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regenerate blast database
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@Donaim
Donaim committed Sep 16, 2023
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Showing 39 changed files with 792 additions and 2,666 deletions.
245 changes: 116 additions & 129 deletions tests/expected-results-large-csv/blast.csv
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97 changes: 46 additions & 51 deletions tests/expected-results-large-csv/errors.csv
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653 changes: 0 additions & 653 deletions tests/expected-results-large-csv/nonintact.fasta
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258 changes: 107 additions & 151 deletions tests/expected-results-large-csv/orfs.csv
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245 changes: 116 additions & 129 deletions tests/expected-results-large/blast.csv
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271 changes: 119 additions & 152 deletions tests/expected-results-large/errors.json
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653 changes: 0 additions & 653 deletions tests/expected-results-large/nonintact.fasta
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842 changes: 197 additions & 645 deletions tests/expected-results-large/orfs.json
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9 changes: 3 additions & 6 deletions tests/expected-results-single-csv/blast.csv
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Original file line number Diff line number Diff line change
@@ -1,7 +1,4 @@
qseqid,sseqid,sgi,qlen,slen,length,qstart,qend,sstart,send,evalue,bitscore,pident,nident,sstrand,btop
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,7214,1,6614,5,7215,0.0,7463,87.316,6299,plus,18-N-N-N5ACAG12TC8AG29-N5GA12-N-N13-A-NGN30TA7-N13-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G-N-N-N3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8-T1GN1GA5AT9GA34GA36-N4AT1-N-N19-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3TG9-N10-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N12-N-NGN21GA1AT6-N7-N9GC18-T2CT56GA3-N21-N9-N18-N19-N-N-T1TN6-N12-N18-N-N-N7-N6-N14-N-N14-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N4TC4-N8AG4-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N9-N-N-NAC12-N-N17-N-N-N-N-N-N8AG15-N-N-N-N6-N-N3-N-N-N-N-N15-N-N-N-NANTNTNTNTA11-N-N-N12-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N40AG9AG6GA36CA27AG3AG11TC27AT7AC32TC25AG51TGGA19AT5TC18-N-N-N5GA6GA8AC1AG21AC7CT3-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N30CA1TC5CG11CT42AG20-N-N-N8AG62TC41AG107CT36-N-N-N-N-N-N-N-N-N29CT41GA8TC17TC17AG3TC10TC17CT14TC8CT39-N-N-N9TG1AG20CT19GCAG38GA17AG8CT18-N-N-N-N-N-N-N-N-N15-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N34GA6GA3-N-N-N29GA5TC1TC79-N-N-N-N-N-N-N-N-N2AG17-N6AG12CT4-N-N-N-N-N-N-N-N-N-N-N-N3GA8AG5CT11GA2-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N18-N-N-N-N-N-N-N-N-N17TC5-T-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-NAN16TC1-N-N-N-N-N-N13TC3CT2GA9-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3T-C-C-7GA10AG106AG47TC24TCCT30GT56AG8TC11CT8TC8AG84AGCT15AG65TC17CT41AG11TC20GA11AC74GA2TC114TA127AGTC26TC109AC23AG11TG26TCGC7CT7AGAG14TC