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ENH run gmscmapper in git action (#17)
* Update test_gmsc_mapper.yml * Update test_gmsc_mapper.yml * Update test_gmsc_mapper.yml * Update test_gmsc_mapper.yml * Update test_gmsc_mapper.yml * ENH git action * Update test_gmsc_mapper.yml * BUG git action * Update main.py * Update main.py * Update main.py * Update test_diamond_gene.py * Update test_diamond_contig.py * Update main.py * ENH run gmscmapper in git action
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‎.github/workflows/test_gmsc_mapper.yml‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -25,12 +25,14 @@ jobs:
2525
python-version: ${{ matrix.python-version }}
2626
auto-activate-base: false
2727
- name: Install dependencies
28+
shell: bash
2829
run: |
2930
pip install pytest
3031
pip install atomicwrites
3132
pip install pyrodigal
3233
pip install pandas
3334
pip install biopython
35+
python ./setup.py install
3436
- name: Test with pytest
3537
run: |
3638
python -m pytest ./tests

‎gmsc_mapper/main.py‎

Lines changed: 58 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -186,13 +186,17 @@ def check_install():
186186
if dep == 'mmseqs':
187187
has_mmseqs = True
188188
if not has_diamond and not has_mmseqs:
189-
sys.stderr.write('GMSC-mapper Error: Neither diamond nor mmseqs appear to be available!\n'
190-
'At least one of them is necessary to run GMSC-mapper.\n')
191-
sys.exit(1)
192-
elif has_diamond and not has_mmseqs:
193-
logger.warning('Warning: mmseqs does not appear to be available.You can only use the `--tool diamond` option(default).')
194-
elif not has_diamond and has_mmseqs:
195-
logger.warning('Warning: diamond does not appear to be available.You can only use the `--tool mmseqs` option.')
189+
logger.warning('GMSC-mapper Warning: Neither diamond nor mmseqs appear to be available! It will download diamond and mmseqs.\n')
190+
subprocess.check_call(['wget','https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz',
191+
'-P','./bin'])
192+
subprocess.check_call(['tar','xvfz',
193+
'./bin/mmseqs-linux-avx2.tar.gz',
194+
'-C','./bin'])
195+
subprocess.check_call(['wget','http://github.com/bbuchfink/diamond/releases/download/v2.1.8/diamond-linux64.tar.gz',
196+
'-P','./bin'])
197+
subprocess.check_call(['tar','xvfz',
198+
'./bin/diamond-linux64.tar.gz',
199+
'-C','./bin'])
196200
else:
197201
logger.info('Dependencies installation is OK\n')
198202
return has_diamond,has_mmseqs
@@ -216,11 +220,19 @@ def expect_file(f):
216220
sys.exit(1)
217221

218222
if args.tool == "diamond" and not has_diamond:
219-
sys.stderr.write("GMSC-mapper Error:diamond is not available.Please add diamond into your path or use the `--tool mmseqs` option.\n")
220-
sys.exit(1)
223+
logger.warning("GMSC-mapper Warning:mmseqs is not available.It will download diamond.\n")
224+
subprocess.check_call(['wget','http://github.com/bbuchfink/diamond/releases/download/v2.1.8/diamond-linux64.tar.gz',
225+
'-P','./bin'])
226+
subprocess.check_call(['tar','xvfz',
227+
'./bin/diamond-linux64.tar.gz',
228+
'-C','./bin'])
221229
if args.tool == "mmseqs" and not has_mmseqs:
222-
sys.stderr.write("GMSC-mapper Error:mmseqs is not available.Please add mmseqs into your path or use the `--tool diamond` option(default).\n")
223-
sys.exit(1)
230+
logger.warning("GMSC-mapper Warning:mmseqs is not available.It will download mmseqs.\n")
231+
subprocess.check_call(['wget','https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz',
232+
'-P','./bin'])
233+
subprocess.check_call(['tar','xvfz',
234+
'./bin/mmseqs-linux-avx2.tar.gz',
235+
'-C','./bin'])
224236

225237
if args.database:
226238
expect_file(args.database)
@@ -300,26 +312,38 @@ def download_db(args):
300312
print('Conserved domain index file already exists. Skip downloading conserved domain index file. Use -f to force download')
301313

302314
def create_db(args):
315+
from shutil import which
316+
303317
if not os.path.exists(args.output):
304318
os.makedirs(args.output)
305319

