def test_search_hmms_input(self):
with tempdir.TempDir() as tmp:
gpkg = tmp + ".gpkg"
Create(prerequisites).main(
sequences=os.path.join(path_to_data, 'create',
'homologs.trimmed.unaligned.faa'),
taxonomy=os.path.join(
path_to_data, 'create',
'homologs.tax2tree.rerooted.decorated.tree-consensus-strings'
),
hmm=os.path.join(
path_to_data, 'create', 'first5.hmm'
), # an HMM created from just the first 5 sequences
search_hmm_files=[
os.path.join(path_to_data, 'create', 'homologs.hmm')
],
prefix=gpkg,
threads=5)
self.assertEqual(
'NAME first10\n',
open(GraftMPackageVersion2.acquire(
gpkg).alignment_hmm_path()).readlines()[1])
self.assertEqual(
1, len(GraftMPackageVersion2.acquire(gpkg).search_hmm_paths()))
self.assertEqual(
'NAME homologs.trimmed.aligned\n',
open(
GraftMPackageVersion2.acquire(gpkg).search_hmm_paths()
[0]).readlines()[1])
def test_search_hmms_input(self):
with tempdir.TempDir() as tmp:
gpkg = tmp+".gpkg"
Create(prerequisites).main(sequences=os.path.join(path_to_data,'create','homologs.trimmed.unaligned.faa'),
taxonomy=os.path.join(path_to_data,'create','homologs.tax2tree.rerooted.decorated.tree-consensus-strings'),
hmm=os.path.join(path_to_data, 'create', 'first5.hmm'), # an HMM created from just the first 5 sequences
search_hmm_files=[os.path.join(path_to_data, 'create', 'homologs.hmm')],
prefix=gpkg,
threads=5)
self.assertEqual('NAME first10\n', open(GraftMPackageVersion2.acquire(gpkg).alignment_hmm_path()).readlines()[1])
self.assertEqual(1, len(GraftMPackageVersion2.acquire(gpkg).search_hmm_paths()))
self.assertEqual('NAME homologs.trimmed.aligned\n', open(GraftMPackageVersion2.acquire(gpkg).search_hmm_paths()[0]).readlines()[1])
def test_create_stars(self):
with tempdir.TempDir() as tmp:
gpkg = tmp+".gpkg"
Create(prerequisites).main(sequences=os.path.join(path_to_data,'create','homologs.trimmed.unaligned.with_stars.faa'),
taxonomy=os.path.join(path_to_data,'create','homologs.tax2tree.rerooted.decorated.tree-consensus-strings'),
prefix=gpkg)
self.assertTrue(os.path.exists(GraftMPackageVersion2.acquire(gpkg).alignment_hmm_path()))
def test_create_dereplication(self):
reads = '''>r1
MSHFLDRLTYFSAPKESFSGGHGLTNAEDRTWEDAYRNRWAHDKIVRSTHGVNCTGSCSWKIYVKGGIVTWETQQTDYPRTRWDMPNHEPRGCARGASYSWYLYSANRVKYPMVRGRLLERWRAALKVAKSPVDAWALIQQDPEARRDYQQVRGMGGFVRSTWDEVNQLIAAANVYTIKQHGPDRVIGFSPIPAMSMVSYAAGSRYLSLIGGVCMSFYDWYCDLPPSSPQVWGEQTDVPESADWYNSTFIIAWGSNVPQTRTPDAHFFTEVRYKGAKTVAVTPDYSEVAKLSDLWLHPKQGTDAALAMAMGHVALKEFYFPGNGKPRSAYFDDYARRYTDLPLLVMLKELTLPDGKVTLVPDRYVRASDFNGKMGQKSNPEWKTVAFDTAGKAVLPNGSIGFRWGEPGREDEGKWNLESKEARSNEDVKLKLSVLEDGEQTHQVVDVAFPYFGGQHNPHFPTNNQKGDVTVAKVPAVQLRLGKAGEERYAMVATVFDLQVAQYGINRGLGSGAKDFDDNAPYTPAWQESITGVPREQVITVARQFAENADKTHGKSMVIIGAAMNHWYHADMNYRGVINLLMMCGCIGQSGGGWSHYVGQEKLRPQTGWVPLAFATDWIRPSRQQNSTSFFYAHTDQWRYEKLGMGEIVSPTLSAQDRQAYSGSMIDFNVKAERMGWLPSAPQLKTNPLQVVKAAEAAGMDAKDYVVKALKDGTLEMSCEDPDASQNWPRNMFVWRSNLLGSSGKGHEYFCKHLLGTENGVQGKDLGKDDARPTEVKWHKDAPQGKLDLLVTLDFRMSTTCLYSDIVLPTASWYEKNDLNTSDMHPFIHPLSAAVDPVWQARSDWEIYKGFAKAFSDMCVGHLGVEKEVVLTPIMHDTAGEMAQPIDVREWKKGQCDLIPGKTAPQITVVERDYPNTFKRFTALGPLLDKLGNGGKGIGWQTGIEVEQLGQLNGLTQEEGISKGRPRIVSDIDACETILQLAPETNGHVAVKAWEALGKQTGRDHTHLALYREDEKIRYRDIQAQPRKIISSPTWSGIESETVSYNAGYTNVHELIPWRTLTGRQQFYQDHKWMIAFGEGFSTYRPPVNLKTTDALQNKRPNGHKEIVLNFITPHQKWGIHSTYSDNLLMLTLNRGGTVIWLSENDAKVAGIEDNDWIELFNVNGAVAGRAVVSQRVNDGMCLMYHSQEKIINTPGSEITGVRGGIHNSVTRIVTKPTHMIGGYAQLSYGFNYYGTIGTNRDEFVIIRKMVKVDWLDTPADDHLVRAYQSQGENP
>r2
MSHFLDRLRYFTAPRPQFSDGHGAVTDEDRQWENAYRQRWQHDKIVRSTHGVNCTGSCSWKIYVKGGIVTWETQQTDYPRTRPDMPNHEPRGCSRGASYSWYLYSANRLKYPLVRSALVKLWRERRVSLEPVQAWQSIVTDEAARRGYQSRRGLGGFIRSTWDEVNEIVAAANVYTVKQHGPDRVVGFSPIPAMSMVSYAAGSRYLSLIGGVCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSTFIVMWGSNVPQTRTPDAHFMTEVRYKGAKIVSIFPDYAEGAKFGDIWLHPKQGTDAALALAMGHVILKEFHLTGKSDYFVDYCRRFTDMPCLVRLVPHGDAYVPERLVRASDFDDALGQANNAEWKTVMIDAASNEFVVPLGSVGFRWGQKEGEDQGKWNLKSEAATGEPLMPRLSLANAHDDVVAVLFPYFGNIAHPHFHHTTHGSQLSRKIGVRRIATRNGEMLVATVHDLFVANYGLDQGLGGEHIARDYDDDLPYTPAWQEAITGVKRADVISVARQFAENAHKTQGKSMVIIGAGINHWFHMDMSYRAIINMLIMCGCVGKSGGGWSHYVGQEKLRPQTGWTALAFALDWHRPPRHMNATSFFYAHTDQWRYDPMNPTALLSPLADASRFHGAPIDYNVRAERMGWLPSAPQLAVNPLDYGRALNDPAQAAATVVRDLKSGSLRMACEDPDHPDNFPRNLFVWRSNLLGSSGKGHEYFLKHLLGTINGVQGEEVVKSGHPRPEEIAWHDEAPRGKLDLLVTLDFRMSTTCMYSDVVLPTATWYEKDDMNTSDMHPFIHPLSAAVDPAWQSKSDWEIFKGIAKRFSELSEGHLGVERDIVLAPIAHDSPAELAQPFDVQDWKRGECEPVPGKTMPSVLVVERDYPATYAKFTSLGPLMDKLGNGGKGVSWDTKDEVALLGDLNYRVADAGCAKGRPRIDTALDAAEVILSLAPETNGAVAVKAWSAVTAMTGIEHAHLADARADEKIRFRDIPGPAAKIISSPTWSGIESEHVSYNAGYTNVHELIPWRTLSGRQQLYQDHLWMRAFGESLCVYKPPIETGSYEHMAGARSNGNPEIVLNFITPHQKWGIHSTYTDNLLMLTLSRGGPIVWLSEADAQAIGLVDNDWIECYNANGALCARAVVSQRVPRGMVMMYHAQEKIVNTPGSEITGTRGGIHNSVTRVALKPTHMIGGYAQLAYGFNYYGTVGSNRDEFLIVRKMKHIDWLDDTPPLTMSPPVQPLRQGEAS
>r3
MSHFLDRLKFMSKVKSTFSNGHGAVVKEDRQWEDAYRQRWQHDKVVRSTHGVNCTGSCSWKVYVKNGLITWETQQTDYPRTRADLPNHEPRGCPRGASYSWYVYSAQRVKYPMMRGKLAQMWREARKTMSAVEAWEYISQDPERAREYKSRRGQGGFVRATWEEANEMVAAANAYTIKNYGPDRVIGFSPIPAMSMVSYAAGSRYLSLIGGVPLSFYDWYCDLPPASPQIWGEQTDVAESADWYNSTYLMVWGSNVPMTRTPDAHFYTEVRYKGTKTVAVSSDFGEMAKFGDIWLAPKQGTDAALAMAMGHVIFKEFHLDNPSEYFTDYIRRLTDMPMLVRLKEEGGHYLPEYFLRASQLADNLGEDNNPDWKTLMIDELTGDVVAPNGSIGFRWGQAEGKTGKWNLETREGTTDREVKGQLSLLGRHDEVVGVAFPYFGAEHDDQLTRNIPAKRVQLADGSSALVTTVFDLMAGNYGIDRGLGGGNVATSYMDDVPYTPAWQQKHTGVKPEMVIQVAREFAQNADQTQGKSMVIVGAGLNHWYHMDMSYRGIINMLMLCGCIGQSGGGWCHYVGQEKLRPQSGWAPLAFAQDWNRPARQMNGTSFFYAHTSQWRHEKLGVNEILCPTAAGNMEHMSLIDYNAKAERMGWLPSAPQLETNPLDLTRMAAEAGMDPAAYTVQGLKDGSIDMSCNDPDNPKNFPRNLFVWRSNILGSSGKGHEYFLKYLLGTQNAVMSDETQCIQPSEITVRPAAEGKLDLLVVLDFRMSTTCLYGDIVLPTATWYEKDDLNTSDMHPFIHPLSEAVQPLWQSKTDWEIYKGFAKAISEVGKDYLGVQKDLVLTPLMHDSPQELGQPFDPRDWKKGECDPIPGKTMPAMTVVERDYGAIYQKFTSIGPLMEKVGNGGKGMAWKTEREVEQLRKMNKVVADGVAKGQPRLDTAIDAAEMIMTLAPETNGHVAVKAWESLSKITGRDHTHLAIPREHDHITFRDIQAQPRKIISSPIWSGLESEEVSYNAGYTNVHELIPWRTLTGRQQFYQDHQWMRAFGEGMCVYRPAVDLKTTAAVHNHKPNGNKEILLNFLTPHQKWGIHSTYSENLRMLTLSRGGPHIWISEKDAREAGIVDNDWVEVFNVNGTLTARVVVSQRIPQGMTLMYHAQEKIVNVPGAEMSGKRGGIHNSVTRAVTKPTHMIGGYAQLAYGFNYYGTVGCNRDEFIVMRKMKNVDWMDQPLSK
>r6
MSRNDASHTDETAGESDDKRRAVDQSDDEQPKKRGANEERTDGGPAVGDPPGGDNPSRRGFLKGVGLASVLGIGSASASDDALFSMDGLQPVGDPIGEYPYRDWEDLYREQWDWDSVSRSTHSVNCTGSCSWNVYVKNGQVWREEQSGDYPRFDESLPDPNPRGCQKGACYTDYVNAEQRIKHPLKRVGERGEGKWKRITWDEALTEIAEHVVDEVEAGRYDAISGFTPIPAMSPVSFASGSRLINLLGGVSHSFYDWYSDLPPGQPITWGTQTDNAESADWYNADYIIAWGSNINVTRIPDAKYFLESGYNGTKRVGIFTDYSQTAIHTDEWLSPDPGSDTALALGMAQTIVSEGLYDEAHLKEQTDMPLLVRQDTGKFLRASDVPSVNSSADRPEWMLLMLDSNGQLREAPGSLGERDGQKDYSKSIDLDFDPRLDAETTVQTDDGSVQVRSVWAELRDELAQYDPETVTKMTGVGTETYQRVAREFADVERAKIIHGKGVNDWYHNDLGNRAIQLLVTLTGNLGRQGTGVDHYVGQEKIWTFHGWKTLSFPTGKVRGVPTTLWTYYHAGILDNTDADTAAKIRESIDKGWMPVYPEEREDGSRPDPTTMFVWRGNYFNQAKGNVAVEEELWPKLDLVVDINFRMDSTALYSDIVLPTASHYEKHDLSMTDMHTYVHPFTPAVEPLGESKTDWQIFKDLAEKIQEVATERGVEPISDRTFDREIDLQSVYDDYVRDWETETDGALAEDRAAAEYILEHSAESNPAGTDEQITFADTVEQPQRLLEAGDHWTSDIEDGEAYAPWKDFVQDKNPWPTVTGRQQYYIDHDWFLELGEQLPTHKEGPTNTGGDYPMEYNTPHGRWAIHSTWRDSEKMLRLQRGEPIVYINPDDAAERGIEDGDTVEVFNDLGAVEVQAKIYPSSERGTLRHFFSWEKFQYASRNNFNTLVPMYMKPTQLVQYPEDTGEHLYFFPNYWGPTGVNSDVRVDVRKKGGDGG
>r5
MMNNQELNPKTTRRSFIKASGMTALTVSAGINLPLQVKAETIPIKNMQDDKEVLSLCSVNCGSRCVLRLHVKNDEVRWVETDNSGDDEYGNHQIRACLRGRSMRYRMNHPDRLKYPMKRIGKRGEGKFQRISWDEALDTIADNLKRIVKDYGNEAVYNNYASGIVGGNMTRSSPFASLFTRLMNCYGGLLSYYGSYSTAQIARAMPFTYGSNVGNSTSDIVNSKLVVFFGNNPMETRMSGAGITYHLEQARERSNAKLIVIDPRYTDTASGREDEWIPIRPGTDAALVAGMAHVMITENLVDQVFLDKYCVGYDEKTLPASAPANGHYKAYILGQGDDGVEKTPEWAAKITGIPAAKIIRLAREIGTTKPCYIAQGWGLQRQSNGELACRAVAMLAILTGNVGISGGNSGAREGSFYPPIQRLPVLENPVKAKISVFSWTDAIDHGDQMTALKDGVQGKDKLDVPIKFMWNYAGNCITNQHSDINRTHEILSDDKKCEMIVVIENFMTDSAKYADILLPDLMTTEQEDIVPNDYAGNMGYLIFSQPATSAKFERRGIYDICCEIAKRLGQDVYDKFTEGGRTQEQWLQFLYSRMQEKDATLPSYDELKQMGVYKRQDPNGHLVAYQKFREDPEANPLKTPSGKIEIYSERLAEIAATWELKEDEVIHPLPIYHSGFNGWDDPKREKYPFQLVSFHYKSRTHSTYGNIDVLESACPQEMWINPIDAQRLTLTDGETVRVFNEIGETRIPVKITPRIMPGVLGMGQGAWHKANMFGDKVDHNGCVNVLTTLRPSPLAKGNPQHSNLVRIEKL
>r7
