#!/usr/bin/env python # -*- coding: utf-8 -*- """test_anim.py Test anim.py module. These tests are intended to be run from the repository root using: pytest -v print() statements will be caught by pytest unless there is an error. (c) The James Hutton Institute 2017 Author: Leighton Pritchard Contact: leighton.pritchard@hutton.ac.uk Leighton Pritchard, Information and Computing Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, DD6 9LH, Scotland, UK The MIT License Copyright (c) 2017 The James Hutton Institute Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ import os import unittest import pandas as pd import pytest from pandas.testing import assert_frame_equal from pyani import anim, pyani_files class TestNUCmerCmdline(unittest.TestCase): """Class defining tests of NUCmer command-line generation.""" def setUp(self): """Set parameters for tests.""" # Basic NUCmer and delta-filter command-line targets self.ntgt = " ".join( [ "nucmer --mum -p", "tests/test_output/anim/nucmer_output/file1_vs_file2", "file1.fna file2.fna", ] ) self.ntgtmax = " ".join( [ "nucmer --maxmatch -p", "tests/test_output/anim/nucmer_output/file1_vs_file2", "file1.fna file2.fna", ] ) self.ftgt = " ".join( [ "delta_filter_wrapper.py delta-filter -1", "tests/test_output/anim/nucmer_output/file1_vs_file2.delta", "tests/test_output/anim/nucmer_output/file1_vs_file2.filter", ] ) self.files = ["file1", "file2", "file3", "file4"] self.ncmdlist = [ "nucmer --mum -p ./nucmer_output/file1_vs_file2 file1 file2", "nucmer --mum -p ./nucmer_output/file1_vs_file3 file1 file3", "nucmer --mum -p ./nucmer_output/file1_vs_file4 file1 file4", "nucmer --mum -p ./nucmer_output/file2_vs_file3 file2 file3", "nucmer --mum -p ./nucmer_output/file2_vs_file4 file2 file4", "nucmer --mum -p ./nucmer_output/file3_vs_file4 file3 file4", ] self.fcmdlist = [ " ".join( [ "delta_filter_wrapper.py delta-filter -1", "./nucmer_output/file1_vs_file2.delta", "./nucmer_output/file1_vs_file2.filter", ] ), " ".join( [ "delta_filter_wrapper.py delta-filter -1", "./nucmer_output/file1_vs_file3.delta", "./nucmer_output/file1_vs_file3.filter", ] ), " ".join( [ "delta_filter_wrapper.py delta-filter -1", "./nucmer_output/file1_vs_file4.delta", "./nucmer_output/file1_vs_file4.filter", ] ), " ".join( [ "delta_filter_wrapper.py delta-filter -1", "./nucmer_output/file2_vs_file3.delta", "./nucmer_output/file2_vs_file3.filter", ] ), " ".join( [ "delta_filter_wrapper.py delta-filter -1", "./nucmer_output/file2_vs_file4.delta", "./nucmer_output/file2_vs_file4.filter", ] ), " ".join( [ "delta_filter_wrapper.py delta-filter -1", "./nucmer_output/file3_vs_file4.delta", "./nucmer_output/file3_vs_file4.filter", ] ), ] self.outdir = os.path.join("tests", "test_output", "anim") self.indir = os.path.join("tests", "test_input", "anim") def test_single_cmd_generation(self): """generate single abstract NUCmer/delta-filter command-line. Tests that a single NUCmer/delta-filter command-line pair is produced correctly """ cmds = anim.construct_nucmer_cmdline("file1.fna", "file2.fna", outdir=self.outdir) assert cmds == (self.ntgt, self.ftgt) def test_maxmatch_cmd_generation(self): """generate NUCmer command line with maxmatch.""" ncmd, fcmd = anim.construct_nucmer_cmdline("file1.fna", "file2.fna", outdir=self.outdir, maxmatch=True) assert ncmd == self.ntgtmax def test_multi_cmd_generation(self): """generate multiple abstract NUCmer/delta-filter command-lines. Tests that all the input files are correctly-paired """ cmds = anim.generate_nucmer_commands(self.files) assert cmds == (self.ncmdlist, self.fcmdlist) def test_nucmer_job_generation(self): """generate dependency tree of NUCmer/delta-filter jobs. Tests that the correct dependency graph and naming scheme is produced. """ joblist = anim.generate_nucmer_jobs(self.files, jobprefix="test") assert len(joblist) == 6 for idx, job in enumerate(joblist): assert job.name == "test_%06d-f" % idx # filter job name assert len(job.dependencies) == 1 # has NUCmer job assert job.dependencies[0].name == "test_%06d-n" % idx # NUCmer job name class TestDeltafileProcessing(unittest.TestCase): """Class defining tests for .delta/.filter file parsing""" def setUp(self): """Set parameters for tests.""" self.indir = os.path.join("tests", "test_input", "anim") self.seqdir = os.path.join("tests", "test_input", "sequences") self.deltafile = os.path.join(self.indir, "test.delta") self.deltadir = os.path.join(self.indir, "deltadir") self.df_pid = pd.DataFrame( [ [1.000000, 0.850994, 0.999974, 0.867940], [0.850994, 1.000000, 0.851074, 0.852842], [0.999974, 0.851074, 1.000000, 0.867991], [0.867940, 0.852842, 0.867991, 1.000000], ], columns=["NC_002696", "NC_010338", "NC_011916", "NC_014100"], index=["NC_002696", "NC_010338", "NC_011916", "NC_014100"], ) def test_deltafile_import(self): """parses NUCmer .delta/.filter file.""" result = anim.parse_delta(self.deltafile) assert result == (4073917, 2191) def test_process_deltadir(self): """processes directory of .delta files into ANIResults.""" seqfiles = pyani_files.get_fasta_files(self.seqdir) orglengths = pyani_files.get_sequence_lengths(seqfiles) result = anim.process_deltadir(self.deltadir, orglengths) assert_frame_equal( result.percentage_identity.sort_index(axis=1).sort_index(), self.df_pid.sort_index(axis=1).sort_index(), )