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#!/usr/bin/env python
# Author: Greg Caporaso (gregcaporaso@gmail.com)
# test_util.py
""" Description
File created on 25 Aug 2009.
"""
from __future__ import division
from os import remove
from cogent import LoadSeqs
from cogent.util.misc import remove_files
from cogent.util.unit_test import TestCase, main
from qiime.util import get_tmp_filename
from qiime.parallel.util import (split_fasta, get_random_job_prefix,
write_jobs_file, compute_seqs_per_file, build_filepaths_from_filepaths,
submit_jobs, merge_to_n_commands)
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
class UtilTests(TestCase):
"""Tests of parallel code utility functions """
def setUp(self):
pass
def test_get_random_job_prefix(self):
""" get_random_job_prefix functions as expected """
s1 = get_random_job_prefix()
s2 = get_random_job_prefix()
self.assertNotEqual(s1,s2)
self.assertEqual(len(s1),10)
self.assertEqual(len(s2),10)
# different max len
s1 = get_random_job_prefix(max_job_prefix_len=22)
self.assertEqual(len(s1),22)
# fixed_prefix added
s1 = get_random_job_prefix(fixed_prefix='TEST')
s2 = get_random_job_prefix(fixed_prefix='TEST')
self.assertNotEqual(s1,s2)
self.assertEqual(len(s1),10)
self.assertTrue(s1.startswith('TEST'))
self.assertTrue(s2.startswith('TEST'))
# leading/trailing underscores added
self.assertTrue(s1.startswith('TEST_'))
self.assertTrue(s1.endswith('_'))
# no leading/trailing underscores
s1 = get_random_job_prefix(leading_trailing_underscores=False)
self.assertFalse(s1.startswith('_'))
self.assertFalse(s1.endswith('_'))
# combo of all parameters
s1 = get_random_job_prefix(leading_trailing_underscores=False,\
fixed_prefix='HELLO',max_job_prefix_len=12)
self.assertEqual(len(s1),12)
self.assertTrue(s1.startswith('HELLO'))
self.assertFalse(s1.endswith('_'))
def test_merge_to_n_commands_even(self):
""" merge_to_n_commands functions as expected (even number of cmds)"""
commands = ['pick_otus.py -h ; mv somthing.txt something_else.txt',
'pick_otus.py -g',
'pick_otus.py -f',
'pick_otus.py -w']
expected = ['/bin/bash ; pick_otus.py -h ; mv somthing.txt something_else.txt ; pick_otus.py -g ; pick_otus.py -f ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,1)
self.assertEqual(actual,expected)
expected = [
'/bin/bash ; pick_otus.py -h ; mv somthing.txt something_else.txt ; pick_otus.py -g ; exit',
'/bin/bash ; pick_otus.py -f ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,2)
self.assertEqual(actual,expected)
# rounds to 2 jobs to start
expected = [
'/bin/bash ; pick_otus.py -h ; mv somthing.txt something_else.txt ; pick_otus.py -g ; exit',
'/bin/bash ; pick_otus.py -f ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,3)
self.assertEqual(actual,expected)
expected = ['/bin/bash ; pick_otus.py -h ; mv somthing.txt something_else.txt ; exit',
'/bin/bash ; pick_otus.py -g ; exit',
'/bin/bash ; pick_otus.py -f ; exit',
'/bin/bash ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,4)
self.assertEqual(actual,expected)
self.assertRaises(ValueError,merge_to_n_commands,commands,0)
self.assertRaises(ValueError,merge_to_n_commands,commands,-42)
# jobs to start is much higer than actual jobs
expected = ['/bin/bash ; pick_otus.py -h ; mv somthing.txt something_else.txt ; exit',
'/bin/bash ; pick_otus.py -g ; exit',
'/bin/bash ; pick_otus.py -f ; exit',
'/bin/bash ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,100)
self.assertEqual(actual,expected)
self.assertRaises(ValueError,merge_to_n_commands,commands,0)
self.assertRaises(ValueError,merge_to_n_commands,commands,-42)