5GA3GA64GA6TC91GA48GA56GA4TA24-N-N-N13GAGATC1AG11AG65CT65TC18TG4TC2AG33GA1CT11GA9TA44CT19AG66AC34AG11CA14CTTC58TC3AG7TC2AG36-N-N-N2AT14CT47GA6-N-N-N1GA28-N-N-N56GA95AG14CT5CT41AT11TC8TCAG2AG4AG4AG21GA11GA5CA80CT17AG26TC102-N-N-N45GA28TC26GA8CT34TC3AG63-N-N56AG32AC27TCGA14-N-N-N-N-N-N50TC40GA24CTAG1CA14GA20TC11AC13GATG3AT10TC8TC5TG24-N-N-N17GA9TC23-N-N-N-N-N-N-N-N-N-N-N-N1GA2GT6CA15GA1AG2GA45CA10TC1TCCA1GT4-N58GT3-N-N-N29CA18AG5-N-N-N38CT2TC2-T-N-N6GA10AG16AG3TC1-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N2CA9AG15AG4-N-N33CT8GA12TACA30TC5CT8GA45-N-N-N-N-N-N12TCCA3AGGA18TC31-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N1TC1AC1CATC2TA3AC1-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3TGCT13AT17CA19TC6TA29-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N11TC15AC3GT22-N-N14GA1ANTNCNANGNGNANANGN2CA5AG2-C-T-T-G-T1CG1CGTA1AG-G-G-G-G27-N-N-N-N-N-N21GA3GACA2TA-N-N-N-N-N-N38AG46GA66GAAGGT5AT21TC7GA4CGCAAC29TC35GA2GA14CT1CG6TG12
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,3136,6626,9387,7308,10443,0.0,2544,79.688,2499,plus,8AG2AG2TG1AGCGAGGA3GTTG3-A-T-G11AG2GA21TACG1TA6AT1GA2AG6GT3TG13CT16GA2GA9GA4AG3ACGT2-C-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-NTNANANTNGNGNTNANANTNTNANTNTNCNTN7GA5TC9TC27-N-N-N2AG5AC22TA15GT1AT12GA6GA4AGCAACAG39-N-N-N2GA50TC18-N-N-N16CT43CAAC14CA13GAGATC10-G-A-ATA4-A-T-CGC1GTGA1TC2CG1TGGA10AGGA6TGAT1GA2-A-T-A-N-N-N-N-N-N-N-N-N-N-N-N3GACA4ANCNAN3GA4-G-N-N-N-N-N-N-N-N-N-N-NAN3AC12TA5AG2AG12CT1GATC7GA2TA1GA3TC1GACGAC8TA2GA6AG1GA3-A-A-T-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N10AT5CATG3CT28AG39AT5AC20-T-T-T3-N-N-N-N-N-N-N-N-N-N-N-N-N-NGNCNANANCAAGCT2AT1-G2TG2AC2GATAAGCGTG1GCGA3GA1TC5GA4AG1-G-A-C-A-C-A33-N-N-N12GA34AT12-N-N-N8CA12TC23-N-N-N-N-N-N-N-N-N-N-N-NANANGNANCNTNANANCNGA1GT7-ACTCG1-G-T10TC23AG40GA15GA24-N-N-N9-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N21-N-N-N-N-N-N9-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3CT44AG1GC2GA3GA2TC17-N-N-N-N-N-N-N-N-N23AG20AG17AG3TC23GA20GA8CG35TA36AC25-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N13GA3AG6GA1GTAC3TC18AC9GA1TC18TC2AT1TC6AGCA9GA1TA3AG6CA8AC7GA8GA13AG16GAGA9CT11CT6AT4TC20AG59CT22GA1TC5GA2-N-N-N-N-N-N9-N-N-N20CA36GACT2CG9AC4TC3AG13TA6AG50ATAG29-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N13TC9CT1TG5GA17CGAT72AG11TG5AG3TC2TG9CT1TG3TC2CA4CG18TG6GACT1-N-N-N-N-N-N-N-N-N-N-N-N9-N-N6GT21TG2GN-N-N-A12AC19-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N21GA12TC10TC6GA21TC9AG3AC8AC22AG11-N-N-N-N-N-N-N-N-N-N-N-N118AG4-N-N-N8TC8AG34GA40-N-N-N-N-N-N16TA21CAAGCA1-A-A2CT3-A3-G-C-C-N-N-N3-A-A-A-G2CG3-A-C-A-C-C-A-G-C-N-N-N3CT1GA7CTAG8GT8AT9GA34GA12AG27AT1-N-N-N-N-N-N-N-N-N12
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,734,9074,9689,5,738,9.18e-154,542,79.428,583,plus,18-N-N-N5ACAG12TC8AG29-N5GA12-N-N13-A-NGN30TA7-N13-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G-N-N-N3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8-T1GN1GA5AT9GA34GA36-N4AT1-N-N19-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3TG9-N10-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N12-N-NGN21GA1AT6-N7-N9GC18-T2CT56GA3-N21-N9-N18-N19-N-N2-N6-N12-N18-N-N-N7-N6-N13
