#!/usr/bin/env python """test_anib.py Test anib.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 anib, pyani_files class TestBLASTCmdline(unittest.TestCase): """Class defining tests of BLAST command-line generation.""" def setUp(self): """Set parameters for tests.""" self.indir = os.path.join("tests", "test_input", "anib") self.outdir = os.path.join("tests", "test_output", "anib") self.seqdir = os.path.join("tests", "test_input", "sequences") self.infiles = [os.path.join(self.seqdir, fname) for fname in os.listdir(self.seqdir)] self.fraglen = 1000 self.fmtdboutdir = os.path.join(self.outdir, "formatdb") self.fmtdbcmd = " ".join( [ "formatdb -p F -i", "tests/test_output/anib/formatdb/NC_002696.fna", "-t NC_002696", ] ) self.makeblastdbdir = os.path.join(self.outdir, "makeblastdb") self.makeblastdbcmd = " ".join( [ "makeblastdb -dbtype nucl -in", "tests/test_input/sequences/NC_002696.fna", "-title NC_002696 -out", os.path.join("tests", "test_output", "anib", "makeblastdb", "NC_002696.fna"), ] ) self.blastdbfnames = [os.path.join(self.seqdir, fname) for fname in ("NC_002696.fna", "NC_010338.fna")] self.blastdbtgt = [ ( " ".join( [ "makeblastdb -dbtype nucl -in", "tests/test_input/sequences/NC_002696.fna", "-title NC_002696 -out", "tests/test_output/anib/NC_002696.fna", ] ), "tests/test_output/anib/NC_002696.fna", ), ( " ".join( [ "makeblastdb -dbtype nucl -in", "tests/test_input/sequences/NC_010338.fna", "-title NC_010338 -out", "tests/test_output/anib/NC_010338.fna", ] ), "tests/test_output/anib/NC_010338.fna", ), ] self.blastdbtgtlegacy = [ ( " ".join( [ "formatdb -p F -i", "tests/test_output/anib/NC_002696.fna", "-t NC_002696", ] ), "tests/test_output/anib/NC_002696.fna", ), ( " ".join( [ "formatdb -p F -i", "tests/test_output/anib/NC_010338.fna", "-t NC_010338", ] ), "tests/test_output/anib/NC_010338.fna", ), ] self.blastncmd = " ".join( [ "blastn -out", os.path.join("tests", "test_output", "anib", "NC_002696_vs_NC_010338.blast_tab"), "-query tests/test_input/sequences/NC_002696.fna", "-db tests/test_input/sequences/NC_010338.fna", "-xdrop_gap_final 150 -dust no -evalue 1e-15", "-max_target_seqs 1 -outfmt '6 qseqid sseqid", "length mismatch pident nident qlen slen qstart", "qend sstart send positive ppos gaps' -task blastn", ] ) self.blastallcmd = " ".join( [ "blastall -p blastn -o", os.path.join("tests", "test_output", "anib", "NC_002696_vs_NC_010338.blast_tab"), "-i tests/test_input/sequences/NC_002696.fna", "-d tests/test_input/sequences/NC_010338.fna", "-X 150 -q -1 -F F -e 1e-15 -b 1 -v 1 -m 8", ] ) self.blastntgt = [ " ".join( [ "blastn -out", os.path.join( "tests", "test_output", "anib", "NC_002696_vs_NC_010338.blast_tab", ), "-query tests/test_input/sequences/NC_002696.fna", "-db tests/test_input/sequences/NC_010338.fna", "-xdrop_gap_final 150 -dust no -evalue 1e-15", "-max_target_seqs 1 -outfmt '6 qseqid sseqid", "length mismatch pident nident qlen slen qstart", "qend sstart send positive ppos gaps' -task blastn", ] ), " ".join( [ "blastn -out", os.path.join( "tests", "test_output", "anib", "NC_010338_vs_NC_002696.blast_tab", ), "-query tests/test_input/sequences/NC_010338.fna", "-db tests/test_input/sequences/NC_002696.fna", "-xdrop_gap_final 150 -dust no -evalue 1e-15", "-max_target_seqs 1 -outfmt '6 qseqid sseqid length", "mismatch