306320
diamond_out_db = path.join(args.output,"diamond_targetdb")
307321
mmseqs_out_db = path.join(args.output,"mmseqs_targetdb")
322+
323+
if which('diamond'):
324+
diamond = 'diamond'
325+
else:
326+
diamond = './bin/diamond'
327+
328+
if which('mmseqs'):
329+
mmseqs = 'mmseqs'
330+
else:
331+
mmseqs = './bin/mmseqs/bin/mmseqs'
308332

309333
if args.quiet:
310-
diamond_cmd = ['diamond','makedb',
334+
diamond_cmd = [diamond,'makedb',
311335
'--in',args.target_faa,
312336
'-d',diamond_out_db,
313337
'--quiet']
314-
mmseqs_cmd = ['mmseqs','createdb',
338+
mmseqs_cmd = [mmseqs,'createdb',
315339
args.target_faa,
316340
mmseqs_out_db,
317341
'-v','0']
318342
else:
319-
diamond_cmd = ['diamond','makedb',
343+
diamond_cmd = [diamond,'makedb',
320344
'--in',args.target_faa,
321345
'-d',diamond_out_db]
322-
mmseqs_cmd = ['mmseqs','createdb',
346+
mmseqs_cmd = [mmseqs,'createdb',
323347
args.target_faa,
324348
mmseqs_out_db]
325349

@@ -380,12 +404,19 @@ def filter_length(queryfile,tmpdir,N):
380404
return filtered_file
381405

382406
def mapdb_diamond(args,queryfile):
407+
from shutil import which
408+
383409
logger.debug('Starting smORF mapping...')
384410

385411
resultfile = path.join(args.output,"alignment.out.smorfs.tsv")
386412
outfmt = '6,qseqid,sseqid,full_qseq,full_sseq,qlen,slen,length,qstart,qend,sstart,send,bitscore,pident,evalue,qcovhsp,scovhsp'
387413

388-
diamond_cmd = ['diamond','blastp',
414+
if which('diamond'):
415+
diamond = 'diamond'
416+
else:
417+
diamond = './bin/diamond'
418+
419+
diamond_cmd = [diamond,'blastp',
389420
'-q',queryfile,
390421
'-d',args.database,
391422
'-o',resultfile,
@@ -405,6 +436,8 @@ def mapdb_diamond(args,queryfile):
405436
return resultfile
406437

407438
def mapdb_mmseqs(args, queryfile, tmpdir):
439+
from shutil import which
440+
408441
logger.info('Start smORF mapping...')
409442

410443
querydb = path.join(tmpdir,"query.db")
@@ -413,8 +446,13 @@ def mapdb_mmseqs(args, queryfile, tmpdir):
413446
resultfile = path.join(args.output,"alignment.out.smorfs.tsv")
414447
outfmt = 'query,target,qseq,tseq,qlen,tlen,alnlen,qstart,qend,tstart,tend,bits,pident,evalue,qcov,tcov'
415448

416-
mmseqs_cmd_db = ['mmseqs', 'createdb', queryfile, querydb]
417-
mmseqs_cmd_search = ['mmseqs','search',
449+
if which('mmseqs'):
450+
mmseqs = 'mmseqs'
451+
else:
452+
mmseqs = './bin/mmseqs/bin/mmseqs'
453+
454+
mmseqs_cmd_db = [mmseqs, 'createdb', queryfile, querydb]
455+
mmseqs_cmd_search = [mmseqs,'search',
418456
querydb,
419457
args.database,
420458
resultdb,
@@ -424,7 +462,7 @@ def mapdb_mmseqs(args, queryfile, tmpdir):
424462
'--min-seq-id',str(args.identity),
425463
'-c',str(args.coverage),
426464
'--threads',str(args.threads)]
427-
mmseqs_cmd_out = ['mmseqs','convertalis',
465+
mmseqs_cmd_out = [mmseqs,'convertalis',
428466
querydb,
429467
args.database,
430468
resultdb,
@@ -510,7 +548,7 @@ def main(args=None):
510548

511549
if not args.cmd:
512550
validate_args(args,has_diamond,has_mmseqs)
513-
551+
514552
if args.tool == 'diamond':
515553
if args.database is None:
516554
args.database = path.join(_ROOT, 'db/diamond_targetdb.dmnd')

