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#!/usr/bin/env python
from __future__ import print_function
"""
test_files_post_merge.py
bug where @files follows merge and extra parenthesis inserted
"""
import os
tempdir = os.path.relpath(os.path.abspath(os.path.splitext(__file__)[0])) + "/"
test_file = tempdir + "test_output"
jobs_per_task = 50
import os
import sys
# 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]
from ruffus import *
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# split_fasta_file
#
def do_write(file_name, what):
with open(file_name, "a") as oo:
oo.write(what)
test_file = tempdir + "task.done"
@posttask(lambda: do_write(test_file, "Split into %d files\n" % jobs_per_task))
@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(jobs_per_task):
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: do_write(test_file, "Sequences aligned\n"))
@transform(split_fasta_file, suffix(".fa"), ".aln") # 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: do_write(test_file, "%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: do_write(test_file, "Results recombined\n"))
@merge(percentage_identity, tempdir + "all.combine_results")
def combine_results (input_files, output_files):
"""
Combine all
"""
(output_filename) = output_files
with open(output_filename, "w") as oo:
for inp, flag in input_files:
with open(inp) as ii:
oo.write(ii.read())
@files(combine_results, os.path.join(tempdir, "check_all_is.well"))
def post_merge_check (input_filename, output_filename):
"""
check that merge sends just one file, not a list to me
"""
with open(output_filename, "w") as oo:
with open(input_filename) as ii:
oo.write(ii.read())
@files(post_merge_check, os.path.join(tempdir, "check_all_is.weller"))
def post_post_merge_check (input_filename, output_filename):
"""
check that @files forwards a single file on when given a single file
"""
with open(output_filename, "w") as oo:
with open(input_filename) as ii:
oo.write(ii.read())
import unittest, shutil
try:
from StringIO import StringIO
except:
from io import StringIO
class Test_ruffus(unittest.TestCase):
def setUp(self):
try:
shutil.rmtree(tempdir)
except:
pass
os.makedirs(tempdir)
open(tempdir + "original.fa", "w").close()
self.expected_text = """Split into %d files
Sequences aligned
%%Identity calculated
Results recombined
""" % jobs_per_task
def tearDown(self):
try:
shutil.rmtree(tempdir)
except:
pass
def test_ruffus (self):
pipeline_run(multiprocess = 50, verbose = 0, pipeline= "main")
with open(test_file) as ii:
post_task_text = ii.read()
self.assertEqual(post_task_text, self.expected_text)
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: do_write(test_file, "Split into %d files\n" % jobs_per_task))
test_pipeline.transform(task_func = align_sequences,
input = split_fasta_file,
filter = suffix(".fa"),
output = ".aln" # fa -> aln
)\
.posttask(lambda: do_write(test_file, "Sequences aligned\n"))
test_pipeline.transform(task_func = percentage_identity,
input = align_sequences, # find all results from align_sequences
filter = suffix(".aln"), # replace suffix with:
output = [r".pcid", # .pcid suffix for the result
r".pcid_success"] # .pcid_success to indicate job completed
)\
.posttask(lambda: do_write(test_file, "%Identity calculated\n"))
test_pipeline.merge(task_func = combine_results,
input = percentage_identity,
output = tempdir + "all.combine_results")\
.posttask(lambda: do_write(test_file, "Results recombined\n"))
test_pipeline.files(post_merge_check, combine_results, os.path.join(tempdir, "check_all_is.well"))
test_pipeline.files(post_post_merge_check, post_merge_check, os.path.join(tempdir, "check_all_is.weller"))
test_pipeline.run(multiprocess = 50, verbose = 0)
with open(test_file) as ii:
post_task_text = ii.read()
self.assertEqual(post_task_text, self.expected_text)
if __name__ == '__main__':
unittest.main()
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