def test_merge_to_n_commands_odd(self):
""" merge_to_n_commands functions as expected (odd number of cmds)"""
commands = ['pick_otus.py -h',
'pick_otus.py -g',
'pick_otus.py -w']
expected = ['/bin/bash ; pick_otus.py -h ; pick_otus.py -g ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,1)
self.assertEqual(actual,expected)
# rounds to 1 job to start
expected = ['/bin/bash ; pick_otus.py -h ; pick_otus.py -g ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,2)
self.assertEqual(actual,expected)
expected = ['/bin/bash ; pick_otus.py -h ; exit',
'/bin/bash ; pick_otus.py -g ; exit',
'/bin/bash ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,3)
self.assertEqual(actual,expected)
expected = ['/bin/bash ; pick_otus.py -h ; exit',
'/bin/bash ; pick_otus.py -g ; exit',
'/bin/bash ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,4)
self.assertEqual(actual,expected)
expected = ['/bin/bash ; pick_otus.py -h ; exit',
'/bin/bash ; pick_otus.py -g ; exit',
'/bin/bash ; pick_otus.py -w ; exit']
actual = merge_to_n_commands(commands,100)
self.assertEqual(actual,expected)
self.assertRaises(ValueError,merge_to_n_commands,commands,0)
self.assertRaises(ValueError,merge_to_n_commands,commands,-42)
def test_merge_to_n_commands_alt_params(self):
""" merge_to_n_commands functions with alt params"""
commands = ['pick_otus.py -h',
'pick_otus.py -g',
'pick_otus.py -w']
expected = ['pick_otus.py -h ; pick_otus.py -g ; pick_otus.py -w']
actual = merge_to_n_commands(commands,2,command_prefix='',command_suffix='')
self.assertEqual(actual,expected)
expected = ['pick_otus.py -h ! pick_otus.py -g ! pick_otus.py -w']
actual = merge_to_n_commands(commands,2,command_prefix='',
command_suffix='',delimiter=' ! ')
self.assertEqual(actual,expected)
commands = map(str,range(10))
actual = merge_to_n_commands(commands,5,command_prefix='',
command_suffix='',delimiter=',')
expected = ['0,1','2,3','4,5','6,7','8,9']
self.assertEqual(actual,expected)
def test_submit_jobs_fail(self):
"""submit jobs fails by raising an error
"""
self.assertRaises(RuntimeError,submit_jobs,
'some_fake_exe','some_fake_fp.txt','JOB')
def test_compute_seqs_per_file(self):
"""compute_seqs_per_file functions as expected
"""
temp_fasta_fp = get_tmp_filename(\
prefix='QiimeScriptUtilTests',suffix='.fasta')
temp_fasta = ['>seq','AAACCCCAAATTGG'] * 25
open(temp_fasta_fp,'w').write('\n'.join(temp_fasta))
actual_25 = compute_seqs_per_file(temp_fasta_fp,25)
actual_2 = compute_seqs_per_file(temp_fasta_fp,2)
actual_10 = compute_seqs_per_file(temp_fasta_fp,10)
actual_5 = compute_seqs_per_file(temp_fasta_fp,5)
actual_40 = compute_seqs_per_file(temp_fasta_fp,40)
remove(temp_fasta_fp)
self.assertEqual(actual_25,1)
self.assertEqual(actual_2,13)
self.assertEqual(actual_10,3)
self.assertEqual(actual_5,5)
self.assertEqual(actual_40,1)
def test_build_filepaths_from_filepaths(self):
""" build_filepaths_from_filepaths functions as expected
"""
# no additional params just strips paths
in_fps = ['in1.txt','somewhere/in2.txt','in3.txt']
actual = build_filepaths_from_filepaths(in_fps)
expected = ['in1.txt','in2.txt','in3.txt']
self.assertEqual(actual,expected)
# replace works as expected
in_fps = ['in1.txt','somewhere/in2.txt','in3.txt']
actual = build_filepaths_from_filepaths(in_fps,replacement=('.txt','.fasta'))
expected = ['in1.fasta','in2.fasta','in3.fasta']
self.assertEqual(actual,expected)
# adding directory works as expected (no trailing / in directory)
in_fps = ['in1.txt','somewhere/in2.txt','in3.txt']
actual = build_filepaths_from_filepaths(in_fps,directory='/home/bob')