MSKIDLYLDNPAFHIVTGACPHDCPDTCTWQVAVDRITGAAVDIWGHPAHPITQGKLCGKVDRYLERTYHKDRLTVPLRRVGPKGSGRFERVSWEEAIADIARRLQAIIEEYGPEAVLPYSYSGTLGFLQGEGMASRFFNRLGASQLARTICAEAGFQGYLYTIGAAEGMLPEDFAHSRLILIWGSNTLTSNLHLWPFIQQARKQGARVLVIDPANTRTAQAGDEWIPIRPGTDAALALAMMQVIIAEERYDADYVARYTLGFKQLAERVRDWTPARSAEITGIPAERIAALAREYATIRPAGIRINYGLQRHYGGGMAVRTIACLPALVGAWRQHGGGIQLSSSGLFRHLDKRGLHRPDLLEKAKAELQKGNAGAVDQTRPFPRVINMNRLGDALSLDPARLARAHYRPRPIDPLPKPEEAGPPVKALIVYNCNPAAVAPDQTAVLAGLRREELFTVVLEHFQTDTADYADYLLPATTQLEHWDIHRAYGHAYLALNRPAIAPVGESLPNSEIFRRLALAMGYDDPCFYESDEEILRAFVAAQTHERFAGLTWERLLNEAFFRLNLPDPYLPFAEGNFPTPSGKCEFFSARMAEDGYDPLPTYTPPRWQDRSGASALSSFDGSLVCISPPAHSFLNSTFANLPRFLQREDRPMLWIHPQDARPRHIEDGTRVRVCNQHGEVMLTARVTDAVVPGTVLAPGVWWPKLSPDGRNINRTTPPDETDMGAGALFYDATVWVEPLPVMANG
>r4
MSESVVVRAACPHDCPDTCAMEIGVRDGRAVSVRGAADMPFTNGALCTKVAHYLERVYSDQRLMHPLRRVGAKGDGRFERIRWDDALDIIAERFRAIAADDPRAILPYSYAGTMGLVQSESLDRRFFNRLGAARLDRTICAAAGAMGWKATVGASIGADPEAVVDARLILIWGGNPVVSNVHGWRYLQEAKRRGAKLICIDPRRSETAAKCHQHVAPLPGTDGALALAMMQVLIAEDLLDHDYIARCTLGFAELAERVRGCTPEWAAGVTGLDAATIRELAQAYGRSAPTLIRLNYGLNRSGGGGMAVRNIACLPALTGAWRHAGGGALLSTSGNFPLDRHALERPDLYRQDPSRPPRTINMTTIGEALLETRDPPIRALYVYNANPVAVAPYSAKVRAGFRREDLFCVVHELFQTDTADYADILLPATSQLEHHDLHTSYGHFYLVANRPAIDAQGEARSNTEVFRQLAARLGFDDTALFETDEAIAAAALRREDGRSLGVGARLAEHGWARLNLPRPFAPFARGGFPTPSGKCEFLSSFLAAQGLDPLPAWHPPYESVVSNPALAARYPLALISPPARNFLNSSFANLPRFTAGEGGPRLDIHRDDAAARGLTDGMRVRIHNDRGAFHAYARVTEAVRRGVVAAPSIWWQKRSGDGENANAVTSDALTDMGGGAVFYDCLVEVAGAPA\n'''
taxonomy = '''r1\td__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Hydrogenophaga;s__
r3\td__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Brachymonas;s__
r2\td__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia;s__
r4\td__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Rhodocyclales;f__Rhodocyclaceae;g__;s__
r5\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Basfia;s__
r7\td__Bacteria;p__Chloroflexi;c__Caldilineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea;s__aerophila
r6\td__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Halobacteriales;f__Halobacteriaceae;g__Halogeometricum;s__\n'''
with tempfile.NamedTemporaryFile(suffix='.fa', mode='w') as fasta:
fasta.write(reads)
fasta.flush()
with tempfile.NamedTemporaryFile(suffix='.tsv', mode='w') as tax:
tax.write(taxonomy)
tax.flush()
sequences_file = fasta.name
taxonomy_file = tax.name
expected_list = [7, 2, 3, 4, 5, 6, 7]
for expected, i in zip(expected_list, list(range(0, 6))):
with tempdir.TempDir() as package:
Create(prerequisites).main(sequences=sequences_file,
taxonomy=taxonomy_file,
prefix=package,
dereplication_level=i,
force=True,
threads=5)
base = os.path.basename(package)
gpkg = GraftMPackageVersion2.acquire(package)
with open(gpkg.taxtastic_seqinfo_path()) as f:
seqinfo = f.readlines()
