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MIN fix tests.sh
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‎gmsc_mapper/main.py‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -460,7 +460,7 @@ def main(args=None):
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fastafile = generate_fasta(args.output,queryfile,resultfile)
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smorf_number = int(predicted_smorf_count(fastafile)/2)
463-
summary.append(f'{smorf_number} smORFs aligned against GMSC in total.\n')
463+
summary.append(f'{smorf_number} smORFs are aligned against GMSC in total.\n')
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if not args.noquality:
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summary.append(f'# Quality')
@@ -476,14 +476,14 @@ def main(args=None):
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if not args.notaxonomy:
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summary.append(f'# Taxonomy')
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annotated_number,rank_number,rank_percentage = taxonomy(args,resultfile,tmpdir)
479-
summary.append(str(annotated_number)+'('+str(round((1-rank_percentage['no rank'])*100,2))+'%) aligned smORFs have taxonomy annotation.')
480-
summary.append(str(rank_number['kingdom'])+'('+str(round(rank_percentage['kingdom']*100,2))+'%) aligned smORFs are annotated on kingdom.')
481-
summary.append(str(rank_number['phylum'])+'('+str(round(rank_percentage['phylum']*100,2))+'%) aligned smORFs are annotated on phylum.')
482-
summary.append(str(rank_number['class'])+'('+str(round(rank_percentage['class']*100,2))+'%) aligned smORFs are annotated on class.')
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summary.append(str(rank_number['order'])+'('+str(round(rank_percentage['order']*100,2))+'%) aligned smORFs are annotated on order.')
484-
summary.append(str(rank_number['family'])+'('+str(round(rank_percentage['family']*100,2))+'%) aligned smORFs are annotated on family.')
485-
summary.append(str(rank_number['genus'])+'('+str(round(rank_percentage['genus']*100,2))+'%) aligned smORFs are annotated on genus.')
486-
summary.append(str(rank_number['species'])+'('+str(round(rank_percentage['species']*100,2))+'%) aligned smORFs are annotated on species.')
479+
summary.append(str(annotated_number)+' ('+str(round((1-rank_percentage['no rank'])*100,2))+'%) aligned smORFs have taxonomy annotation.')
480+
summary.append(str(rank_number['kingdom'])+' ('+str(round(rank_percentage['kingdom']*100,2))+'%) aligned smORFs are annotated on kingdom.')
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summary.append(str(rank_number['phylum'])+' ('+str(round(rank_percentage['phylum']*100,2))+'%) aligned smORFs are annotated on phylum.')
482+
summary.append(str(rank_number['class'])+' ('+str(round(rank_percentage['class']*100,2))+'%) aligned smORFs are annotated on class.')
483+
summary.append(str(rank_number['order'])+' ('+str(round(rank_percentage['order']*100,2))+'%) aligned smORFs are annotated on order.')
484+
summary.append(str(rank_number['family'])+' ('+str(round(rank_percentage['family']*100,2))+'%) aligned smORFs are annotated on family.')
485+
summary.append(str(rank_number['genus'])+' ('+str(round(rank_percentage['genus']*100,2))+'%) aligned smORFs are annotated on genus.')
486+
summary.append(str(rank_number['species'])+' ('+str(round(rank_percentage['species']*100,2))+'%) aligned smORFs are annotated on species.')
487487

488488
with atomic_write(f'{args.output}/summary.txt', overwrite=True) as ofile:
489489
for s in summary:

‎tests/diamond_contig/summary.txt‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -3,18 +3,18 @@
33
28 smORFs are aligned against GMSC in total.
44

55
# Quality
6-
8(28.57%) aligned smORFs are high quality.
6+
8 (28.57%) aligned smORFs are high quality.
77

88
# Habitat
9-
25(89.29%) aligned smORFs are single-habitat.
10-
3(10.71%) aligned smORFs are multi-habitat.
9+
25 (89.29%) aligned smORFs are single-habitat.
10+
3 (10.71%) aligned smORFs are multi-habitat.
1111

1212
# Taxonomy
13-
8(28.57%) aligned smORFs have taxonomy annotation.
14-
3(10.71%) aligned smORFs are annotated on kingdom.
15-
0(0%) aligned smORFs are annotated on phylum.
16-
1(3.57%) aligned smORFs are annotated on class.
17-
1(3.57%) aligned smORFs are annotated on order.
18-
0(0%) aligned smORFs are annotated on family.
19-
0(0%) aligned smORFs are annotated on genus.
20-
3(10.71%) aligned smORFs are annotated on species.
13+
8 (28.57%) aligned smORFs have taxonomy annotation.
14+
3 (10.71%) aligned smORFs are annotated on kingdom.
15+
0 (0%) aligned smORFs are annotated on phylum.
16+
1 (3.57%) aligned smORFs are annotated on class.
17+
1 (3.57%) aligned smORFs are annotated on order.
18+
0 (0%) aligned smORFs are annotated on family.
19+
0 (0%) aligned smORFs are annotated on genus.
20+
3 (10.71%) aligned smORFs are annotated on species.

