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ENH integrate test.sh in pytest
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+252
-4
lines changed

5 files changed

+252
-4
lines changed

‎tests/mmseqs_contig.py‎

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@@ -11,10 +11,6 @@ def checkf(f):
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ok = False
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print('\nContig input of MMseqs2 mode predicted fasta results have something wrong.\n')
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if not checkf("alignment.out.smorfs.tsv"):
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ok = False
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print('\nContig input of MMseqs2 mode alignment results have something wrong.\n')
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if not checkf("mapped.smorfs.faa"):
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ok = False
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print('\nContig input of MMseqs2 mode mapped fasta results have something wrong.\n')

‎tests/test_diamond_contig.py‎

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import filecmp
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import sys
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import pytest
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import subprocess
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def checkf(f):
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return filecmp.cmp(f"./tests/diamond_contig/{f}",
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f"./examples_output/{f}")
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def test_diamond_contig():
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ok = True
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subprocess.check_call(['gmsc-mapper','createdb',
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'-i','examples/target.faa',
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'-o','examples/',
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'-m','diamond',
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'--quiet'])
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subprocess.check_call(['gmsc-mapper',
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'-i','examples/example.fa',
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'-o','examples_output/',
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'--db','examples/diamond_targetdb.dmnd',
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'--habitat','examples/ref_habitat.npy',
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'--habitat-index','examples/ref_habitat_index.tsv',
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'--quality','examples/ref_quality.txt',
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'--taxonomy','examples/ref_taxonomy.npy',
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'--taxonomy-index','examples/ref_taxonomy_index.tsv',
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'--domain','examples/ref_domain.txt','--quiet'])
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if not checkf("predicted.filterd.smorf.faa"):
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ok = False
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print('\nContig input of Diamond mode predicted fasta results have something wrong.\n')
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if not checkf("alignment.out.smorfs.tsv"):
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ok = False
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print('\nContig input of Diamond mode alignment results have something wrong.\n')
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if not checkf("mapped.smorfs.faa"):
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ok = False
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print('\nContig input of Diamond mode mapped fasta results have something wrong.\n')
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if not checkf("habitat.out.smorfs.tsv"):
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ok = False
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print('\nContig input of Diamond mode habitat results have something wrong.\n')
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if not checkf("taxonomy.out.smorfs.tsv"):
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ok = False
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print('\nContig input of Diamond mode taxonomy results have something wrong.\n')
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if not checkf("quality.out.smorfs.tsv"):
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ok = False
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print('\nContig input of Diamond mode quality results have something wrong.\n')
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if not checkf("domain.out.smorfs.tsv"):
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ok = False
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print('\nContig input of Diamond mode domain results have something wrong.\n')
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if not checkf("summary.txt"):
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ok = False
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print('\nContig input of Diamond mode summary results have something wrong.\n')
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assert ok
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if __name__ == '__main__':
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pytest.main()

‎tests/test_diamond_gene.py‎

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import filecmp
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import sys
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import subprocess
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import pytest
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def checkf(f):
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return filecmp.cmp(f"./tests/diamond_gene/{f}",
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f"./examples_output/{f}")
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def test_diamond_contig():
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ok = True
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subprocess.check_call(['gmsc-mapper','createdb',
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'-i','examples/target.faa',
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'-o','examples/',
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'-m','diamond',
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'--quiet'])
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subprocess.check_call(['gmsc-mapper',
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'--nt-genes','examples/example.fna',
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'-o','examples_output/',
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'--db','examples/diamond_targetdb.dmnd',
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'--habitat','examples/ref_habitat.npy',
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'--habitat-index','examples/ref_habitat_index.tsv',
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'--quality','examples/ref_quality.txt',
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'--taxonomy','examples/ref_taxonomy.npy',
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'--taxonomy-index','examples/ref_taxonomy_index.tsv',
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'--domain','examples/ref_domain.txt','--quiet'])
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if not checkf("alignment.out.smorfs.tsv"):
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ok = False
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print('\nGene input of Diamond mode alignment results have something wrong.\n')
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if not checkf("mapped.smorfs.faa"):
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ok = False
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print('\nGene input of Diamond mode mapped fasta results have something wrong.\n')
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if not checkf("habitat.out.smorfs.tsv"):
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ok = False
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print('\nGene input of Diamond mode habitat results have something wrong.\n')
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if not checkf("taxonomy.out.smorfs.tsv"):
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ok = False
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print('\nGene input of Diamond mode taxonomy results have something wrong.\n')
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if not checkf("quality.out.smorfs.tsv"):
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ok = False
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print('\nGene input of Diamond mode quality results have something wrong.\n')
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if not checkf("domain.out.smorfs.tsv"):
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ok = False
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print('\nGene input of Diamond mode domain results have something wrong.\n')
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if not checkf("summary.txt"):
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ok = False
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print('\nGene input of Diamond mode summary results have something wrong.\n')
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assert ok
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if __name__ == '__main__':
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pytest.main()
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‎tests/test_diamond_protein.py‎