with open(gpkg.search_hmm_paths()[0]) as hmm:
nseq = [
int(x.strip().split()[1])
for x in hmm.readlines()
if x.startswith("NSEQ")
][0]
self.assertEqual(nseq, expected)
def test_dna_package(self):
with tempdir.TempDir() as tmp:
gpkg = tmp+".gpkg"
Create(prerequisites).main(sequences=os.path.join(path_to_data,'create','61_otus.fasta'),
taxtastic_taxonomy=os.path.join(path_to_data,'61_otus.gpkg','61_otus.refpkg','61_otus_taxonomy.csv'),
taxtastic_seqinfo=os.path.join(path_to_data,'61_otus.gpkg','61_otus.refpkg','61_otus_seqinfo.csv'),
alignment=os.path.join(path_to_data,'61_otus.gpkg','61_otus.refpkg','61_otus.aln.fa'),
prefix=gpkg,
threads=5)
pkg = GraftMPackageVersion2.acquire(gpkg)
self.assertEqual('NAME 61_otus.aln\n', open(pkg.alignment_hmm_path()).readlines()[1])
self.assertEqual(pkg.diamond_database_path(), None)
def test_create_dereplication(self):
reads = '''>r1
MSHFLDRLTYFSAPKESFSGGHGLTNAEDRTWEDAYRNRWAHDKIVRSTHGVNCTGSCSWKIYVKGGIVTWETQQTDYPRTRWDMPNHEPRGCARGASYSWYLYSANRVKYPMVRGRLLERWRAALKVAKSPVDAWALIQQDPEARRDYQQVRGMGGFVRSTWDEVNQLIAAANVYTIKQHGPDRVIGFSPIPAMSMVSYAAGSRYLSLIGGVCMSFYDWYCDLPPSSPQVWGEQTDVPESADWYNSTFIIAWGSNVPQTRTPDAHFFTEVRYKGAKTVAVTPDYSEVAKLSDLWLHPKQGTDAALAMAMGHVALKEFYFPGNGKPRSAYFDDYARRYTDLPLLVMLKELTLPDGKVTLVPDRYVRASDFNGKMGQKSNPEWKTVAFDTAGKAVLPNGSIGFRWGEPGREDEGKWNLESKEARSNEDVKLKLSVLEDGEQTHQVVDVAFPYFGGQHNPHFPTNNQKGDVTVAKVPAVQLRLGKAGEERYAMVATVFDLQVAQYGINRGLGSGAKDFDDNAPYTPAWQESITGVPREQVITVARQFAENADKTHGKSMVIIGAAMNHWYHADMNYRGVINLLMMCGCIGQSGGGWSHYVGQEKLRPQTGWVPLAFATDWIRPSRQQNSTSFFYAHTDQWRYEKLGMGEIVSPTLSAQDRQAYSGSMIDFNVKAERMGWLPSAPQLKTNPLQVVKAAEAAGMDAKDYVVKALKDGTLEMSCEDPDASQNWPRNMFVWRSNLLGSSGKGHEYFCKHLLGTENGVQGKDLGKDDARPTEVKWHKDAPQGKLDLLVTLDFRMSTTCLYSDIVLPTASWYEKNDLNTSDMHPFIHPLSAAVDPVWQARSDWEIYKGFAKAFSDMCVGHLGVEKEVVLTPIMHDTAGEMAQPIDVREWKKGQCDLIPGKTAPQITVVERDYPNTFKRFTALGPLLDKLGNGGKGIGWQTGIEVEQLGQLNGLTQEEGISKGRPRIVSDIDACETILQLAPETNGHVAVKAWEALGKQTGRDHTHLALYREDEKIRYRDIQAQPRKIISSPTWSGIESETVSYNAGYTNVHELIPWRTLTGRQQFYQDHKWMIAFGEGFSTYRPPVNLKTTDALQNKRPNGHKEIVLNFITPHQKWGIHSTYSDNLLMLTLNRGGTVIWLSENDAKVAGIEDNDWIELFNVNGAVAGRAVVSQRVNDGMCLMYHSQEKIINTPGSEITGVRGGIHNSVTRIVTKPTHMIGGYAQLSYGFNYYGTIGTNRDEFVIIRKMVKVDWLDTPADDHLVRAYQSQGENP
>r2
MSHFLDRLRYFTAPRPQFSDGHGAVTDEDRQWENAYRQRWQHDKIVRSTHGVNCTGSCSWKIYVKGGIVTWETQQTDYPRTRPDMPNHEPRGCSRGASYSWYLYSANRLKYPLVRSALVKLWRERRVSLEPVQAWQSIVTDEAARRGYQSRRGLGGFIRSTWDEVNEIVAAANVYTVKQHGPDRVVGFSPIPAMSMVSYAAGSRYLSLIGGVCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSTFIVMWGSNVPQTRTPDAHFMTEVRYKGAKIVSIFPDYAEGAKFGDIWLHPKQGTDAALALAMGHVILKEFHLTGKSDYFVDYCRRFTDMPCLVRLVPHGDAYVPERLVRASDFDDALGQANNAEWKTVMIDAASNEFVVPLGSVGFRWGQKEGEDQGKWNLKSEAATGEPLMPRLSLANAHDDVVAVLFPYFGNIAHPHFHHTTHGSQLSRKIGVRRIATRNGEMLVATVHDLFVANYGLDQGLGGEHIARDYDDDLPYTPAWQEAITGVKRADVISVARQFAENAHKTQGKSMVIIGAGINHWFHMDMSYRAIINMLIMCGCVGKSGGGWSHYVGQEKLRPQTGWTALAFALDWHRPPRHMNATSFFYAHTDQWRYDPMNPTALLSPLADASRFHGAPIDYNVRAERMGWLPSAPQLAVNPLDYGRALNDPAQAAATVVRDLKSGSLRMACEDPDHPDNFPRNLFVWRSNLLGSSGKGHEYFLKHLLGTINGVQGEEVVKSGHPRPEEIAWHDEAPRGKLDLLVTLDFRMSTTCMYSDVVLPTATWYEKDDMNTSDMHPFIHPLSAAVDPAWQSKSDWEIFKGIAKRFSELSEGHLGVERDIVLAPIAHDSPAELAQPFDVQDWKRGECEPVPGKTMPSVLVVERDYPATYAKFTSLGPLMDKLGNGGKGVSWDTKDEVALLGDLNYRVADAGCAKGRPRIDTALDAAEVILSLAPETNGAVAVKAWSAVTAMTGIEHAHLADARADEKIRFRDIPGPAAKIISSPTWSGIESEHVSYNAGYTNVHELIPWRTLSGRQQLYQDHLWMRAFGESLCVYKPPIETGSYEHMAGARSNGNPEIVLNFITPHQKWGIHSTYTDNLLMLTLSRGGPIVWLSEADAQAIGLVDNDWIECYNANGALCARAVVSQRVPRGMVMMYHAQEKIVNTPGSEITGTRGGIHNSVTRVALKPTHMIGGYAQLAYGFNYYGTVGSNRDEFLIVRKMKHIDWLDDTPPLTMSPPVQPLRQGEAS
>r3
MSHFLDRLKFMSKVKSTFSNGHGAVVKEDRQWEDAYRQRWQHDKVVRSTHGVNCTGSCSWKVYVKNGLITWETQQTDYPRTRADLPNHEPRGCPRGASYSWYVYSAQRVKYPMMRGKLAQMWREARKTMSAVEAWEYISQDPERAREYKSRRGQGGFVRATWEEANEMVAAANAYTIKNYGPDRVIGFSPIPAMSMVSYAAGSRYLSLIGGVPLSFYDWYCDLPPASPQIWGEQTDVAESADWYNSTYLMVWGSNVPMTRTPDAHFYTEVRYKGTKTVAVSSDFGEMAKFGDIWLAPKQGTDAALAMAMGHVIFKEFHLDNPSEYFTDYIRRLTDMPMLVRLKEEGGHYLPEYFLRASQLADNLGEDNNPDWKTLMIDELTGDVVAPNGSIGFRWGQAEGKTGKWNLETREGTTDREVKGQLSLLGRHDEVVGVAFPYFGAEHDDQLTRNIPAKRVQLADGSSALVTTVFDLMAGNYGIDRGLGGGNVATSYMDDVPYTPAWQQKHTGVKPEMVIQVAREFAQNADQTQGKSMVIVGAGLNHWYHMDMSYRGIINMLMLCGCIGQSGGGWCHYVGQEKLRPQSGWAPLAFAQDWNRPARQMNGTSFFYAHTSQWRHEKLGVNEILCPTAAGNMEHMSLIDYNAKAERMGWLPSAPQLETNPLDLTRMAAEAGMDPAAYTVQGLKDGSIDMSCNDPDNPKNFPRNLFVWRSNILGSSGKGHEYFLKYLLGTQNAVMSDETQCIQPSEITVRPAAEGKLDLLVVLDFRMSTTCLYGDIVLPTATWYEKDDLNTSDMHPFIHPLSEAVQPLWQSKTDWEIYKGFAKAISEVGKDYLGVQKDLVLTPLMHDSPQELGQPFDPRDWKKGECDPIPGKTMPAMTVVERDYGAIYQKFTSIGPLMEKVGNGGKGMAWKTEREVEQLRKMNKVVADGVAKGQPRLDTAIDAAEMIMTLAPETNGHVAVKAWESLSKITGRDHTHLAIPREHDHITFRDIQAQPRKIISSPIWSGLESEEVSYNAGYTNVHELIPWRTLTGRQQFYQDHQWMRAFGEGMCVYRPAVDLKTTAAVHNHKPNGNKEILLNFLTPHQKWGIHSTYSENLRMLTLSRGGPHIWISEKDAREAGIVDNDWVEVFNVNGTLTARVVVSQRIPQGMTLMYHAQEKIVNVPGAEMSGKRGGIHNSVTRAVTKPTHMIGGYAQLAYGFNYYGTVGCNRDEFIVMRKMKNVDWMDQPLSK
>r6
MSRNDASHTDETAGESDDKRRAVDQSDDEQPKKRGANEERTDGGPAVGDPPGGDNPSRRGFLKGVGLASVLGIGSASASDDALFSMDGLQPVGDPIGEYPYRDWEDLYREQWDWDSVSRSTHSVNCTGSCSWNVYVKNGQVWREEQSGDYPRFDESLPDPNPRGCQKGACYTDYVNAEQRIKHPLKRVGERGEGKWKRITWDEALTEIAEHVVDEVEAGRYDAISGFTPIPAMSPVSFASGSRLINLLGGVSHSFYDWYSDLPPGQPITWGTQTDNAESADWYNADYIIAWGSNINVTRIPDAKYFLESGYNGTKRVGIFTDYSQTAIHTDEWLSPDPGSDTALALGMAQTIVSEGLYDEAHLKEQTDMPLLVRQDTGKFLRASDVPSVNSSADRPEWMLLMLDSNGQLREAPGSLGERDGQKDYSKSIDLDFDPRLDAETTVQTDDGSVQVRSVWAELRDELAQYDPETVTKMTGVGTETYQRVAREFADVERAKIIHGKGVNDWYHNDLGNRAIQLLVTLTGNLGRQGTGVDHYVGQEKIWTFHGWKTLSFPTGKVRGVPTTLWTYYHAGILDNTDADTAAKIRESIDKGWMPVYPEEREDGSRPDPTTMFVWRGNYFNQAKGNVAVEEELWPKLDLVVDINFRMDSTALYSDIVLPTASHYEKHDLSMTDMHTYVHPFTPAVEPLGESKTDWQIFKDLAEKIQEVATERGVEPISDRTFDREIDLQSVYDDYVRDWETETDGALAEDRAAAEYILEHSAESNPAGTDEQITFADTVEQPQRLLEAGDHWTSDIEDGEAYAPWKDFVQDKNPWPTVTGRQQYYIDHDWFLELGEQLPTHKEGPTNTGGDYPMEYNTPHGRWAIHSTWRDSEKMLRLQRGEPIVYINPDDAAERGIEDGDTVEVFNDLGAVEVQAKIYPSSERGTLRHFFSWEKFQYASRNNFNTLVPMYMKPTQLVQYPEDTGEHLYFFPNYWGPTGVNSDVRVDVRKKGGDGG
>r5
MMNNQELNPKTTRRSFIKASGMTALTVSAGINLPLQVKAETIPIKNMQDDKEVLSLCSVNCGSRCVLRLHVKNDEVRWVETDNSGDDEYGNHQIRACLRGRSMRYRMNHPDRLKYPMKRIGKRGEGKFQRISWDEALDTIADNLKRIVKDYGNEAVYNNYASGIVGGNMTRSSPFASLFTRLMNCYGGLLSYYGSYSTAQIARAMPFTYGSNVGNSTSDIVNSKLVVFFGNNPMETRMSGAGITYHLEQARERSNAKLIVIDPRYTDTASGREDEWIPIRPGTDAALVAGMAHVMITENLVDQVFLDKYCVGYDEKTLPASAPANGHYKAYILGQGDDGVEKTPEWAAKITGIPAAKIIRLAREIGTTKPCYIAQGWGLQRQSNGELACRAVAMLAILTGNVGISGGNSGAREGSFYPPIQRLPVLENPVKAKISVFSWTDAIDHGDQMTALKDGVQGKDKLDVPIKFMWNYAGNCITNQHSDINRTHEILSDDKKCEMIVVIENFMTDSAKYADILLPDLMTTEQEDIVPNDYAGNMGYLIFSQPATSAKFERRGIYDICCEIAKRLGQDVYDKFTEGGRTQEQWLQFLYSRMQEKDATLPSYDELKQMGVYKRQDPNGHLVAYQKFREDPEANPLKTPSGKIEIYSERLAEIAATWELKEDEVIHPLPIYHSGFNGWDDPKREKYPFQLVSFHYKSRTHSTYGNIDVLESACPQEMWINPIDAQRLTLTDGETVRVFNEIGETRIPVKITPRIMPGVLGMGQGAWHKANMFGDKVDHNGCVNVLTTLRPSPLAKGNPQHSNLVRIEKL
>r7
MSKIDLYLDNPAFHIVTGACPHDCPDTCTWQVAVDRITGAAVDIWGHPAHPITQGKLCGKVDRYLERTYHKDRLTVPLRRVGPKGSGRFERVSWEEAIADIARRLQAIIEEYGPEAVLPYSYSGTLGFLQGEGMASRFFNRLGASQLARTICAEAGFQGYLYTIGAAEGMLPEDFAHSRLILIWGSNTLTSNLHLWPFIQQARKQGARVLVIDPANTRTAQAGDEWIPIRPGTDAALALAMMQVIIAEERYDADYVARYTLGFKQLAERVRDWTPARSAEITGIPAERIAALAREYATIRPAGIRINYGLQRHYGGGMAVRTIACLPALVGAWRQHGGGIQLSSSGLFRHLDKRGLHRPDLLEKAKAELQKGNAGAVDQTRPFPRVINMNRLGDALSLDPARLARAHYRPRPIDPLPKPEEAGPPVKALIVYNCNPAAVAPDQTAVLAGLRREELFTVVLEHFQTDTADYADYLLPATTQLEHWDIHRAYGHAYLALNRPAIAPVGESLPNSEIFRRLALAMGYDDPCFYESDEEILRAFVAAQTHERFAGLTWERLLNEAFFRLNLPDPYLPFAEGNFPTPSGKCEFFSARMAEDGYDPLPTYTPPRWQDRSGASALSSFDGSLVCISPPAHSFLNSTFANLPRFLQREDRPMLWIHPQDARPRHIEDGTRVRVCNQHGEVMLTARVTDAVVPGTVLAPGVWWPKLSPDGRNINRTTPPDETDMGAGALFYDATVWVEPLPVMANG
>r4
MSESVVVRAACPHDCPDTCAMEIGVRDGRAVSVRGAADMPFTNGALCTKVAHYLERVYSDQRLMHPLRRVGAKGDGRFERIRWDDALDIIAERFRAIAADDPRAILPYSYAGTMGLVQSESLDRRFFNRLGAARLDRTICAAAGAMGWKATVGASIGADPEAVVDARLILIWGGNPVVSNVHGWRYLQEAKRRGAKLICIDPRRSETAAKCHQHVAPLPGTDGALALAMMQVLIAEDLLDHDYIARCTLGFAELAERVRGCTPEWAAGVTGLDAATIRELAQAYGRSAPTLIRLNYGLNRSGGGGMAVRNIACLPALTGAWRHAGGGALLSTSGNFPLDRHALERPDLYRQDPSRPPRTINMTTIGEALLETRDPPIRALYVYNANPVAVAPYSAKVRAGFRREDLFCVVHELFQTDTADYADILLPATSQLEHHDLHTSYGHFYLVANRPAIDAQGEARSNTEVFRQLAARLGFDDTALFETDEAIAAAALRREDGRSLGVGARLAEHGWARLNLPRPFAPFARGGFPTPSGKCEFLSSFLAAQGLDPLPAWHPPYESVVSNPALAARYPLALISPPARNFLNSSFANLPRFTAGEGGPRLDIHRDDAAARGLTDGMRVRIHNDRGAFHAYARVTEAVRRGVVAAPSIWWQKRSGDGENANAVTSDALTDMGGGAVFYDCLVEVAGAPA\n'''