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,356,1,314,10088,10443,4.12e-84,311,82.584,294,plus,24AG4-N-N-N8TC8AG34GA40-N-N-N-N-N-N16TA21CAAGCA1-A-A2CT3-A3-G-C-C-N-N-N3-A-A-A-G2CG3-A-C-A-C-C-A-G-C-N-N-N3CT1GA7CTAG8GT8AT9GA34GA12AG27AT1-N-N-N-N-N-N-N-N-N12
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,286,364,616,10644,10929,2.47e-64,245,86.364,247,plus,6-N9-A-NGCCTAN6-N6-N9-N-N-N1GC10-N8-T2CT2-N10-N21-N7-N-N14-N-N-N-N-N2GA9-N10-N7-N6-N13-N27-N-N-N-N-N17-N-N-N45
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,286,9437,9689,10644,10929,2.47e-64,245,86.364,247,plus,6-N9-A-NGCCTAN6-N6-N9-N-N-N1GC10-N8-T2CT2-N10-N21-N7-N-N14-N-N-N-N-N2GA9-N10-N7-N6-N13-N27-N-N-N-N-N17-N-N-N45
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,9719,9753,1,9689,1,9719,0.0,11990,93.264,9096,plus,23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA153TC12AG13AC37AG40T-T-T-T-63AG9AG6GA36CA27AG3AG11TC27AT7AC32TC25AG51TGGA19AT5TC23GA6GA8AC1AG21AC7CT33CA1TC5CG11CT42AG28AG62TC41AG107CT65CT41GA8TC17TC17AG3TC10TC17CT14TC8CT48TG1AG20CT19GCAG38GA17AG8CT67GA6GA32GA5TC1TC81AG23AG12CT7GA8AG5CT11GA37TC5AT16TC14TC3CT2GA12T-C-C-7GA10AG106AG47TC24TCCT30GT56AG8TC11CT8TC8AG84AGCT15AG65TC17CT41AG11TC20GA11AC74GA2TC114TA127AGTC26TC109AC23AG11TG26TCGC7CT7AGAG14TC5GA3GA64GA6TC91GA48GA56GA4TA37GAGATC1AG11AG65CT65TC18TG4TC2AG33GA1CT11GA9TA44CT19AG66AC34AG11CA14CTTC58TC3AG7TC2AG38AT14CT47GA7GA84GA95AG14CT5CT41AT11TC8TCAG2AG4AG4AG21GA11GA5CA80CT17AG26TC147GA28TC26GA8CT34TC3AG119AG32AC27TCGA64TC40GA24CTAG1CA14GA20TC11AC13GATG3AT10TC8TC5TG41GA9TC24GA2GT6CA15GA1AG2GA45CA10TC1TCCA1GT62GT32CA18AG43CT2TC2-T6GA10AG16AG3TC3CA9AG15AG37CT8GA12TACA30TC5CT8GA57TCCA3AGGA18TC32TC1AC1CATC2TA3AC4TGCT13AT17CA19TC6TA40TC15AC3GT36GA2TACAATGAGTAC2AC3A-1CGATAGCG2CAATCGTGTGAG-G48GA3GACA2TA38AG46GA66GAAGGT5AT21TC7GA4CGCAAC29TC35GA2GA14CT1CG6TG12GAGAAGCA1GT2GT1GC-T-A-A8AG2AG2TG1AGCGAGGA3GTTG3-A-T-G11AG2GA21TACG1TA6AT1GA2AG6GT3TG13CT16GA2GA9GA4AG3A-G-A-3A-T-G-G-T-A-A-T-T-A-T-T-1TC7GA5TC9TC29AG5AC22TA15GT1AT12GA6GA4AGCAACAG41GA50TC34CT43CAAC14CA13GAGATC10TG2GA1GA1GAGA1TC1AGCT2GC-C-A-G-A-G-A10AGGA6TGAT1GA2GAGT2CG2TA2CT4GA4AG3AC12TA5AG2AG12CT1GATC7GA2TA1GA3TC1GACGAC8TA2GA6AG1GA-A-A-T13AT5CATG3CT28AG39AT5AC20ATAT1G-C-2CT1CG-T2AT1-G2TG2AC2GATAAGCGTG1GCGA3GA1TC5GA4AG1-G-A-C-A-C-A45GA34AT20CA12TC25GT1CGTC3GA1-T3CTA-A-C-A-C-C-A-10TC23AG40GA15GA66CT44AG1GC2GA3GA2TC40AG20AG17AG3TC23GA20GA8CG35TA36AC38GA3AG6GA1GTAC3TC18AC9GA1TC18TC2AT1TC6AGCA9GA1TA3AG6CA8AC7GA8GA13AG16GAGA9CT11CT6AT4TC20AG59CT22GA1TC5GA31CA36GACT2CG9AC4TC3AG13TA6AG50ATAG42TC9CT1TG5GA17CGAT72AG11TG5AG3TC2TG9CT1TG3TC2CA4CG18TG6GACT16GT21TG2GA12AC40GA12TC10TC6GA21TC9AG3AC8AC22AG129AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT23TG31G-21GA1AT22GC20CT-T56GA134
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,9719,635,1,616,9086,9719,0.0,760,92.283,586,plus,24AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT23TG31G-21GA1AT22GC18-T2CT56GA134
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,9719,635,9074,9689,1,634,0.0,752,91.811,583,plus,23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA134
1 change: 0 additions & 1 deletion tests/expected-results-single-csv/errors.csv
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@@ -1,4 +1,3 @@
sequence_name,error,message
MN692145,FrameshiftInOrf,Smaller ORF vpr at 5558-5850 contains out of frame indels that impact 79 positions.
