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cocodyqcocodyq
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Merge pull request #14 from luispedro/cleanup_tests
TST Refactor testing-related code
2 parents ed28a5d + 3482225 commit 0078d24

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+74
-59
lines changed

3 files changed

+74
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lines changed

‎tests.sh‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,11 +10,13 @@ gmsc-mapper createdb -i examples/target.faa -o examples/ -m mmseqs --quiet
1010
echo "Testing basic usage"
1111
gmsc-mapper -i ./examples/example.fa -o ./examples_output/ --db ./examples/targetdb.dmnd --habitat ./examples/ref_habitat.npy --habitat-index ./examples/ref_habitat_index.tsv --quality ./examples/ref_quality.txt --taxonomy ./examples/ref_taxonomy.npy --taxonomy-index ./examples/ref_taxonomy_index.tsv --quiet
1212
python tests/diamond_contig.py
13+
1314
gmsc-mapper --aa-genes examples/example.faa -o examples_output/ --db examples/targetdb.dmnd --habitat ./examples/ref_habitat.npy --habitat-index ./examples/ref_habitat_index.tsv --quality examples/ref_quality.txt --taxonomy ./examples/ref_taxonomy.npy --taxonomy-index ./examples/ref_taxonomy_index.tsv --quiet
1415
python tests/diamond_protein.py
16+
1517
gmsc-mapper --nt-genes examples/example.fna -o examples_output/ --db examples/targetdb.dmnd --habitat ./examples/ref_habitat.npy --habitat-index ./examples/ref_habitat_index.tsv --quality examples/ref_quality.txt --taxonomy ./examples/ref_taxonomy.npy --taxonomy-index ./examples/ref_taxonomy_index.tsv --quiet
1618
python tests/diamond_gene.py
1719

1820
echo "Testing tool flag - MMSeqs"
1921
gmsc-mapper -i examples/example.fa -o examples_output/ --db examples/targetdb --habitat ./examples/ref_habitat.npy --habitat-index ./examples/ref_habitat_index.tsv --quality examples/ref_quality.txt --taxonomy ./examples/ref_taxonomy.npy --taxonomy-index ./examples/ref_taxonomy_index.tsv --tool mmseqs --quiet
20-
python tests/mmseqs_contig.py
22+
python tests/mmseqs_contig.py

‎tests/diamond_contig.py‎

Lines changed: 33 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -1,37 +1,43 @@
1-
def diamond_contig_test():
2-
import filecmp
1+
import filecmp
2+
import sys
33

4-
alignment_flag = filecmp.cmp("./tests/diamond_contig/alignment.out.smorfs.tsv", "./examples_output/alignment.out.smorfs.tsv")
5-
if not alignment_flag:
6-
print('\nContig input of Diamond mode alignment results have something wrong.\n')
4+
def checkf(f):
5+
return filecmp.cmp(f"./tests/diamond_contig/${f}",
6+
f"./examples_output/${f}")
77

8-
predict_flag = filecmp.cmp("./tests/diamond_contig/predicted.filterd.smorf.faa", "./examples_output/predicted.filterd.smorf.faa")
9-
if not predict_flag:
10-
print('\nContig input of Diamond mode predicted fasta results have something wrong.\n')
8+
ok = True
119

12-
fasta_flag = filecmp.cmp("./tests/diamond_contig/mapped.smorfs.faa", "./examples_output/mapped.smorfs.faa")
13-
if not fasta_flag:
14-
print('\nContig input of Diamond mode mapped fasta results have something wrong.\n')
10+
if not checkf("alignment.out.smorfs.tsv"):
11+
ok = False
12+
print('\nContig input of Diamond mode alignment results have something wrong.\n')
1513

16-
habitat_flag = filecmp.cmp("./tests/diamond_contig/habitat.out.smorfs.tsv", "./examples_output/habitat.out.smorfs.tsv")
17-
if not habitat_flag:
18-
print('\nContig input of Diamond mode habitat results have something wrong.\n')
14+
if not checkf("predicted.filterd.smorf.faa"):
15+
ok = False
16+
print('\nContig input of Diamond mode predicted fasta results have something wrong.\n')
1917

20-
taxonomy_flag = filecmp.cmp("./tests/diamond_contig/taxonomy.out.smorfs.tsv", "./examples_output/taxonomy.out.smorfs.tsv")
21-
if not taxonomy_flag:
22-
print('\nContig input of Diamond mode taxonomy results have something wrong.\n')
18+
if not checkf("mapped.smorfs.faa"):
19+
ok = False
20+
print('\nContig input of Diamond mode mapped fasta results have something wrong.\n')
2321

24-
quality_flag = filecmp.cmp("./tests/diamond_contig/quality.out.smorfs.tsv", "./examples_output/quality.out.smorfs.tsv")
25-
if not quality_flag:
26-
print('\nContig input of Diamond mode quality results have something wrong.\n')
22+
if not checkf("habitat.out.smorfs.tsv"):
23+
ok = False
24+
print('\nContig input of Diamond mode habitat results have something wrong.\n')
2725

