test_alpha_diversity.py

#!/usr/bin/env python
# File created on 13 Jul 2012
from __future__ import division

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"

from shutil import rmtree
from glob import glob
from os import close
from os.path import exists, join
from tempfile import mkstemp, mkdtemp

from skbio.util import remove_files
from unittest import TestCase, main
from qiime.parallel.alpha_diversity import ParallelAlphaDiversity
from qiime.util import get_qiime_temp_dir, count_seqs_in_filepaths
from qiime.test import initiate_timeout, disable_timeout


class ParallelAlphaDiversityTests(TestCase):

    def setUp(self):
        """ """
        self.files_to_remove = []
        self.dirs_to_remove = []

        tmp_dir = get_qiime_temp_dir()
        self.test_out = mkdtemp(dir=tmp_dir,
                                prefix='qiime_parallel_tests_',
                                suffix='')
        self.dirs_to_remove.append(self.test_out)

        self.rt_fps = []
        for rt in [rt1, rt2, rt3, rt4]:
            fd, rt_fp = mkstemp(dir=self.test_out,
                               prefix='qiime_rt',
                               suffix='.biom')
            close(fd)
            rt_f = open(rt_fp, 'w')
            rt_f.write(rt)
            rt_f.close()
            self.rt_fps.append(rt_fp)
            self.files_to_remove.append(rt_fp)

        fd, self.tree_fp = mkstemp(dir=self.test_out,
                                  prefix='qiime',
                                  suffix='.tre')
        close(fd)
        tree_f = open(self.tree_fp, 'w')
        tree_f.write(tree)
        tree_f.close()
        self.files_to_remove.append(self.tree_fp)

        initiate_timeout(60)

    def tearDown(self):
        """ """
        disable_timeout()
        remove_files(self.files_to_remove)
        # remove directories last, so we don't get errors
        # trying to remove files which may be in the directories
        for d in self.dirs_to_remove:
            if exists(d):
                rmtree(d)

    def test_parallel_alpha_diversity(self):
        """parallel alpha diversity functions as expected with basic input
        """
        params = {'metrics': 'observed_species,chao1,PD_whole_tree',
                  'tree_path': self.tree_fp,
                  'jobs_to_start': 2
                  }
        app = ParallelAlphaDiversity()
        r = app(self.rt_fps,
                self.test_out,
                params,
                job_prefix='ATEST',
                poll_directly=True,
                suppress_submit_jobs=False)
        # confirm that the total number of output sequences equals the total
        # number of input sequences
        output_fps = glob(join(self.test_out, '*txt'))
        self.assertEqual(len(output_fps), len(self.rt_fps))

    def test_parallel_alpha_diversity_wo_tree(self):
        """parallel alpha diversity functions as expected without tree
        """
        params = {'metrics': 'observed_species,chao1',
                  'tree_path': None,
                  'jobs_to_start': 2
                  }
        app = ParallelAlphaDiversity()
        r = app(self.rt_fps,
                self.test_out,
                params,
                job_prefix='ATEST',
                poll_directly=True,
                suppress_submit_jobs=False)
        # confirm that the total number of output sequences equals the total
        # number of input sequences
        output_fps = glob(join(self.test_out, '*txt'))
        self.assertEqual(len(output_fps), len(self.rt_fps))


