## ## JHCepas ## CPCantalapiedra 2020 import unittest import os, shutil from .common import run, check_gff, check_fasta, check_seed_orthologs, check_annotations, check_hmm_hits, check_orthologs, check_pfam # General eggnog-mapper settings DECORATED_GFF_SUFFIX = '.emapper.decorated.gff' GENEPRED_GFF_SUFFIX = '.emapper.genepred.gff' GENEPRED_FASTA_SUFFIX = '.emapper.genepred.fasta' HMM_HITS_SUFFIX = '.emapper.hits' SEED_ORTHOLOGS_SUFFIX = '.emapper.seed_orthologs' ANNOTATIONS_SUFFIX = '.emapper.annotations' ORTHOLOGS_SUFFIX = '.emapper.orthologs' PFAM_SUFFIX = '.emapper.pfam' class Test(unittest.TestCase): # Tests def test_emapper_diamond(self): ''' Tests the whole emapper (-m diamond) command ''' # ./emapper.py -m diamond -i tests/fixtures/test_queries.fa --data_dir tests/fixtures --output_dir tmp -o test_output ## # Setup test in_file = "tests/fixtures/test_queries.fa" data_dir = "tests/fixtures" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_seed_orthologs = os.path.join(outdir, outprefix+SEED_ORTHOLOGS_SUFFIX) obs_annotations = os.path.join(outdir, outprefix+ANNOTATIONS_SUFFIX) exp_seed_orthologs = os.path.join(data_dir, 'test_output.emapper.seed_orthologs') exp_annotations = os.path.join(data_dir, 'test_output.emapper.annotations') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = f'./emapper.py -m diamond -i {in_file} --data_dir {data_dir} --output_dir {outdir} -o {outprefix}' # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check alignment phase: detection of seed orthologs check_seed_orthologs(obs_seed_orthologs, exp_seed_orthologs) # Check annotation phase check_annotations(obs_annotations, exp_annotations) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_emapper_novel_fams(self): ''' Test annotation using novel families (-m novel_fams) command ''' # ./emapper.py -m novel_fams -i tests/fixtures/novel_fams/novel_fams_queries.fa --data_dir tests/fixtures/novel_fams # --output_dir tmp -o test # --dmnd_db tests/fixtures/novel_fams/novel_fams.dmnd ## # Setup test in_file = "tests/fixtures/novel_fams/novel_fams_queries.fa" data_dir = "tests/fixtures/novel_fams" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_seed_orthologs = os.path.join(outdir, outprefix+SEED_ORTHOLOGS_SUFFIX) obs_annotations = os.path.join(outdir, outprefix+ANNOTATIONS_SUFFIX) exp_seed_orthologs = os.path.join(data_dir, 'test.emapper.seed_orthologs') exp_annotations = os.path.join(data_dir, 'test.emapper.annotations') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = f'./emapper.py -m novel_fams -i {in_file} --data_dir {data_dir} --output_dir {outdir} -o {outprefix}' cmd += f' --dmnd_db tests/fixtures/novel_fams/novel_fams.dmnd' # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check alignment phase: detection of seed orthologs check_seed_orthologs(obs_seed_orthologs, exp_seed_orthologs) # Check annotation phase check_annotations(obs_annotations, exp_annotations) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_emapper_mmseqs(self): ''' Tests the whole emapper (-m mmseqs) command ''' # ./emapper.py -m mmseqs -i tests/fixtures/test_queries.fa --data_dir tests/fixtures --output_dir tmp -o test_mmseqs ## # Setup test in_file = "tests/fixtures/test_queries.fa" data_dir = "tests/fixtures" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_seed_orthologs = os.path.join(outdir, outprefix+SEED_ORTHOLOGS_SUFFIX) obs_annotations = os.path.join(outdir, outprefix+ANNOTATIONS_SUFFIX) exp_seed_orthologs = os.path.join(data_dir, 'test_mmseqs.emapper.seed_orthologs') exp_annotations = os.path.join(data_dir, 'test_mmseqs.emapper.annotations') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = f'./emapper.py -m mmseqs -i {in_file} --data_dir {data_dir} --output_dir {outdir} -o {outprefix}' # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check alignment phase: detection of seed orthologs check_seed_orthologs(obs_seed_orthologs, exp_seed_orthologs) # Check annotation phase check_annotations(obs_annotations, exp_annotations) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_emapper_no_search(self): ''' Tests