‎tests/diamond_contig/domain.out.smorfs.tsv‎

Lines changed: 29 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,29 @@
1+
qseqid cdd
2+
smORF_00 198061,429887
3+
smORF_01
4+
smORF_02 197696
5+
smORF_05
6+
smORF_06 381607
7+
smORF_07
8+
smORF_08
9+
smORF_09 425695
10+
smORF_10
11+
smORF_11
12+
smORF_12
13+
smORF_13
14+
smORF_14 433792
15+
smORF_15
16+
smORF_16
17+
smORF_17
18+
smORF_18
19+
smORF_19 426994
20+
smORF_20 429147
21+
smORF_21
22+
smORF_22
23+
smORF_24
24+
smORF_25
25+
smORF_26 425742
26+
smORF_27 429147
27+
smORF_28
28+
smORF_29 197911,429147
29+
smORF_30

‎tests/diamond_contig/summary.txt‎

Lines changed: 11 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -11,10 +11,14 @@
1111

1212
# Taxonomy
1313
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.
14+
3 (10.71%) aligned smORFs are annotated at level of kingdom.
15+
0 (0.00%) aligned smORFs are annotated at level of phylum.
16+
1 (3.57%) aligned smORFs are annotated at level of class.
17+
1 (3.57%) aligned smORFs are annotated at level of order.
18+
0 (0.00%) aligned smORFs are annotated at level of family.
19+
0 (0.00%) aligned smORFs are annotated at level of genus.
20+
3 (10.71%) aligned smORFs are annotated at level of species.
21+
22+
# Conserved domain
23+
10 aligned smORFs are annotated with CDD database.
24+

‎tests/diamond_gene/domain.out.smorfs.tsv‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
1+
qseqid cdd
2+
GMSC10.90AA.000_000_000_003
3+
GMSC10.90AA.000_000_000_007
4+
GMSC10.90AA.000_000_000_009

‎tests/diamond_gene/summary.txt‎

Lines changed: 12 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -9,11 +9,15 @@
99
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 (0.00%) aligned smORFs have taxonomy annotation.
13+
0 (0.00%) aligned smORFs are annotated at level of kingdom.
14+
0 (0.00%) aligned smORFs are annotated at level of phylum.
15+
0 (0.00%) aligned smORFs are annotated at level of class.
16+
0 (0.00%) aligned smORFs are annotated at level of order.
17+
0 (0.00%) aligned smORFs are annotated at level of family.
18+
0 (0.00%) aligned smORFs are annotated at level of genus.
19+
0 (0.00%) aligned smORFs are annotated at level of species.
20+
21+
# Conserved domain
22+
0 aligned smORFs are annotated with CDD database.
23+

‎tests/diamond_protein/domain.out.smorfs.tsv‎

Lines changed: 30 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,30 @@
1+
qseqid cdd
2+
smORF_00 198061,429887
3+
smORF_01
4+
smORF_02 197696
5+
smORF_03
6+
smORF_04
7+
smORF_05 381607
8+
smORF_06
9+
smORF_07
10+
smORF_08 425695
11+
smORF_09
12+
smORF_10
13+
smORF_11
14+
smORF_12
15+
smORF_13 433792
16+
smORF_14
17+
smORF_15
18+
smORF_16
19+
smORF_17
20+
smORF_18 426994
21+
smORF_19 429147
22+
smORF_20
23+
smORF_21
24+
smORF_22
25+
smORF_23
26+
smORF_24 425742
27+
smORF_25 429147
28+
smORF_26
29+
smORF_27 197911,429147
30+
smORF_28

‎tests/diamond_protein/summary.txt‎

Lines changed: 11 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -10,10 +10,14 @@
1010

1111
# Taxonomy
1212
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.
13+
3 (10.34%) aligned smORFs are annotated at level of kingdom.
14+
0 (0.00%) aligned smORFs are annotated at level of phylum.
15+
1 (3.45%) aligned smORFs are annotated at level of class.
16+
1 (3.45%) aligned smORFs are annotated at level of order.
17+
0 (0.00%) aligned smORFs are annotated at level of family.
18+
0 (0.00%) aligned smORFs are annotated at level of genus.
19+
3 (10.34%) aligned smORFs are annotated at level of species.
20+
21+
# Conserved domain
22+
10 aligned smORFs are annotated with CDD database.
23+