pident nident qlen slen qstart qend", "sstart send positive ppos gaps' -task blastn", ] ), ] self.blastalltgt = [ " ".join( [ "blastall -p blastn -o", os.path.join( "tests", "test_output", "anib", "NC_002696_vs_NC_010338.blast_tab", ), "-i tests/test_input/sequences/NC_002696.fna", "-d tests/test_input/sequences/NC_010338.fna", "-X 150 -q -1 -F F -e 1e-15 -b 1 -v 1 -m 8", ] ), " ".join( [ "blastall -p blastn -o", os.path.join( "tests", "test_output", "anib", "NC_010338_vs_NC_002696.blast_tab", ), "-i tests/test_input/sequences/NC_010338.fna", "-d tests/test_input/sequences/NC_002696.fna", "-X 150 -q -1 -F F -e 1e-15 -b 1 -v 1 -m 8", ] ), ] self.blastnjobdict = sorted( [ ( "tests/test_output/anib/NC_002696.fna", "makeblastdb -dbtype nucl " + "-in tests/test_input/sequences/NC_002696.fna " + "-title NC_002696 -out tests/test_output/anib/NC_002696.fna", ), ( "tests/test_output/anib/NC_010338.fna", "makeblastdb -dbtype nucl " + "-in tests/test_input/sequences/NC_010338.fna " + "-title NC_010338 -out tests/test_output/anib/NC_010338.fna", ), ( "tests/test_output/anib/NC_011916.fna", "makeblastdb -dbtype nucl " + "-in tests/test_input/sequences/NC_011916.fna " + "-title NC_011916 -out tests/test_output/anib/NC_011916.fna", ), ( "tests/test_output/anib/NC_014100.fna", "makeblastdb -dbtype nucl " + "-in tests/test_input/sequences/NC_014100.fna " + "-title NC_014100 -out tests/test_output/anib/NC_014100.fna", ), ] ) self.blastalljobdict = sorted( [ ( "tests/test_output/anib/NC_002696.fna", "formatdb -p F -i tests/test_output/anib/NC_002696.fna " + "-t NC_002696", ), ( "tests/test_output/anib/NC_010338.fna", "formatdb -p F -i tests/test_output/anib/NC_010338.fna " + "-t NC_010338", ), ( "tests/test_output/anib/NC_011916.fna", "formatdb -p F -i tests/test_output/anib/NC_011916.fna " + "-t NC_011916", ), ( "tests/test_output/anib/NC_014100.fna", "formatdb -p F -i tests/test_output/anib/NC_014100.fna " + "-t NC_014100", ), ] ) os.makedirs(self.outdir, exist_ok=True) os.makedirs(self.fmtdboutdir, exist_ok=True) os.makedirs(self.makeblastdbdir, exist_ok=True) @pytest.mark.skip(reason="legacy BLAST deprecated") def test_formatdb_generation(self): """generate formatdb command-line.""" cmd = anib.construct_formatdb_cmd(os.path.join(self.seqdir, "NC_002696.fna"), self.fmtdboutdir) assert cmd[0] == self.fmtdbcmd # correct command assert os.path.isfile(cmd[1]) # creates new file def test_makeblastdb_generation(self): """generate makeblastdb command-line.""" cmd = anib.construct_makeblastdb_cmd(os.path.join(self.seqdir, "NC_002696.fna"), self.makeblastdbdir) assert cmd[0] == self.makeblastdbcmd # correct command def test_blastdb_commands(self): """generate BLAST+ db commands.""" # BLAST+ cmds = anib.generate_blastdb_commands(self.blastdbfnames, self.outdir, mode="ANIb") assert cmds == self.blastdbtgt @pytest.mark.skip(reason="legacy BLAST deprecated") def test_legacy_blastdb_commands(self): """generate legacy BLAST db commands.""" # legacy cmds = anib.generate_blastdb_commands(self.blastdbfnames, self.outdir, mode="ANIblastall") assert cmds == self.blastdbtgtlegacy def test_blastn_generation(self): """generate BLASTN+ command-line.""" cmd = anib.construct_blastn_cmdline(self.blastdbfnames[0], self.blastdbfnames[1], self.outdir) assert cmd == self.blastncmd @pytest.mark.skip(reason="legacy BLAST deprecated") def test_blastall_generation(self): """generate legacy BLASTN command-line.""" cmd = anib.construct_blastall_cmdline(self.blastdbfnames[0], self.blastdbfnames[1], self.outdir) assert cmd == self.blastallcmd def test_blastn_commands(self): """generate BLASTN+ commands.""" # BLAST+ cmds = anib.generate_blastn_commands(self.blastdbfnames, self.outdir, mode="ANIb") assert cmds == self.blastntgt @pytest.mark.skip(reason="legacy BLAST deprecated") def test_legacy_blastn_commands(self): """generate legacy BLASTN commands.""" cmds = anib.generate_blastn_commands(self.blastdbfnames, self.outdir, mode="ANIblastall") assert cmds == self.blastalltgt @pytest.mark.skip(reason="legacy BLAST deprecated") def test_blastall_dbjobdict(self): """generate dictionary of legacy BLASTN database jobs.""" blastcmds = anib.make_blastcmd_builder("ANIblastall", self.outdir) jobdict = anib.build_db_jobs(self.infiles, blastcmds) assert sorted([(k, v.script) for (k, v) in jobdict.items()]) == self.blastalljobdict def test_blastn_dbjobdict(self): """generate dictionary of BLASTN+ database jobs.""" blastcmds = anib.make_blastcmd_builder("ANIb", self.outdir) jobdict = anib.build_db_jobs(self.infiles, blastcmds) assert sorted([(k, v.script) for (k, v) in jobdict.items()]) == self.blastnjobdict def test_blastn_graph(self): """create jobgraph for BLASTN+ jobs.""" fragresult = anib.fragment_fasta_files(self.infiles, self.outdir, self.fraglen) blastcmds = anib.make_blastcmd_builder("ANIb", self.outdir) jobgraph = anib.make_job_graph(self.infiles, fragresult[0], blastcmds) # We check that the main script job is a blastn job, and that there # is a single dependency, which is a makeblastdb job for job in jobgraph: assert job.script.startswith("blastn") assert 1 == len(job.dependencies) dep = job.dependencies[0] assert dep.script.startswith("makeblastdb") @pytest.mark.skip(reason="legacy BLAST deprecated") def test_blastall_graph(self): """create jobgraph for legacy BLASTN jobs.""" fragresult = anib.fragment_fasta_files(self.infiles, self.outdir, self.fraglen) blastcmds = anib.make_blastcmd_builder("ANIblastall", self.outdir) jobgraph = anib.make_job_graph(self.infiles, fragresult[0], blastcmds) # We check that the main script job is a blastn job, and that there # is a single dependency, which is a makeblastdb job for job in jobgraph: assert job.script.startswith("blastall -p blastn") assert 1 == len(job.dependencies) dep = job.dependencies[0] assert dep.script.startswith("formatdb") class TestFragments(unittest.TestCase): """Class defining tests of ANIb FASTA fragmentation""" def setUp(self): """Initialise parameters for tests.""" self.outdir = os.path.join("tests", "test_output", "anib") self.seqdir = os.path.join("tests", "test_input", "sequences") self.infnames = [ os.path.join(self.seqdir, fname) for fname in ( "NC_002696.fna", "NC_010338.fna", "NC_011916.fna", "NC_014100.fna", ) ] self.outfnames = [ os.path.join(self.outdir, fname) for fname in ( "NC_002696-fragments.fna", "NC_010338-fragments.fna", "NC_011916-fragments.fna", "NC_014100-fragments.fna", ) ] self.fraglen = 1000 os.makedirs(self.outdir, exist_ok=True) def test_fragment_files(self): """fragment files for ANIb/ANIblastall.""" result = anib.fragment_fasta_files(self.infnames, self.outdir, self.fraglen) # Are