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.. include:: ../../global.inc
.. include:: manual_chapter_numbers.inc
.. _new_manual.subdivide_collate.code:
#############################################################################################################################################################################################################################################################################################################################
|new_manual.subdivide_collate.chapter_num|: Python Code for :ref:`@subdivide <decorators.subdivide>` tasks to run efficiently and regroup with :ref:`@collate <decorators.collate>`
#############################################################################################################################################################################################################################################################################################################################
.. seealso::
* :ref:`Manual Table of Contents <new_manual.table_of_contents>`
* :ref:`@jobs_limit <decorators.jobs_limit>` syntax
* :ref:`pipeline_run() <pipeline_functions.pipeline_run>` syntax
* :ref:`drmaa_wrapper.run_job() <drmaa_wrapper.run_job>` syntax
* Back to |new_manual.subdivide_collate.chapter_num|: :ref:`:ref:`@subdivide tasks to run efficiently and regroup with @collate <new_manual.subdivide_collate>`
*****************************************************************************************************************************
:ref:`@subdivide <decorators.subdivide>` and regroup with :ref:`@collate <decorators.collate>` example
*****************************************************************************************************************************
.. code-block:: python
:emphasize-lines: 17
from ruffus import *
import os, random, sys
# Create files a random number of lines
@originate(["a.start",
"b.start",
"c.start"])
def create_test_files(output_file):
cnt_lines = random.randint(1,3) * 2
with open(output_file, "w") as oo:
for ii in range(cnt_lines):
oo.write("data item = %d\n" % ii)
print " %s has %d lines" % (output_file, cnt_lines)
#
# subdivide the input files into NNN fragment files of 2 lines each
#
@subdivide( create_test_files,
formatter(),
"{path[0]}/{basename[0]}.*.fragment",
"{path[0]}/{basename[0]}")
def subdivide_files(input_file, output_files, output_file_name_stem):
#
# cleanup any previous results
#
for oo in output_files:
os.unlink(oo)
#
# Output files contain two lines each
# (new output files every even line)
#
cnt_output_files = 0
for ii, line in enumerate(open(input_file)):
if ii % 2 == 0:
cnt_output_files += 1
output_file_name = "%s.%d.fragment" % (output_file_name_stem, cnt_output_files)
output_file = open(output_file_name, "w")
print " Subdivide %s -> %s" % (input_file, output_file_name)
output_file.write(line)
#
# Analyse each fragment independently
#
@transform(subdivide_files, suffix(".fragment"), ".analysed")
def analyse_fragments(input_file, output_file):
print " Analysing %s -> %s" % (input_file, output_file)
with open(output_file, "w") as oo:
for line in open(input_file):
oo.write("analysed " + line)
#
# Group results using original names
#
@collate( analyse_fragments,
# split file name into [abc].NUMBER.analysed
formatter("/(?P<NAME>[abc]+)\.\d+\.analysed$"),
"{path[0]}/{NAME[0]}.final_result")
def recombine_analyses(input_file_names, output_file):
with open(output_file, "w") as oo:
for input_file in input_file_names:
print " Recombine %s -> %s" % (input_file, output_file)
for line in open(input_file):
oo.write(line)
#pipeline_printout(sys.stdout, verbose = 3)
pipeline_run(verbose = 1)
Results in
.. code-block:: pycon
>>> pipeline_run(verbose = 1)
a.start has 2 lines
Job = [None -> a.start] completed
b.start has 6 lines
Job = [None -> b.start] completed
c.start has 6 lines
Job = [None -> c.start] completed
Completed Task = create_test_files
Subdivide a.start -> /home/lg/temp/a.1.fragment
Job = [a.start -> a.*.fragment, a] completed
Subdivide b.start -> /home/lg/temp/b.1.fragment
Subdivide b.start -> /home/lg/temp/b.2.fragment
Subdivide b.start -> /home/lg/temp/b.3.fragment
Job = [b.start -> b.*.fragment, b] completed
Subdivide c.start -> /home/lg/temp/c.1.fragment
Subdivide c.start -> /home/lg/temp/c.2.fragment
Subdivide c.start -> /home/lg/temp/c.3.fragment
Job = [c.start -> c.*.fragment, c] completed
Completed Task = subdivide_files
Analysing /home/lg/temp/a.1.fragment -> /home/lg/temp/a.1.analysed
Job = [a.1.fragment -> a.1.analysed] completed
Analysing /home/lg/temp/b.1.fragment -> /home/lg/temp/b.1.analysed
Job = [b.1.fragment -> b.1.analysed] completed
Analysing /home/lg/temp/b.2.fragment -> /home/lg/temp/b.2.analysed
Job = [b.2.fragment -> b.2.analysed] completed
Analysing /home/lg/temp/b.3.fragment -> /home/lg/temp/b.3.analysed
Job = [b.3.fragment -> b.3.analysed] completed
Analysing /home/lg/temp/c.1.fragment -> /home/lg/temp/c.1.analysed
Job = [c.1.fragment -> c.1.analysed] completed
Analysing /home/lg/temp/c.2.fragment -> /home/lg/temp/c.2.analysed
Job = [c.2.fragment -> c.2.analysed] completed
Analysing /home/lg/temp/c.3.fragment -> /home/lg/temp/c.3.analysed
Job = [c.3.fragment -> c.3.analysed] completed
Completed Task = analyse_fragments
Recombine /home/lg/temp/a.1.analysed -> /home/lg/temp/a.final_result
Job = [[a.1.analysed] -> a.final_result] completed
Recombine /home/lg/temp/b.1.analysed -> /home/lg/temp/b.final_result
Recombine /home/lg/temp/b.2.analysed -> /home/lg/temp/b.final_result
Recombine /home/lg/temp/b.3.analysed -> /home/lg/temp/b.final_result
Job = [[b.1.analysed, b.2.analysed, b.3.analysed] -> b.final_result] completed
Recombine /home/lg/temp/c.1.analysed -> /home/lg/temp/c.final_result
Recombine /home/lg/temp/c.2.analysed -> /home/lg/temp/c.final_result
Recombine /home/lg/temp/c.3.analysed -> /home/lg/temp/c.final_result
Job = [[c.1.analysed, c.2.analysed, c.3.analysed] -> c.final_result] completed
Completed Task = recombine_analyses
|