‎tests/mmseqs_contig/alignment.out.smorfs.tsv‎

Lines changed: 28 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
1+
smORF_00 GMSC10.90AA.000_000_000_080 MQEEMSALTQNHTWDLVPASPDMNLLGCKWVFRVKLNADGSLDKLKARLVAKGFLIPTRKKLVG* MQEEMSALTQNHTWDLVPASPDMNLLGCKWVFRVKLNADGSLDKLKARLVAKGFLIPTRKKLVG* 65 65 64 1 64 1 64 136 98.600 1.180E-41 0.985 0.985
2+
smORF_01 GMSC10.90AA.000_000_000_081 MPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAVEGNEIIREACKWSPELAAACEVWKEITFNFPTIDKLDGQE* MPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAVEGNEIIREACKWSPELAAACEVWKEITFNFPTIDKLDGQE* 94 94 93 1 93 1 93 200 100.000 1.456E-63 0.989 0.989
3+
smORF_02 GMSC10.90AA.000_000_000_082 MGCCSTERRDAPDRWDPVPTKLIEGSANPTKLKKEWRTKENGRRSAVPKGCYSADRREVNSGIRMLRCQRSDGISSCQDRGMM* MGCCSTERRDAPDRWDPVPTKLIEGSANPTKLKKEWRTKENGRRSAVPKGCYSADRREVNSGIRMLRCQRSDGISSCQDRGMM* 84 84 83 1 83 1 83 181 100.000 4.761E-57 0.988 0.988
4+
smORF_05 GMSC10.90AA.000_000_000_086 MVYILLLIAWRIKNMTIAFQLAVFALIITSSILLISVPVVFASPDGWSSNKNVVFSGTSLWIGLVFLVGILNSLIS* MVYILLLIAWRIKNMTIAFQLAVFALIITSSILLISVPVVFASPDGWSSNKNVVFSGTSLWIGLVFLVGILNSLIS* 77 77 76 1 76 1 76 143 88.600 7.209E-44 0.987 0.987
5+
smORF_06 GMSC10.90AA.000_000_000_088 MPRSRINGNFIDKTFTIVADILLRVIPTTSGEKEAFTYYRDGAIWLSLFFFLADFDWNRKKNEYWKKIYAFEGEVYNIKKTIPSVMYPRLMQP* MPRSRINGNFIDKTFTIVADILLRVIPTTSGEKEAFTYYRDGAIWLSLFFFLADFDWNRKKNEYWKKIYAFEGEVYNIKKTIPSVMYPRLMQP* 94 94 93 1 93 1 93 199 99.900 5.156E-63 0.989 0.989
6+
smORF_07 GMSC10.90AA.000_000_000_013 MAKGKDVRVTIILECTSCVRNDIKKEAAGISRYITQKNRHNTPSRLELRKFCPYCYKHTIHGEIKK* MAKGKDVRVTIILECTSCVRNDIKKEAAGISRYITQKNRHNTPSRLELRKFCPYCYKHTIHGEIKK* 67 67 66 1 66 1 66 144 100.000 1.688E-44 0.985 0.985
7+
smORF_08 GMSC10.90AA.000_000_000_014 MRDLKTYLSVAPVLSTLWFGSLAGLLIEINRLFPDALTFPFFSF* MRDLKTYLSVAPVLSTLWFGSLAGLLIEINRLFPDALTFPFFSF* 45 45 44 1 44 1 44 91 95.700 1.535E-26 0.978 0.978
8+
smORF_09 GMSC10.90AA.000_000_000_016 MSSPEFARTIPVSPPMVNKKMNPTANNMGVLYCIEPPHMVAIQLKILIPVGTAMIMVAAVK* MSSPEFARTIPVSPPMVNKKMNPTANNMGVLYCIEPPHMVAIQLKILIPVGTAMIMVAAVK* 62 62 61 1 61 1 61 122 93.600 4.834E-37 0.984 0.984
9+
smORF_10 GMSC10.90AA.000_000_000_021 MVFSRMFRMSRLLNSLTDWLLELTNGLPASLLFVLEPLLAMDLLWLTGPEMS* MVFSRMFRMSRLLNSLTDWLLELTNGLPASLLFVLEPLLAMDLLWLTGPEMS* 53 53 52 1 52 1 52 104 93.200 6.587E-31 0.981 0.981
10+
smORF_11 GMSC10.90AA.000_000_000_023 MCLELILNAVNMNFVTFSDFFDNSQLQGEIFCIFVIAIAAAEAAIGLAIVSSIYRNRKSIRINQSTLLNK* MCLELILNAVNMNFVTFSDFFDNSQLQGEIFCIFVIAIAAAEAAIGLAIVSSIYRNRKSIRINQSTLLNK* 71 71 70 1 70 1 70 133 89.400 1.466E-40 0.986 0.986
11+
smORF_12 GMSC10.90AA.000_000_000_024 MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY* MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY* 82 82 81 1 81 1 81 183 100.000 1.216E-57 0.988 0.988
12+