rt1 = """{"rows": [{"id": "0", "metadata": {}}, {"id": "1", "metadata": {}}, {"id": "2", "metadata": {}}, {"id": "3", "metadata": {}}, {"id": "4", "metadata": {}}, {"id": "5", "metadata": {}}, {"id": "6", "metadata": {}}, {"id": "8", "metadata": {}}, {"id": "9", "metadata": {}}, {"id": "10", "metadata": {}}, {"id": "11", "metadata": {}}, {"id": "12", "metadata": {}}, {"id": "13", "metadata": {}}, {"id": "14", "metadata": {}}, {"id": "16", "metadata": {}}, {"id": "17", "metadata": {}}, {"id": "23", "metadata": {}}, {"id": "24", "metadata": {}}, {"id": "25", "metadata": {}}, {"id": "26", "metadata": {}}, {"id": "27", "metadata": {}}, {"id": "29", "metadata": {}}, {"id": "30", "metadata": {}}, {"id": "31", "metadata": {}}, {"id": "32", "metadata": {}}, {"id": "33", "metadata": {}}, {"id": "34", "metadata": {}}, {"id": "35", "metadata": {}}, {"id": "37", "metadata": {}}, {"id": "38", "metadata": {}}, {"id": "39", "metadata": {}}, {"id": "41", "metadata": {}}, {"id": "42", "metadata": {}}, {"id": "43", "metadata": {}}, {"id": "44", "metadata": {}}, {"id": "45", "metadata": {}}, {"id": "46", "metadata": {}}, {"id": "48", "metadata": {}}, {"id": "49", "metadata": {}}, {"id": "51", "metadata": {}}, {"id": "52", "metadata": {}}, {"id": "53", "metadata": {}}, {"id": "54", "metadata": {}}, {"id": "56", "metadata": {}}, {"id": "57", "metadata": {}}, {"id": "58", "metadata": {}}, {"id": "59", "metadata": {}}, {"id": "60", "metadata": {}}, {"id": "62", "metadata": {}}, {"id": "63", "metadata": {}}, {"id": "64", "metadata": {}}, {"id": "65", "metadata": {}}, {"id": "66", "metadata": {}}, {"id": "70", "metadata": {}}, {"id": "71", "metadata": {}}, {"id": "72", "metadata": {}}, {"id": "73", "metadata": {}}, {"id": "74", "metadata": {}}, {"id": "75", "metadata": {}}, {"id": "76", "metadata": {}}, {"id": "77", "metadata": {}}, {"id": "78", "metadata": {}}, {"id": "81", "metadata": {}}, {"id": "82", "metadata": {}}, {"id": "83", "metadata": {}}, {"id": "84", "metadata": {}}, {"id": 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"metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2826", "matrix_type": "sparse", "shape": [316, 9], "format_url": "http://biom-format.org", "date": "2012-03-14T16:24:01.170353", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""

rt2 = """{"rows": [{"id": "1", "metadata": {}}, {"id": "3", "metadata": {}}, {"id": "5", "metadata": {}}, {"id": "8", "metadata": {}}, {"id": "10", "metadata": {}}, {"id": "11", "metadata": {}}, {"id": "12", "metadata": {}}, {"id": "13", "metadata": {}}, {"id": "14", "metadata": {}}, {"id": "15", "metadata": {}}, {"id": "16", "metadata": {}}, {"id": "17", "metadata": {}}, {"id": "18", "metadata": {}}, {"id": "20", "metadata": {}}, {"id": "21", "metadata": {}}, {"id": "23", "metadata": {}}, {"id": "24", "metadata": {}}, {"id": "25", "metadata": {}}, {"id": "26", "metadata": {}}, {"id": "27", "metadata": {}}, {"id": "28", "metadata": {}}, {"id": "29", "metadata": {}}, {"id": "30", "metadata": {}}, {"id": "31", "metadata": {}}, {"id": "32", "metadata": {}}, {"id": "33", "metadata": {}}, {"id": "34", "metadata": {}}, {"id": "35", "metadata": {}}, {"id": "36", "metadata": {}}, {"id": "37", "metadata": {}}, {"id": "39", "metadata": {}}, {"id": "40", "metadata": {}}, {"id": "41", "metadata": 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[285, 8, 1.0], [286, 0, 1.0], [286, 1, 3.0], [286, 7, 4.0], [286, 8, 6.0], [287, 0, 3.0], [287, 1, 3.0], [287, 3, 1.0], [287, 4, 1.0], [287, 6, 15.0], [287, 8, 16.0], [288, 2, 1.0], [289, 2, 1.0], [290, 3, 1.0], [291, 6, 1.0], [291, 7, 1.0], [292, 2, 1.0], [293, 4, 1.0], [294, 2, 1.0], [295, 2, 1.0], [296, 2, 1.0], [297, 2, 1.0], [298, 8, 1.0], [299, 2, 2.0], [299, 5, 2.0], [299, 6, 13.0], [299, 8, 2.0], [300, 2, 1.0], [301, 3, 1.0], [302, 2, 1.0], [302, 6, 1.0], [303, 0, 2.0], [303, 2, 1.0], [303, 5, 5.0], [303, 6, 1.0], [303, 7, 1.0], [303, 8, 1.0], [304, 7, 1.0], [305, 8, 1.0], [306, 0, 3.0], [306, 2, 1.0], [306, 3, 1.0], [306, 5, 2.0], [306, 6, 2.0], [306, 8, 2.0], [307, 8, 1.0], [308, 6, 1.0], [309, 4, 1.0], [310, 3, 1.0], [311, 0, 1.0], [311, 2, 1.0], [311, 3, 1.0], [311, 6, 2.0], [311, 8, 1.0], [312, 8, 1.0], [313, 8, 1.0], [314, 0, 1.0], [315, 3, 6.0], [315, 8, 2.0], [316, 0, 1.0], [317, 0, 1.0], [318, 0, 2.0], [318, 1, 3.0], [318, 8, 7.0], [319, 6, 1.0], [320, 3, 1.0], [321, 0, 1.0]], "columns": [{"id": "PC.636", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.354", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2826", "matrix_type": "sparse", "shape": [322, 9], "format_url": "http://biom-format.org", "date": "2012-03-14T16:24:01.254089", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""