MN692145,InsertionInOrf,"Smaller ORF nef at 8796-9417 can have maximum insertions 90, got 231"
MN692145,Scramble,Sequence is plus-scrambled.
9 changes: 3 additions & 6 deletions tests/expected-results-single/blast.csv
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@@ -1,7 +1,4 @@
qseqid,sseqid,sgi,qlen,slen,length,qstart,qend,sstart,send,evalue,bitscore,pident,nident,sstrand,btop
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,7214,1,6614,5,7215,0.0,7463,87.316,6299,plus,18-N-N-N5ACAG12TC8AG29-N5GA12-N-N13-A-NGN30TA7-N13-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G-N-N-N3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8-T1GN1GA5AT9GA34GA36-N4AT1-N-N19-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3TG9-N10-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N12-N-NGN21GA1AT6-N7-N9GC18-T2CT56GA3-N21-N9-N18-N19-N-N-T1TN6-N12-N18-N-N-N7-N6-N14-N-N14-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N4TC4-N8AG4-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N9-N-N-NAC12-N-N17-N-N-N-N-N-N8AG15-N-N-N-N6-N-N3-N-N-N-N-N15-N-N-N-NANTNTNTNTA11-N-N-N12-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N40AG9AG6GA36CA27AG3AG11TC27AT7AC32TC25AG51TGGA19AT5TC18-N-N-N5GA6GA8AC1AG21AC7CT3-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N30CA1TC5CG11CT42AG20-N-N-N8AG62TC41AG107CT36-N-N-N-N-N-N-N-N-N29CT41GA8TC17TC17AG3TC10TC17CT14TC8CT39-N-N-N9TG1AG20CT19GCAG38GA17AG8CT18-N-N-N-N-N-N-N-N-N15-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N34GA6GA3-N-N-N29GA5TC1TC79-N-N-N-N-N-N-N-N-N2AG17-N6AG12CT4-N-N-N-N-N-N-N-N-N-N-N-N3GA8AG5CT11GA2-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N18-N-N-N-N-N-N-N-N-N17TC5-T-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-NAN16TC1-N-N-N-N-N-N13TC3CT2GA9-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3T-C-C-7GA10AG106AG47TC24TCCT30GT56AG8TC11CT8TC8AG84AGCT15AG65TC17CT41AG11TC20GA11AC74GA2TC114TA127AGTC26TC109AC23AG11TG26TCGC7CT7AGAG14TC5GA3GA64GA6TC91GA48GA56GA4TA24-N-N-N13GAGATC1AG11AG65CT65TC18TG4TC2AG33GA1CT11GA9TA44CT19AG66AC34AG11CA14CTTC58TC3AG7TC2AG36-N-N-N2AT14CT47GA6-N-N-N1GA28-N-N-N56GA95AG14CT5CT41AT11TC8TCAG2AG4AG4AG21GA11GA5CA80CT17AG26TC102-N-N-N45GA28TC26GA8CT34TC3AG63-N-N56AG32AC27TCGA14-N-N-N-N-N-N50TC40GA24CTAG1CA14GA20TC11AC13GATG3AT10TC8TC5TG24-N-N-N17GA9TC23-N-N-N-N-N-N-N-N-N-N-N-N1GA2GT6CA15GA1AG2GA45CA10TC1TCCA1GT4-N58GT3-N-N-N29CA18AG5-N-N-N38CT2TC2-T-N-N6GA10AG16AG3TC1-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N2CA9AG15AG4-N-N33CT8GA12TACA30TC5CT8GA45-N-N-N-N-N-N12TCCA3AGGA18TC31-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N1TC1AC1CATC2TA3AC1-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3TGCT13AT17CA19TC6TA29-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N11TC15AC3GT22-N-N14GA1ANTNCNANGNGNANANGN2CA5AG2-C-T-T-G-T1CG1CGTA1AG-G-G-G-G27-N-N-N-N-N-N21GA3GACA2TA-N-N-N-N-N-N38AG46GA66GAAGGT5AT21TC7GA4CGCAAC29TC35GA2GA14CT1CG6TG12