smORF_13 GMSC10.90AA.000_000_000_028 MSGSTGERSFADIITSIRYWVIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTESRQGIPLITGRFDPLEQLDEFSRSF* MSGSTGERSFADIITSIRYWVIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTESRQGIPLITGRFDPLEQLDEFSRSF* 84 84 83 1 83 1 83 176 99.000 2.909E-55 0.988 0.988
13+
smORF_14 GMSC10.90AA.000_000_000_032 MKTGLWESKKSVVLLGEAVECRTLDGESPVAESITSLCSDPSSMGHVESRVNQQGPPCKAKYSWVTDSEVVP* MKTGLWESKKSVVLLGEAVECRTLDGESPVAESITSLCSDPSSMGHVESRVNQQGPPCKAKYSWVTDSEVVP* 73 73 72 1 72 1 72 151 97.700 1.050E-46 0.986 0.986
14+
smORF_15 GMSC10.90AA.000_000_000_033 MPLEPRASWFSPKCVEAQQLTGHLGVKHCFGAGRESGTKSRQTLNTRYDLKITGVKVGQ* MPLEPRASWFSPKCVEAQQLTGHLGVKHCFGAGRESGTKSRQTLNTRYDLKITGVKVGQ* 60 60 59 1 59 1 59 132 100.000 1.583E-40 0.983 0.983
15+
smORF_16 GMSC10.90AA.000_000_000_034 MKNLTDSFVYLGHWPSAGSFGFNTDILATNPINLSVVFGVLIFFGKGVCVSCSFQE* MKNLTDSFVYLGHWPSAGSFGFNTDILATNPINLSVVFGVLIFFGKGVCVSCSFQE* 57 57 56 1 56 1 56 124 100.000 7.672E-38 0.982 0.982
16+
smORF_17 GMSC10.90AA.000_000_000_037 MFLISRLAETNRAPFDLPEAEAESVAGYNVEYARDAILNSPLLAEANVPGSRGLILTETRGGSLPTQKYSIFGKTKNVIA* MFLISRLAETNRAPFDLPEAEAESVAGYNVEYARDAILNSPLLAEANVPGSRGLILTETRGGSLPTQKYSIFGKTKNVIA* 81 81 80 1 80 1 80 162 95.000 1.615E-50 0.988 0.988
17+
smORF_18 GMSC10.90AA.000_000_000_043 MVDTRDSKSRAKERGGSSPLQGIILKWNKFGSGSRNIGDLLYLMNGEGESALKSSALRPAVYDSTGITQG* MVDTRDSKSRAKERGGSSPLQGIILKWNKFGSGSRNIGDLLYLMNGEGESALKSSALRPAVYDSTGITQG* 71 71 70 1 70 1 70 142 94.900 1.006E-43 0.986 0.986
18+
smORF_19 GMSC10.90AA.000_000_000_044 MLLLKHGRIEILDQNTMYGWYELPKQEFLNSEQPELLLTTSKKFPLIKDGNPLENQKYACRIKLLLLSVPITNQLNN* MLLLKHGRIEILDQNTMYGWYELPKQEFLNSEQPELLLTTSKKFPLIKDGNPLENQKYACRIKLLLLSVPITNQLNN* 78 78 77 1 77 1 77 164 99.200 3.923E-51 0.987 0.987
19+
smORF_30 GMSC10.90AA.000_000_000_079 MEYKVLNLSLIQYYFLLFKDMKESKCESSSLWLNAKKSSKLIRLYVVLIVTGLLNLLDYLSLLSFFIWYLYGTGTGISSCFLYY* MEYKVLNLSLIQYYFLLFKDMKESKCESSSLWLNAKKSSKLIRLYVVLIVTGLLNLLDYLSLLSFFIWYLYGTGTGISSCFLYY* 85 85 84 1 84 1 84 164 92.200 2.950E-51 0.988 0.988
20+
smORF_20 GMSC10.90AA.000_000_000_047 MTTFNNLPSIFVPLVGLVFPAIAMASLFLHIQKNKIF* MTTFNNLPSIFVPLVGLVFPAIAMASLFLHIQKNKIF* 38 38 37 1 37 1 37 75 93.200 4.815E-21 0.974 0.974
21+
smORF_21 GMSC10.90AA.000_000_000_054 MTRNVRRGGKIWVRIFPDKPVTVRPAETRMGSGKGSPEYWVAVVKPGKILYEMGGVPENIARKAISIAASKMPIKTQFIISE* MTRNVRRGGKIWVRIFPDKPVTVRPAETRMGSGKGSPEYWVAVVKPGKILYEMGGVPENIARKAISIAASKMPIKTQFIISE* 83 83 82 1 82 1 82 171 97.800 8.984E-54 0.988 0.988
22+
smORF_22 GMSC10.90AA.000_000_000_055 MKGNRKVCGFSGRMKEREKKLNINDI* MKGNRKVCGFSGRMKEREKKLNINDI* 27 27 26 1 26 1 26 57 99.500 4.356E-15 0.963 0.963
23+
smORF_24 GMSC10.90AA.000_000_000_059 MDGIKYAVFTDKSIRLLGKNQYTFNVESGSTRTEIKHWVELFFGVKVIAMNSHRLPGKVKRMGPILGHTMHYRRMIITLQPGYSIPPLRKKRT* MDGIKYAVFTDKSIRLLGKNQYTFNVESGSTRTEIKHWVELFFGVKVIAMNSHRLPGKVKRMGPILGHTMHYRRMIITLQPGYSIPPLRKKRT* 94 94 93 1 93 1 93 196 98.800 3.438E-62 0.989 0.989