taxonomy = '''r1\td__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Hydrogenophaga;s__
r3\td__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Brachymonas;s__
r2\td__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia;s__
r4\td__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Rhodocyclales;f__Rhodocyclaceae;g__;s__
r5\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Basfia;s__
r7\td__Bacteria;p__Chloroflexi;c__Caldilineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea;s__aerophila
r6\td__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Halobacteriales;f__Halobacteriaceae;g__Halogeometricum;s__\n'''
with tempfile.NamedTemporaryFile(suffix='.fa') as fasta:
fasta.write(reads)
fasta.flush()
with tempfile.NamedTemporaryFile(suffix='.tsv') as tax:
tax.write(taxonomy)
tax.flush()
sequences_file = fasta.name
taxonomy_file = tax.name
expected_list = [7, 2 ,3, 4, 5, 6, 7]
for expected, i in zip( expected_list, range(0,6) ):
with tempdir.TempDir() as package:
Create(prerequisites).main(sequences = sequences_file,
taxonomy = taxonomy_file,
prefix = package,
dereplication_level = i,
force = True,
threads = 5)
base = os.path.basename(package)
gpkg = GraftMPackageVersion2.acquire(package)
seqinfo = open(gpkg.taxtastic_seqinfo_path())\
.readlines()
hmm = gpkg.search_hmm_paths()[0]
nseq = [int(x.strip().split()[1])
for x in open(hmm).readlines()
if x.startswith("NSEQ")][0]
self.assertEqual(nseq, expected)
def test_create_stars(self):
with tempdir.TempDir() as tmp:
gpkg = tmp + ".gpkg"
Create(prerequisites).main(
sequences=os.path.join(
path_to_data, 'create',
'homologs.trimmed.unaligned.with_stars.faa'),
taxonomy=os.path.join(
path_to_data, 'create',
'homologs.tax2tree.rerooted.decorated.tree-consensus-strings'
),
prefix=gpkg)
self.assertTrue(
os.path.exists(
GraftMPackageVersion2.acquire(gpkg).alignment_hmm_path()))
def test_dna_package(self):
with tempdir.TempDir() as tmp:
gpkg = tmp + ".gpkg"
Create(prerequisites).main(
sequences=os.path.join(path_to_data, 'create',
'61_otus.fasta'),
taxtastic_taxonomy=os.path.join(path_to_data, '61_otus.gpkg',
'61_otus.refpkg',
'61_otus_taxonomy.csv'),
taxtastic_seqinfo=os.path.join(path_to_data, '61_otus.gpkg',
'61_otus.refpkg',
'61_otus_seqinfo.csv'),
alignment=os.path.join(path_to_data, '61_otus.gpkg',
'61_otus.refpkg', '61_otus.aln.fa'),
prefix=gpkg,
threads=5)
pkg = GraftMPackageVersion2.acquire(gpkg)
with open(pkg.alignment_hmm_path()) as f:
self.assertEqual('NAME 61_otus.aln\n', f.readlines()[1])
self.assertEqual(pkg.diamond_database_path(), None)
