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#!/usr/bin/env python
from __future__ import print_function
import shutil
import unittest
from ruffus import posttask, split, merge, transform, pipeline_printout, pipeline_run, Pipeline, suffix
"""
test_split_and_combine.py
test branching dependencies
"""
import sys
import os
tempdir = os.path.relpath(os.path.abspath(os.path.splitext(__file__)[0])) + "/"
verbose_output = sys.stderr
# add grandparent to search path for testing
grandparent_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", ".."))
sys.path.insert(0, grandparent_dir)
# module name = script name without extension
module_name = os.path.splitext(os.path.basename(__file__))[0]
# funky code to import by file name
parent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# split_fasta_file
#
@posttask(lambda: verbose_output.write(" Split into %d files\n" % 10))
@split(tempdir + "original.fa", [tempdir + "files.split.success", tempdir + "files.split.*.fa"])
def split_fasta_file(input_file, outputs):
#
# remove previous fasta files
#
success_flag = outputs[0]
output_file_names = outputs[1:]
for f in output_file_names:
os.unlink(f)
#
# create as many files as we are simulating in jobs_per_task
#
for i in range(10):
with open(tempdir + "files.split.%03d.fa" % i, "w") as oo:
pass
with open(success_flag, "w") as oo:
pass
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# align_sequences
#
@posttask(lambda: verbose_output.write(" Sequences aligned\n"))
# fa -> aln
@transform(split_fasta_file, suffix(".fa"), ".aln")
def align_sequences(input_file, output_filename):
with open(output_filename, "w") as oo:
oo.write("%s\n" % output_filename)
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# percentage_identity
#
@posttask(lambda: verbose_output.write(" %Identity calculated\n"))
@transform(align_sequences, # find all results from align_sequences
suffix(".aln"), # replace suffix with:
[r".pcid", # .pcid suffix for the result
r".pcid_success"]) # .pcid_success to indicate job completed
def percentage_identity(input_file, output_files):
(output_filename, success_flag_filename) = output_files
with open(output_filename, "w") as oo:
oo.write("%s\n" % output_filename)
with open(success_flag_filename, "w") as oo:
pass
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# combine_results
#
@posttask(lambda: verbose_output.write(" Results recombined\n"))
@merge(percentage_identity, [tempdir + "all.combine_results",
tempdir + "all.combine_results_success"])
def combine_results(input_files, output_files):
"""
Combine all
"""
(output_filename, success_flag_filename) = output_files
with open(output_filename, "w") as out:
for inp, flag in input_files:
with open(inp) as ii:
out.write(ii.read())
with open(success_flag_filename, "w") as oo:
pass
class Test_ruffus(unittest.TestCase):
def setUp(self):
try:
shutil.rmtree(tempdir)
except:
pass
os.makedirs(tempdir)
open(tempdir + "original.fa", "w").close()
def tearDown(self):
try:
shutil.rmtree(tempdir)
pass
except:
pass
def test_ruffus(self):
pipeline_run(multiprocess=50, verbose=0, pipeline="main")
if not os.path.exists(tempdir + "all.combine_results"):
raise Exception("Missing %s" % (tempdir + "all.combine_results"))
def test_newstyle_ruffus(self):
test_pipeline = Pipeline("test")
test_pipeline.split(task_func=split_fasta_file,
input=tempdir + "original.fa",
output=[tempdir + "files.split.success",
tempdir + "files.split.*.fa"])\
.posttask(lambda: verbose_output.write(" Split into %d files\n" % 10))
test_pipeline.transform(task_func=align_sequences,
input=split_fasta_file,
filter=suffix(".fa"),
output=".aln" # fa -> aln
)\
.posttask(lambda: verbose_output.write(" Sequences aligned\n"))
test_pipeline.transform(task_func=percentage_identity,
input=align_sequences, # find all results from align_sequences
# replace suffix with:
filter=suffix(".aln"),
output=[r".pcid", # .pcid suffix for the result
r".pcid_success"] # .pcid_success to indicate job completed
)\
.posttask(lambda: verbose_output.write(" %Identity calculated\n"))
test_pipeline.merge(task_func=combine_results,
input=percentage_identity,
output=[tempdir + "all.combine_results",
tempdir + "all.combine_results_success"])\
.posttask(lambda: verbose_output.write(" Results recombined\n"))
test_pipeline.run(multiprocess=50, verbose=0)
if not os.path.exists(tempdir + "all.combine_results"):
raise Exception("Missing %s" % (tempdir + "all.combine_results"))
if __name__ == '__main__':
unittest.main()
|