24+
smORF_25 GMSC10.90AA.000_000_000_062 MTRSLKKNPFVAKHLLRKIEKLNTKAEKEIIITWSRASTIIPTMIGHTIAIHNGREHLPVYIIDLMVGHKLGEFSPTINFRGHAKNDNRSRR* MTRSLKKNPFVAKHLLRKIEKLNTKAEKEIIITWSRASTIIPTMIGHTIAIHNGREHLPVYIIDLMVGHKLGEFSPTINFRGHAKNDNRSRR* 93 93 92 1 92 1 92 188 95.800 3.437E-59 0.989 0.989
25+
smORF_26 GMSC10.90AA.000_000_000_065 MIKNIVISFEEQKEESRGSVEFQVFSFTNKIRRLTSHLELHRKDYLSQRGLRKILGKRQRLLAYLSKKNRVRYKELINQLNIRELKTR* MIKNIVISFEEQKEESRGSVEFQVFSFTNKIRRLTSHLELHRKDYLSQRGLRKILGKRQRLLAYLSKKNRVRYKELINQLNIRELKTR* 89 89 88 1 88 1 88 168 90.000 2.860E-52 0.989 0.989
26+
smORF_27 GMSC10.90AA.000_000_000_068 MSAQSEGNYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYVRLSPL* MSAQSEGNYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYVRLSPL* 83 83 82 1 82 1 82 173 98.500 3.477E-54 0.988 0.988
27+
smORF_28 GMSC10.90AA.000_000_000_075 MIYLSIEKDTKDLYLFINSPGGWVISGMAIYDTMQFVRPDVQTICMGLAASIASFILVGGAITKRIAFPHAWRQ* MIYLSIEKDTKDLYLFINSPGGWVISGMAIYDTMQFVRPDVQTICMGLAASIASFILVGGAITKRIAFPHAWRQ* 75 75 74 1 74 1 74 158 99.600 2.836E-49 0.987 0.987
28+
smORF_29 GMSC10.90AA.000_000_000_078 MATQTVEDSSRSGPRSTTVGKLLKPLNSEYGKVAPGWGTTPLMGVAMALFAVFLSIILEIYNSSVLLDGISVN* MATQTVEDSSRSGPRSTTVGKLLKPLNSEYGKVAPGWGTTPLMGVAMALFAVFLSIILEIYNSSVLLDGISVN* 74 74 73 1 73 1 73 143 91.900 6.208E-44 0.986 0.986

‎tests/mmseqs_contig/domain.out.smorfs.tsv‎

Lines changed: 29 additions & 0 deletions
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qseqid cdd
2+
smORF_00 198061,429887
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smORF_01
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smORF_02 197696
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smORF_05
6+
smORF_06 381607
7+
smORF_07
8+
smORF_08
9+
smORF_09 425695
10+
smORF_10
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smORF_11
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smORF_12
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smORF_13
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smORF_14 433792
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smORF_15
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smORF_16
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smORF_17
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smORF_18
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smORF_19 426994
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smORF_20 429147
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smORF_21
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smORF_22
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smORF_24
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smORF_25
25+
smORF_26 425742
26+
smORF_27 429147
27+
smORF_28
28+
smORF_29 197911,429147
29+
smORF_30

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