28-
summary_flag = filecmp.cmp("./tests/diamond_contig/summary.txt", "./examples_output/summary.txt")
29-
if not summary_flag:
30-
print('\nContig input of Diamond mode summary results have something wrong.\n')
26+
if not checkf("taxonomy.out.smorfs.tsv"):
27+
ok = False
28+
print('\nContig input of Diamond mode taxonomy results have something wrong.\n')
3129

32-
if alignment_flag and predict_flag and fasta_flag and habitat_flag and taxonomy_flag and quality_flag and summary_flag:
33-
print('\nContig input of Diamond mode checking has passed.\n')
30+
if not checkf("quality.out.smorfs.tsv"):
31+
ok = False
32+
print('\nContig input of Diamond mode quality results have something wrong.\n')
33+
34+
if not checkf("summary.txt"):
35+
ok = False
36+
print('\nContig input of Diamond mode summary results have something wrong.\n')
37+
38+
if ok:
39+
print('\nContig input of Diamond mode checking has passed.\n')
40+
else:
41+
sys.exit(1)
3442

35-
return(alignment_flag,predict_flag,fasta_flag,habitat_flag,taxonomy_flag,quality_flag,summary_flag)
3643

37-
diamond_contig_test()

‎tests/diamond_gene.py‎

Lines changed: 38 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -1,33 +1,40 @@
1-
def diamond_gene_test():
2-
import filecmp
1+
import filecmp
2+
import sys
3+
4+
alignment_flag = filecmp.cmp("./tests/diamond_gene/alignment.out.smorfs.tsv", "./examples_output/alignment.out.smorfs.tsv")
5+
ok = True
6+
if not alignment_flag:
7+
ok = False
8+
print('\nGene input of Diamond mode alignment results have something wrong.\n')
9+
10+
fasta_flag = filecmp.cmp("./tests/diamond_gene/mapped.smorfs.faa", "./examples_output/mapped.smorfs.faa")
11+
if not fasta_flag:
12+
ok = False
13+
print('\nGene input of Diamond mode mapped fasta results have something wrong.\n')
14+
15+
habitat_flag = filecmp.cmp("./tests/diamond_gene/habitat.out.smorfs.tsv", "./examples_output/habitat.out.smorfs.tsv")
16+
if not habitat_flag:
17+
ok = False
18+
print('\nGene input of Diamond mode habitat results have something wrong.\n')
19+
20+
taxonomy_flag = filecmp.cmp("./tests/diamond_gene/taxonomy.out.smorfs.tsv", "./examples_output/taxonomy.out.smorfs.tsv")
21+
if not taxonomy_flag:
22+
ok = False
23+
print('\nGene input of Diamond mode taxonomy results have something wrong.\n')
24+
25+
quality_flag = filecmp.cmp("./tests/diamond_gene/quality.out.smorfs.tsv", "./examples_output/quality.out.smorfs.tsv")
26+
if not quality_flag:
27+
ok = False
28+
print('\nGene input of Diamond mode quality results have something wrong.\n')
29+
30+
summary_flag = filecmp.cmp("./tests/diamond_gene/summary.txt", "./examples_output/summary.txt")
31+
if not summary_flag:
32+
ok = False
33+
print('\nGene input of Diamond mode summary results have something wrong.\n')
34+
35+
if ok:
36+
print('\nGene input of Diamond mode checking has passed.\n')
37+
else:
38+
sys.exit(1)
339

4-
alignment_flag = filecmp.cmp("./tests/diamond_gene/alignment.out.smorfs.tsv", "./examples_output/alignment.out.smorfs.tsv")
5-
if not alignment_flag:
6-
print('\nGene input of Diamond mode alignment results have something wrong.\n')
740

8-
fasta_flag = filecmp.cmp("./tests/diamond_gene/mapped.smorfs.faa", "./examples_output/mapped.smorfs.faa")
9-
if not fasta_flag:
10-
print('\nGene input of Diamond mode mapped fasta results have something wrong.\n')
11-
12-
habitat_flag = filecmp.cmp("./tests/diamond_gene/habitat.out.smorfs.tsv", "./examples_output/habitat.out.smorfs.tsv")
13-
if not habitat_flag:
14-
print('\nGene input of Diamond mode habitat results have something wrong.\n')
15-
16-
taxonomy_flag = filecmp.cmp("./tests/diamond_gene/taxonomy.out.smorfs.tsv", "./examples_output/taxonomy.out.smorfs.tsv")
17-
if not taxonomy_flag:
18-
print('\nGene input of Diamond mode taxonomy results have something wrong.\n')
19-
20-
quality_flag = filecmp.cmp("./tests/diamond_gene/quality.out.smorfs.tsv", "./examples_output/quality.out.smorfs.tsv")
21-
if not quality_flag:
22-
print('\nGene input of Diamond mode quality results have something wrong.\n')
23-
24-
summary_flag = filecmp.cmp("./tests/diamond_gene/summary.txt", "./examples_output/summary.txt")
25-
if not summary_flag:
26-
print('\nGene input of Diamond mode summary results have something wrong.\n')
27-
28-
if alignment_flag and fasta_flag and habitat_flag and taxonomy_flag and quality_flag and summary_flag:
29-
print('\nGene input of Diamond mode checking has passed.\n')
30-
31-
return(alignment_flag,fasta_flag,habitat_flag,taxonomy_flag,quality_flag,summary_flag)
32-
33-
diamond_gene_test()

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