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import filecmp
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import sys
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import subprocess
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import pytest
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def checkf(f):
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return filecmp.cmp(f"./tests/diamond_protein/{f}",
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f"./examples_output/{f}")
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def test_diamond_contig():
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ok = True
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subprocess.check_call(['gmsc-mapper','createdb',
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'-i','examples/target.faa',
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'-o','examples/',
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'-m','diamond',
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'--quiet'])
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subprocess.check_call(['gmsc-mapper',
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'--aa-genes','examples/example.faa',
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'-o','examples_output/',
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'--db','examples/diamond_targetdb.dmnd',
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'--habitat','examples/ref_habitat.npy',
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'--habitat-index','examples/ref_habitat_index.tsv',
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'--quality','examples/ref_quality.txt',
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'--taxonomy','examples/ref_taxonomy.npy',
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'--taxonomy-index','examples/ref_taxonomy_index.tsv',
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'--domain','examples/ref_domain.txt','--quiet'])
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if not checkf("alignment.out.smorfs.tsv"):
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ok = False
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print('\nProtein input of Diamond mode alignment results have something wrong.\n')
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if not checkf("mapped.smorfs.faa"):
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ok = False
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print('\nProtein input of Diamond mode mapped fasta results have something wrong.\n')
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if not checkf("habitat.out.smorfs.tsv"):
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ok = False
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print('\nProtein input of Diamond mode habitat results have something wrong.\n')
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if not checkf("taxonomy.out.smorfs.tsv"):
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ok = False
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print('\nProtein input of Diamond mode taxonomy results have something wrong.\n')
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if not checkf("quality.out.smorfs.tsv"):
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ok = False
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print('\nProtein input of Diamond mode quality results have something wrong.\n')
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if not checkf("domain.out.smorfs.tsv"):
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ok = False
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print('\nProtein input of Diamond mode quality results have something wrong.\n')
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if not checkf("summary.txt"):
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ok = False
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print('\nProtein input of Diamond mode summary results have something wrong.\n')
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assert ok
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if __name__ == '__main__':
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pytest.main()
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‎tests/test_mmseqs_contig.py‎

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import filecmp
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import sys
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import pytest
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import subprocess
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def checkf(f):
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return filecmp.cmp(f"./tests/mmseqs_contig/{f}",
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f"./examples_output/{f}")
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def test_mmseqs_contig():
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ok = True
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subprocess.check_call(['gmsc-mapper','createdb',
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'-i','examples/target.faa',
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'-o','examples/',
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'-m','mmseqs',
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'--quiet'])
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subprocess.check_call(['gmsc-mapper',
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'-i','examples/example.fa',
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'-o','examples_output/',
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'--db','examples/mmseqs_targetdb',
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'--habitat','examples/ref_habitat.npy',
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'--habitat-index','examples/ref_habitat_index.tsv',
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'--quality','examples/ref_quality.txt',
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'--taxonomy','examples/ref_taxonomy.npy',
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'--taxonomy-index','examples/ref_taxonomy_index.tsv',
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'--domain','examples/ref_domain.txt','--quiet',
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'--tool','mmseqs'])
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if not checkf("predicted.filterd.smorf.faa"):
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ok = False
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print('\nContig input of MMseqs2 mode predicted fasta results have something wrong.\n')
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if not checkf("mapped.smorfs.faa"):
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ok = False
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print('\nContig input of MMseqs2 mode mapped fasta results have something wrong.\n')
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if not checkf("habitat.out.smorfs.tsv"):
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ok = False
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print('\nContig input of MMseqs2 mode habitat results have something wrong.\n')
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if not checkf("taxonomy.out.smorfs.tsv"):
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ok = False
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print('\nContig input of MMseqs2 mode taxonomy results have something wrong.\n')
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if not checkf("quality.out.smorfs.tsv"):
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ok = False
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print('\nContig input of MMseqs2 mode quality results have something wrong.\n')
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if not checkf("domain.out.smorfs.tsv"):
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ok = False
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print('\nContig input of MMseqs2 mode domain results have something wrong.\n')
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if not checkf("summary.txt"):
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ok = False
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print('\nContig input of MMseqs2 mode summary results have something wrong.\n')
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assert ok
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if __name__ == '__main__':
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pytest.main()

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