annotation (-m no_search) of an existing hits table, and reports orthologs (--report_orthologs, --target_orthologs, --target_taxa and --excluded_taxa) ''' # ./emapper.py -m no_search --annotate_hits_table tests/fixtures/test_output.emapper.seed_orthologs # --data_dir tests/fixtures --output_dir tmp -o tmp --report_orthologs --target_orthologs one2one # --target_taxa 72274,1123487 --excluded_taxa 205918,1395571 ## # Setup test in_file = "tests/fixtures/test_output.emapper.seed_orthologs" data_dir = "tests/fixtures" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_annotations = os.path.join(outdir, outprefix+ANNOTATIONS_SUFFIX) obs_orthologs = os.path.join(outdir, outprefix+ORTHOLOGS_SUFFIX) exp_annotations = os.path.join(data_dir, 'test_no_search.emapper.annotations') exp_orthologs = os.path.join(data_dir, 'test_no_search.emapper.orthologs') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = (f'./emapper.py -m no_search --annotate_hits_table {in_file} --data_dir {data_dir} --output_dir {outdir} -o {outprefix} --report_orthologs ' f'--target_orthologs one2one --target_taxa 72274,1123487 --excluded_taxa 205918,1395571') # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check orthologs check_orthologs(obs_orthologs, exp_orthologs) # Check annotation phase check_annotations(obs_annotations, exp_annotations) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_emapper_hmmer_eggnogdb(self): ''' Tests the whole emapper (-m hmmer) command against a eggNOG DB ''' # ./emapper.py -m hmmer -i tests/fixtures/test_queries.fa --data_dir tests/fixtures -d bact --output_dir tmp -o bact ## # Setup test in_file = "tests/fixtures/test_queries.fa" data_dir = "tests/fixtures" outdir = "tests/integration/out" outprefix = "bact" database = "bact" # Observed and expected files obs_hmm_hits = os.path.join(outdir, outprefix+HMM_HITS_SUFFIX) obs_seed_orthologs = os.path.join(outdir, outprefix+SEED_ORTHOLOGS_SUFFIX) obs_annotations = os.path.join(outdir, outprefix+ANNOTATIONS_SUFFIX) exp_files_dir = "tests/fixtures/hmmer_expected_output/" exp_hmm_hits = os.path.join(exp_files_dir, "bact.emapper.hmm_hits") exp_seed_orthologs = os.path.join(exp_files_dir, "bact.emapper.seed_orthologs") exp_annotations = os.path.join(exp_files_dir, "bact.emapper.annotations") ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = f'./emapper.py -m hmmer -i {in_file} --data_dir {data_dir} -d {database} --output_dir {outdir} -o {outprefix}' # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check HMM hits from alignment phase check_hmm_hits(obs_hmm_hits, exp_hmm_hits) # Check seed orthologs from alignment phase check_seed_orthologs(obs_seed_orthologs, exp_seed_orthologs) # Check annotation phase check_annotations(obs_annotations, exp_annotations) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_scratch_dir(self): ''' Tests the use of scratch_dir ''' # ./emapper.py -m hmmer -i tests/fixtures/test_queries.fa --data_dir tests/fixtures # -d bact -o bact --output_dir tmp --scratch_dir tmp_scratch ## # Setup test in_file = "tests/fixtures/test_queries.fa" data_dir = "tests/fixtures" outdir = "tests/integration/out" scratchdir = "tests/integration/scratch" outprefix = "bact" database = "bact" # Observed and expected files obs_hmm_hits = os.path.join(outdir, outprefix+HMM_HITS_SUFFIX) obs_seed_orthologs = os.path.join(outdir, outprefix+SEED_ORTHOLOGS_SUFFIX) obs_annotations = os.path.join(outdir, outprefix+ANNOTATIONS_SUFFIX) scratch_hmm_hits = os.path.join(scratchdir, outprefix+HMM_HITS_SUFFIX) scratch_seed_orthologs = os.path.join(scratchdir, outprefix+SEED_ORTHOLOGS_SUFFIX) scratch_annotations = os.path.join(scratchdir, outprefix+ANNOTATIONS_SUFFIX) exp_files_dir = "tests/fixtures/hmmer_expected_output/" exp_hmm_hits = os.path.join(exp_files_dir, "bact.emapper.hmm_hits") exp_seed_orthologs = os.path.join(exp_files_dir, "bact.emapper.seed_orthologs") exp_annotations = os.path.join(exp_files_dir, "bact.emapper.annotations") ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) if os.path.isdir(scratchdir): shutil.rmtree(scratchdir) os.mkdir(scratchdir) cmd = f'./emapper.py -m hmmer -i {in_file} --data_dir {data_dir} -d {database} --output_dir {outdir} -o {outprefix} --scratch_dir {scratchdir}' # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check HMM hits from alignment phase check_hmm_hits(obs_hmm_hits, exp_hmm_hits) check_hmm_hits(scratch_hmm_hits, exp_hmm_hits) # Check seed orthologs from alignment phase check_seed_orthologs(obs_seed_orthologs, exp_seed_orthologs) check_seed_orthologs(scratch_seed_orthologs, exp_seed_orthologs) # Check annotation phase check_annotations(obs_annotations, exp_annotations) check_annotations(scratch_annotations, exp_annotations) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) if os.path.isdir(scratchdir): shutil.rmtree(scratchdir) return def test_pfam_realign(self): ''' Tests --pfam_realign realign ''' # ./emapper.py -m no_search --annotate_hits_table tests/fixtures/test_pfam_groups.seed_orthologs # -i tests/fixtures/test_pfam_groups.fa --data_dir tests/fixtures # --output_dir tmp -o test --pfam_realign realign ## # Setup test in_file = "tests/fixtures/test_pfam_groups.fa" seeds_file = "tests/fixtures/test_pfam_groups.seed_orthologs" data_dir = "tests/fixtures" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_annotations = os.path.join(outdir, outprefix+ANNOTATIONS_SUFFIX) obs_pfam = os.path.join(outdir, outprefix+PFAM_SUFFIX) exp_annotations = os.path.join(data_dir, 'pfam_realign_output', 'test.emapper.annotations') exp_pfam = os.path.join(data_dir, 'pfam_realign_output', 'test.emapper.pfam') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = ( f'./emapper.py -m no_search --annotate_hits_table {seeds_file} -i {in_file} --data_dir {data_dir} ' f'--output_dir {outdir} -o {outprefix} --pfam_realign realign' ) # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check PFAM check_pfam(obs_pfam, exp_pfam) # Check annotation phase check_annotations(obs_annotations, exp_annotations) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_pfam_denovo(self): ''' Tests --pfam_realign denovo ''' # ./emapper.py -m no_search --annotate_hits_table tests/fixtures/test_pfam_groups.seed_orthologs # -i tests/fixtures/test_pfam_groups.fa --data_dir tests/fixtures # --output_dir tmp -o test --pfam_realign denovo ## # Setup test in_file = "tests/fixtures/test_pfam_groups.fa" seeds_file = "tests/fixtures/test_pfam_groups.seed_orthologs" data_dir = "tests/fixtures" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_annotations = os.path.join(outdir, outprefix+ANNOTATIONS_SUFFIX) obs_pfam = os.path.join(outdir, outprefix+PFAM_SUFFIX) exp_annotations = os.path.join(data_dir, 'pfam_denovo_output', 'test.emapper.annotations') exp_pfam = os.path.join(data_dir, 'pfam_denovo_output', 'test.emapper.pfam') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = ( f'./emapper.py -m no_search --annotate_hits_table {seeds_file} -i {in_file} --data_dir {data_dir} ' f'--output_dir {outdir} -o {outprefix} --pfam_realign denovo' ) # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check PFAM check_pfam(obs_pfam, exp_pfam) # Check annotation phase check_annotations(obs_annotations, exp_annotations) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_genepred_prodigal(self): ''' Test gene prediction with prodigal ''' # rm -r tmp_borrar; mkdir tmp_borrar; # emapper.py -i tests/fixtures/genepred_contig/contig.fna \ # --itype metagenome --genepred prodigal --data_dir tests/fixtures \ # -m diamond --sensmode sensitive --no_annot \ # --dmnd_db tests/fixtures/genepred_contig/contig.dmnd -o test --output_dir tmp_borrar ## # Setup test in_file = "tests/fixtures/genepred_contig/contig.fna" data_dir = "tests/fixtures/genepred_contig/prodigal_out" dmnd_db = "tests/fixtures/genepred_contig/contig.dmnd" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_genepred_gff = os.path.join(outdir, outprefix+GENEPRED_GFF_SUFFIX) obs_genepred_fasta = os.path.join(outdir, outprefix+GENEPRED_FASTA_SUFFIX) obs_seed_orthologs = os.path.join(outdir, outprefix+SEED_ORTHOLOGS_SUFFIX) exp_genepred_gff = os.path.join(data_dir, 'out.emapper.genepred.gff') exp_genepred_fasta = os.path.join(data_dir, 'out.emapper.genepred.fasta') exp_seed_orthologs = os.path.join(data_dir, 'out.emapper.seed_orthologs') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = (f'./emapper.py -i {in_file} --itype metagenome --genepred prodigal --data_dir tests/fixtures ' f'-m diamond --sensmode sensitive --no_annot ' f'--dmnd_db {dmnd_db} ' f'-o {outprefix} --output_dir {outdir}') # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check GFF from gene prediction check_gff(obs_genepred_gff, exp_genepred_gff) # Check FASTA from gene prediction check_fasta(obs_genepred_fasta, exp_genepred_fasta) # Check alignment phase: detection of seed orthologs check_seed_orthologs(obs_seed_orthologs, exp_seed_orthologs) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_genepred_diamond(self): ''' Test gene prediction with diamond ''' # rm -r tmp_test; mkdir tmp_test; # emapper.py -i tests/fixtures/genepred_contig/contig.fna --itype metagenome --genepred search \ # --data_dir tests/fixtures \ # -m diamond --sensmode sensitive --no_annot --dmnd_db tests/fixtures/genepred_contig/contig.dmnd \ # -o test --output_dir tmp_test ## # Setup test in_file = "tests/fixtures/genepred_contig/contig.fna" data_dir = "tests/fixtures/genepred_contig/diamond_out" dmnd_db = "tests/fixtures/genepred_contig/contig.dmnd" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_genepred_gff = os.path.join(outdir, outprefix+GENEPRED_GFF_SUFFIX) obs_genepred_fasta = os.path.join(outdir, outprefix+GENEPRED_FASTA_SUFFIX) obs_seed_orthologs = os.path.join(outdir, outprefix+SEED_ORTHOLOGS_SUFFIX) exp_genepred_gff = os.path.join(data_dir, 'out.emapper.genepred.gff') exp_genepred_fasta = os.path.join(data_dir, 'out.emapper.genepred.fasta') exp_seed_orthologs = os.path.join(data_dir, 'out.emapper.seed_orthologs') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = (f'./emapper.py -i {in_file} --itype metagenome --genepred search --data_dir tests/fixtures ' f'-m diamond --sensmode sensitive --no_annot ' f'--dmnd_db {dmnd_db} ' f'-o {outprefix} --output_dir {outdir}') # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check GFF from gene prediction check_gff(obs_genepred_gff, exp_genepred_gff) # Check FASTA from gene prediction check_fasta(obs_genepred_fasta, exp_genepred_fasta) # Check alignment phase: detection of seed orthologs check_seed_orthologs(obs_seed_orthologs, exp_seed_orthologs) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_genepred_mmseqs(self): ''' Test gene prediction with mmseqs ''' # rm -r tmp_test; mkdir tmp_test; # emapper.py -i tests/fixtures/genepred_contig/contig.fna --itype metagenome --genepred search \ # --data_dir tests/fixtures \ # -m mmseqs --no_annot --mmseqs_db tests/fixtures/genepred_contig/contig.mmseqs/contig.0.hits.mmseqs.db \ # -o test --output_dir tmp_test ## # Setup test in_file = "tests/fixtures/genepred_contig/contig.fna" data_dir = "tests/fixtures/genepred_contig/mmseqs_out" mmseqs_db = "tests/fixtures/genepred_contig/contig.mmseqs/contig.0.hits.mmseqs.db" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_genepred_gff = os.path.join(outdir, outprefix+GENEPRED_GFF_SUFFIX) obs_genepred_fasta = os.path.join(outdir, outprefix+GENEPRED_FASTA_SUFFIX) obs_seed_orthologs = os.path.join(outdir, outprefix+SEED_ORTHOLOGS_SUFFIX) exp_genepred_gff = os.path.join(data_dir, 'out.emapper.genepred.gff') exp_genepred_fasta = os.path.join(data_dir, 'out.emapper.genepred.fasta') exp_seed_orthologs = os.path.join(data_dir, 'out.emapper.seed_orthologs') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = (f'./emapper.py -i {in_file} --itype metagenome --genepred search --data_dir tests/fixtures ' f'-m mmseqs --no_annot ' f'--mmseqs_db {mmseqs_db} ' f'-o {outprefix} --output_dir {outdir}') # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check GFF from gene prediction check_gff(obs_genepred_gff, exp_genepred_gff) # Check FASTA from gene prediction check_fasta(obs_genepred_fasta, exp_genepred_fasta) # Check alignment phase: detection of seed orthologs