files created? for outfname in self.outfnames: assert os.path.isfile(outfname) # Test fragment lengths for accession, fragdict in result[-1].items(): for fragname, fraglen in fragdict.items(): assert fraglen <= self.fraglen class TestParsing(unittest.TestCase): """Class defining tests of BLAST output parsing.""" def setUp(self): self.indir = os.path.join("tests", "test_input", "anib") self.seqdir = os.path.join("tests", "test_input", "sequences") self.fragdir = os.path.join("tests", "test_input", "anib", "fragfiles") self.anibdir = os.path.join("tests", "test_input", "anib", "blastn") self.aniblastalldir = os.path.join("tests", "test_input", "anib", "blastall") self.fname_legacy = os.path.join(self.indir, "NC_002696_vs_NC_010338.blast_tab") self.fname = os.path.join(self.indir, "NC_002696_vs_NC_011916.blast_tab") self.fragfname = os.path.join(self.indir, "NC_002696-fragments.fna") self.fraglens = 1000 self.infnames = [ os.path.join(self.seqdir, fname) for fname in ( "NC_002696.fna", "NC_010338.fna", "NC_011916.fna", "NC_014100.fna", ) ] self.fragfiles = [ os.path.join(self.fragdir, fname) for fname in ( "NC_002696-fragments.fna", "NC_010338-fragments.fna", "NC_011916-fragments.fna", "NC_014100-fragments.fna", ) ] self.anibtgt = pd.DataFrame( [ [1.000000, 0.796974, 0.999977, 0.837285], [0.795958, 1.000000, 0.795917, 0.798250], [0.999922, 0.795392, 1.000000, 0.837633], [0.836780, 0.798704, 0.836823, 1.000000], ], columns=["NC_002696", "NC_010338", "NC_011916", "NC_014100"], index=["NC_002696", "NC_010338", "NC_011916", "NC_014100"], ) self.aniblastalltgt = pd.DataFrame( [ [1.000000, 0.785790, 0.999977, 0.830641], [0.781319, 1.000000, 0.781281, 0.782723], [0.999937, 0.782968, 1.000000, 0.830431], [0.828919, 0.784533, 0.828853, 1.000000], ], columns=["NC_002696", "NC_010338", "NC_011916", "NC_014100"], index=["NC_002696", "NC_010338", "NC_011916", "NC_014100"], ) @pytest.mark.skip(reason="legacy BLAST deprecated") def test_parse_blasttab(self): """parses ANIblastall .blast_tab output.""" fragdata = anib.get_fraglength_dict([self.fragfname]) # ANIb output result = anib.parse_blast_tab(self.fname, fragdata, 0.3, 0.7, mode="ANIb") assert result == (4016551, 93, 99.997693577050029) # ANIblastall output result = anib.parse_blast_tab(self.fname_legacy, fragdata, 0.3, 0.7, mode="ANIblastall") assert result == (1966922, 406104, 78.578978313253018) def test_blastdir_processing(self): """parses directory of .blast_tab output.""" orglengths = pyani_files.get_sequence_lengths(self.infnames) fraglengths = anib.get_fraglength_dict(self.fragfiles) # ANIb result = anib.process_blast(self.anibdir, orglengths, fraglengths, mode="ANIb") assert_frame_equal( result.percentage_identity.sort_index(axis=1).sort_index(), self.anibtgt.sort_index(axis=1).sort_index(), ) @pytest.mark.skip(reason="legacy BLAST deprecated") def test_legacy_blastdir_processing(self): """parse directory of legacy .blast_tab output""" orglengths = pyani_files.get_sequence_lengths(self.infnames) fraglengths = anib.get_fraglength_dict(self.fragfiles) # ANIblastall result = anib.process_blast(self.aniblastalldir, orglengths, fraglengths, mode="ANIblastall") assert_frame_equal( result.percentage_identity.sort_index(axis=1).sort_index(), self.aniblastalltgt.sort_index(axis=1).sort_index(), )