rt3 = """{"rows": [{"id": "0", "metadata": {}}, {"id": "2", "metadata": {}}, {"id": "4", "metadata": {}}, {"id": "5", "metadata": {}}, {"id": "7", "metadata": {}}, {"id": "8", "metadata": {}}, {"id": "9", "metadata": {}}, {"id": "10", "metadata": {}}, {"id": "11", "metadata": {}}, {"id": "12", "metadata": {}}, {"id": "13", "metadata": {}}, {"id": "14", "metadata": {}}, {"id": "18", "metadata": {}}, {"id": "19", "metadata": {}}, {"id": "20", "metadata": {}}, {"id": "21", "metadata": {}}, {"id": "24", "metadata": {}}, {"id": "25", "metadata": {}}, {"id": "27", "metadata": {}}, {"id": "28", "metadata": {}}, {"id": "29", "metadata": {}}, {"id": "30", "metadata": {}}, {"id": "31", "metadata": {}}, {"id": "32", "metadata": {}}, {"id": "33", "metadata": {}}, {"id": "34", "metadata": {}}, {"id": "35", "metadata": {}}, {"id": "36", "metadata": {}}, {"id": "37", "metadata": {}}, {"id": "38", "metadata": {}}, {"id": "39", "metadata": {}}, {"id": "40", "metadata": {}}, {"id": "41", "metadata": 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[318, 0, 1.0], [319, 3, 6.0], [319, 8, 2.0], [320, 6, 1.0], [321, 0, 2.0], [321, 1, 7.0], [321, 8, 5.0], [322, 6, 1.0], [323, 2, 1.0], [323, 3, 1.0], [324, 6, 1.0], [325, 0, 1.0]], "columns": [{"id": "PC.636", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.354", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2826", "matrix_type": "sparse", "shape": [326, 9], "format_url": "http://biom-format.org", "date": "2012-03-14T16:24:01.347554", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""

rt4 = """{"rows": [{"id": "0", "metadata": {}}, {"id": "2", "metadata": {}}, {"id": "4", "metadata": {}}, {"id": "5", "metadata": {}}, {"id": "6", "metadata": {}}, {"id": "7", "metadata": {}}, {"id": "8", "metadata": {}}, {"id": "9", "metadata": {}}, {"id": "10", "metadata": {}}, {"id": "11", "metadata": {}}, {"id": "13", "metadata": {}}, {"id": "14", "metadata": {}}, {"id": "15", "metadata": {}}, {"id": "16", "metadata": {}}, {"id": "17", "metadata": {}}, {"id": "19", "metadata": {}}, {"id": "20", "metadata": {}}, {"id": "21", "metadata": {}}, {"id": "22", "metadata": {}}, {"id": "24", "metadata": {}}, {"id": "25", "metadata": {}}, {"id": "26", "metadata": {}}, {"id": "27", "metadata": {}}, {"id": "29", "metadata": {}}, {"id": "30", "metadata": {}}, {"id": "31", "metadata": {}}, {"id": "32", "metadata": {}}, {"id": "33", "metadata": {}}, {"id": "34", "metadata": {}}, {"id": "35", "metadata": {}}, {"id": "37", "metadata": {}}, {"id": "38", "metadata": {}}, {"id": "39", "metadata": {}}, 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tree = 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if __name__ == "__main__":
    main()