‎tests/diamond_gene/summary.txt‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -2,18 +2,18 @@
22
3 smORFs are aligned against GMSC in total.
33

44
# Quality
5-
2(66.67%) aligned smORFs are high quality.
5+
2 (66.67%) aligned smORFs are high quality.
66

77
# Habitat
8-
3(100.0%) aligned smORFs are single-habitat.
9-
0(0.0%) aligned smORFs are multi-habitat.
8+
3 (100.00%) aligned smORFs are single-habitat.
9+
0 (0.00%) aligned smORFs are multi-habitat.
1010

1111
# Taxonomy
12-
0(0.0%) aligned smORFs have taxonomy annotation.
13-
0(0%) aligned smORFs are annotated on kingdom.
14-
0(0%) aligned smORFs are annotated on phylum.
15-
0(0%) aligned smORFs are annotated on class.
16-
0(0%) aligned smORFs are annotated on order.
17-
0(0%) aligned smORFs are annotated on family.
18-
0(0%) aligned smORFs are annotated on genus.
19-
0(0%) aligned smORFs are annotated on species.
12+
0 (0.0%) aligned smORFs have taxonomy annotation.
13+
0 (0%) aligned smORFs are annotated on kingdom.
14+
0 (0%) aligned smORFs are annotated on phylum.
15+
0 (0%) aligned smORFs are annotated on class.
16+
0 (0%) aligned smORFs are annotated on order.
17+
0 (0%) aligned smORFs are annotated on family.
18+
0 (0%) aligned smORFs are annotated on genus.
19+
0 (0%) aligned smORFs are annotated on species.

‎tests/diamond_protein/summary.txt‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -2,18 +2,18 @@
22
29 smORFs are aligned against GMSC in total.
33

44
# Quality
5-
8(27.59%) aligned smORFs are high quality.
5+
8 (27.59%) aligned smORFs are high quality.
66

77
# Habitat
8-
26(89.66%) aligned smORFs are single-habitat.
9-
3(10.34%) aligned smORFs are multi-habitat.
8+
26 (89.66%) aligned smORFs are single-habitat.
9+
3 (10.34%) aligned smORFs are multi-habitat.
1010

1111
# Taxonomy
12-
8(27.59%) aligned smORFs have taxonomy annotation.
13-
3(10.34%) aligned smORFs are annotated on kingdom.
14-
0(0%) aligned smORFs are annotated on phylum.
15-
1(3.45%) aligned smORFs are annotated on class.
16-
1(3.45%) aligned smORFs are annotated on order.
17-
0(0%) aligned smORFs are annotated on family.
18-
0(0%) aligned smORFs are annotated on genus.
19-
3(10.34%) aligned smORFs are annotated on species.
12+
8 (27.59%) aligned smORFs have taxonomy annotation.
13+
3 (10.34%) aligned smORFs are annotated on kingdom.
14+
0 (0%) aligned smORFs are annotated on phylum.
15+
1 (3.45%) aligned smORFs are annotated on class.
16+
1 (3.45%) aligned smORFs are annotated on order.
17+
0 (0%) aligned smORFs are annotated on family.
18+
0 (0%) aligned smORFs are annotated on genus.
19+
3 (10.34%) aligned smORFs are annotated on species.

‎tests/mmseqs_contig/summary.txt‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -3,18 +3,18 @@
33
28 smORFs are aligned against GMSC in total.
44

55
# Quality
6-
8(28.57%) aligned smORFs are high quality.
6+
8 (28.57%) aligned smORFs are high quality.
77

88
# Habitat
9-
25(89.29%) aligned smORFs are single-habitat.
10-
3(10.71%) aligned smORFs are multi-habitat.
9+
25 (89.29%) aligned smORFs are single-habitat.
10+
3 (10.71%) aligned smORFs are multi-habitat.
1111

1212
# Taxonomy
13-
8(28.57%) aligned smORFs have taxonomy annotation.
14-
3(10.71%) aligned smORFs are annotated on kingdom.
15-
0(0%) aligned smORFs are annotated on phylum.
16-
1(3.57%) aligned smORFs are annotated on class.
17-
1(3.57%) aligned smORFs are annotated on order.
18-
0(0%) aligned smORFs are annotated on family.
19-
0(0%) aligned smORFs are annotated on genus.
20-
3(10.71%) aligned smORFs are annotated on species.
13+
8 (28.57%) aligned smORFs have taxonomy annotation.
14+
3 (10.71%) aligned smORFs are annotated on kingdom.
15+
0 (0%) aligned smORFs are annotated on phylum.
16+
1 (3.57%) aligned smORFs are annotated on class.
17+
1 (3.57%) aligned smORFs are annotated on order.
18+
0 (0%) aligned smORFs are annotated on family.
19+
0 (0%) aligned smORFs are annotated on genus.
20+
3 (10.71%) aligned smORFs are annotated on species.

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