check_seed_orthologs(obs_seed_orthologs, exp_seed_orthologs) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_decorate_gff_blastx_annot(self): ''' Test gene prediction with mmseqs with GFF decoration ''' # ./emapper.py -i tests/fixtures/genepred_contig/contig.fna --itype metagenome --genepred search \ # --decorate_gff yes --data_dir tests/fixtures \ # -m mmseqs --mmseqs_db tests/fixtures/genepred_contig/contig.mmseqs/contig.0.hits.mmseqs.db -o test --output_dir tmp ## # Setup test in_file = "tests/fixtures/genepred_contig/contig.fna" data_dir = "tests/fixtures" mmseqs_db = "tests/fixtures/genepred_contig/contig.mmseqs/contig.0.hits.mmseqs.db" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_genepred_gff = os.path.join(outdir, outprefix+DECORATED_GFF_SUFFIX) exp_genepred_gff = os.path.join(data_dir, 'decorate_gff', 'blastx_annot', 'out.emapper.genepred.gff') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = (f'./emapper.py -i {in_file} --itype metagenome --genepred search --decorate_gff yes ' f'-m mmseqs --data_dir tests/fixtures ' f'--mmseqs_db {mmseqs_db} ' f'-o {outprefix} --output_dir {outdir}') # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check GFF from gene prediction check_gff(obs_genepred_gff, exp_genepred_gff) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_decorate_gff_file(self): ''' Test decoration of existing GFF file from seed_orthologs file and annotations ''' # ./emapper.py -m no_search # --annotate_hits_table tests/fixtures/decorate_gff/decorate_file/test.emapper.seed_orthologs # --data_dir tests/fixtures # --decorate_gff tests/fixtures/decorate_gff/decorate_file/test.emapper.genepred.gff --output_dir tmp -o test ## # Setup test in_file = "tests/fixtures/decorate_gff/decorate_file/test.emapper.seed_orthologs" data_dir = "tests/fixtures" gff_to_decorate = "tests/fixtures/decorate_gff/decorate_file/test.emapper.genepred.gff" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_genepred_gff = os.path.join(outdir, outprefix+DECORATED_GFF_SUFFIX) exp_genepred_gff = os.path.join(data_dir, 'decorate_gff', 'decorate_file', 'out.emapper.genepred.gff') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = (f'./emapper.py -m no_search --annotate_hits_table {in_file} --decorate_gff {gff_to_decorate} --data_dir tests/fixtures ' f'-o {outprefix} --output_dir {outdir}') # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check GFF from gene prediction check_gff(obs_genepred_gff, exp_genepred_gff) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return def test_decorate_gff_file_short(self): ''' Test decoration of existing GFF file from seed_orthologs file (short format) and annotations ''' # ./emapper.py -m no_search --data_dir tests/fixtures # --annotate_hits_table tests/fixtures/decorate_gff/decorate_file/test.emapper.seed_orthologs.short # --decorate_gff tests/fixtures/decorate_gff/decorate_file/test.emapper.genepred.gff --output_dir tmp -o test ## # Setup test in_file = "tests/fixtures/decorate_gff/decorate_file/test.emapper.seed_orthologs.short" data_dir = "tests/fixtures" gff_to_decorate = "tests/fixtures/decorate_gff/decorate_file/test.emapper.genepred.gff" outdir = "tests/integration/out" outprefix = "test" # Observed and expected files obs_genepred_gff = os.path.join(outdir, outprefix+DECORATED_GFF_SUFFIX) exp_genepred_gff = os.path.join(data_dir, 'decorate_gff', 'decorate_file', 'out.emapper.short.genepred.gff') ## # Run test # Remove (just in case) and recreate the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) os.mkdir(outdir) cmd = (f'./emapper.py -m no_search --annotate_hits_table {in_file} --decorate_gff {gff_to_decorate} --data_dir tests/fixtures ' f'-o {outprefix} --output_dir {outdir}') # print(f"\t{cmd}") st, out, err = run(cmd) if st != 0: # print(out) # print(err) print(out.decode("utf-8")) print(err.decode("utf-8")) assert st == 0 # check exit status is ok ## # Check test # Check GFF from gene prediction check_gff(obs_genepred_gff, exp_genepred_gff) ## # Teardown test # Remove the output dir if os.path.isdir(outdir): shutil.rmtree(outdir) return if __name__ == '__main__': unittest.main() ## END