D
B - C - D

Example code for @combinations_with_replacement

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_with_replacement
@combinations_with_replacement(create_initial_files_ABCD,   # Input
              formatter(),                                  # match input files

              # tuple of 2 at a time
              2,

              # Output Replacement string
              "{path[0][0]}/"
              "{basename[0][1]}_vs_"
              "{basename[1][1]}.combinations_with_replacement",

              # 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]}",  #              2rd
               ])
def combinations_with_replacement_task(input_file, output_parameter, shared_path, basenames):
    print " - ".join(basenames)


#
#       Run
#
pipeline_run(verbose=0)

This results in:

>>> pipeline_run(verbose=0)
A - A
A - B
A - C
A - D
B - B
B - C
B - D
C - C
C - D
D - D