expected = ['/home/bob/in1.txt','/home/bob/in2.txt','/home/bob/in3.txt']
self.assertEqual(actual,expected)
# adding directory works as expected (trailing / in directory)
in_fps = ['in1.txt','somewhere/in2.txt','in3.txt']
actual = build_filepaths_from_filepaths(in_fps,directory='/home/bob/')
expected = ['/home/bob/in1.txt','/home/bob/in2.txt','/home/bob/in3.txt']
self.assertEqual(actual,expected)
# prefix works as expected
in_fps = ['in1.txt','somewhere/in2.txt','in3.txt']
actual = build_filepaths_from_filepaths(in_fps,prefix='blah_')
expected = ['blah_in1.txt','blah_in2.txt','blah_in3.txt']
self.assertEqual(actual,expected)
# suffix works as expected
in_fps = ['in1.txt','somewhere/in2.txt','in3.txt']
actual = build_filepaths_from_filepaths(in_fps,suffix='.out')
expected = ['in1.txt.out','in2.txt.out','in3.txt.out']
self.assertEqual(actual,expected)
# combination works as expected (including order of operations)
in_fps = ['txt_dir/in1.txt','somewhere/in2.txt','txt_dir/in3.txt']
actual = build_filepaths_from_filepaths(in_fps,replacement=('txt','fasta'),\
prefix='blah_',suffix='.out',directory='out/')
expected = ['out/blah_in1.fasta.out','out/blah_in2.fasta.out',\
'out/blah_in3.fasta.out']
self.assertEqual(actual,expected)
actual = build_filepaths_from_filepaths(in_fps,prefix='',\
directory='',suffix='',replacement=('',''))
def test_split_fasta_equal_num_seqs_per_file(self):
"""split_fasta funcs as expected when equal num seqs go to each file
"""
filename_prefix = get_random_job_prefix(fixed_prefix='/tmp/')
infile = ['>seq1','AACCTTAA','>seq2','TTAACC','AATTAA',\
'>seq3','CCTT--AA']
actual = split_fasta(infile, 1, filename_prefix)
actual_seqs = []
for fp in actual:
actual_seqs += list(open(fp))
remove_files(actual)
expected = ['%s.%d.fasta' % (filename_prefix,i) for i in range(3)]
self.assertEqual(actual,expected)
self.assertEqual(\
LoadSeqs(data=infile,aligned=False),\
LoadSeqs(data=actual_seqs,aligned=False))
def test_split_fasta_diff_num_seqs_per_file(self):
"""split_fasta funcs as expected when diff num seqs go to each file
"""
filename_prefix = get_random_job_prefix(fixed_prefix='/tmp/')
infile = ['>seq1','AACCTTAA','>seq2','TTAACC','AATTAA',\
'>seq3','CCTT--AA']
actual = split_fasta(infile, 2, filename_prefix)
actual_seqs = []
for fp in actual:
actual_seqs += list(open(fp))
remove_files(actual)
expected = ['%s.%d.fasta' % (filename_prefix,i) for i in range(2)]
# list of file paths is as expected
self.assertEqual(actual,expected)
# building seq collections from infile and the split files result in
# equivalent seq collections
self.assertEqual(\
LoadSeqs(data=infile,aligned=False),\
LoadSeqs(data=actual_seqs,aligned=False))
def test_split_fasta_diff_num_seqs_per_file_alt(self):
"""split_fasta funcs always catches all seqs
"""
# start with 59 seqs (b/c it's prime, so should make more
# confusing splits)
in_seqs = LoadSeqs(data=[('seq%s' % k,'AACCTTAA') for k in range(59)])
infile = in_seqs.toFasta().split('\n')
# test seqs_per_file from 1 to 1000
for i in range(1,1000):
filename_prefix = get_random_job_prefix(fixed_prefix='/tmp/')
actual = split_fasta(infile, i, filename_prefix)
actual_seqs = []
for fp in actual:
actual_seqs += list(open(fp))
# remove the files now, so if the test fails they still get
# cleaned up
remove_files(actual)
# building seq collections from infile and the split files result in
# equivalent seq collections
self.assertEqual(\
LoadSeqs(data=infile,aligned=False),\
LoadSeqs(data=actual_seqs,aligned=False))
if __name__ == "__main__":
main()
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