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,3136,6626,9387,7308,10443,0.0,2544,79.688,2499,plus,8AG2AG2TG1AGCGAGGA3GTTG3-A-T-G11AG2GA21TACG1TA6AT1GA2AG6GT3TG13CT16GA2GA9GA4AG3ACGT2-C-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-NTNANANTNGNGNTNANANTNTNANTNTNCNTN7GA5TC9TC27-N-N-N2AG5AC22TA15GT1AT12GA6GA4AGCAACAG39-N-N-N2GA50TC18-N-N-N16CT43CAAC14CA13GAGATC10-G-A-ATA4-A-T-CGC1GTGA1TC2CG1TGGA10AGGA6TGAT1GA2-A-T-A-N-N-N-N-N-N-N-N-N-N-N-N3GACA4ANCNAN3GA4-G-N-N-N-N-N-N-N-N-N-N-NAN3AC12TA5AG2AG12CT1GATC7GA2TA1GA3TC1GACGAC8TA2GA6AG1GA3-A-A-T-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N10AT5CATG3CT28AG39AT5AC20-T-T-T3-N-N-N-N-N-N-N-N-N-N-N-N-N-NGNCNANANCAAGCT2AT1-G2TG2AC2GATAAGCGTG1GCGA3GA1TC5GA4AG1-G-A-C-A-C-A33-N-N-N12GA34AT12-N-N-N8CA12TC23-N-N-N-N-N-N-N-N-N-N-N-NANANGNANCNTNANANCNGA1GT7-ACTCG1-G-T10TC23AG40GA15GA24-N-N-N9-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N21-N-N-N-N-N-N9-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3CT44AG1GC2GA3GA2TC17-N-N-N-N-N-N-N-N-N23AG20AG17AG3TC23GA20GA8CG35TA36AC25-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N13GA3AG6GA1GTAC3TC18AC9GA1TC18TC2AT1TC6AGCA9GA1TA3AG6CA8AC7GA8GA13AG16GAGA9CT11CT6AT4TC20AG59CT22GA1TC5GA2-N-N-N-N-N-N9-N-N-N20CA36GACT2CG9AC4TC3AG13TA6AG50ATAG29-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N13TC9CT1TG5GA17CGAT72AG11TG5AG3TC2TG9CT1TG3TC2CA4CG18TG6GACT1-N-N-N-N-N-N-N-N-N-N-N-N9-N-N6GT21TG2GN-N-N-A12AC19-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N21GA12TC10TC6GA21TC9AG3AC8AC22AG11-N-N-N-N-N-N-N-N-N-N-N-N118AG4-N-N-N8TC8AG34GA40-N-N-N-N-N-N16TA21CAAGCA1-A-A2CT3-A3-G-C-C-N-N-N3-A-A-A-G2CG3-A-C-A-C-C-A-G-C-N-N-N3CT1GA7CTAG8GT8AT9GA34GA12AG27AT1-N-N-N-N-N-N-N-N-N12
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,734,9074,9689,5,738,9.18e-154,542,79.428,583,plus,18-N-N-N5ACAG12TC8AG29-N5GA12-N-N13-A-NGN30TA7-N13-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G-N-N-N3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8-T1GN1GA5AT9GA34GA36-N4AT1-N-N19-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N3TG9-N10-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N-N12-N-NGN21GA1AT6-N7-N9GC18-T2CT56GA3-N21-N9-N18-N19-N-N2-N6-N12-N18-N-N-N7-N6-N13
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,356,1,314,10088,10443,4.12e-84,311,82.584,294,plus,24AG4-N-N-N8TC8AG34GA40-N-N-N-N-N-N16TA21CAAGCA1-A-A2CT3-A3-G-C-C-N-N-N3-A-A-A-G2CG3-A-C-A-C-C-A-G-C-N-N-N3CT1GA7CTAG8GT8AT9GA34GA12AG27AT1-N-N-N-N-N-N-N-N-N12
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,286,364,616,10644,10929,2.47e-64,245,86.364,247,plus,6-N9-A-NGCCTAN6-N6-N9-N-N-N1GC10-N8-T2CT2-N10-N21-N7-N-N14-N-N-N-N-N2GA9-N10-N7-N6-N13-N27-N-N-N-N-N17-N-N-N45
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,11027,286,9437,9689,10644,10929,2.47e-64,245,86.364,247,plus,6-N9-A-NGCCTAN6-N6-N9-N-N-N1GC10-N8-T2CT2-N10-N21-N7-N-N14-N-N-N-N-N2GA9-N10-N7-N6-N13-N27-N-N-N-N-N17-N-N-N45
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,9719,9753,1,9689,1,9719,0.0,11990,93.264,9096,plus,23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA153TC12AG13AC37AG40T-T-T-T-63AG9AG6GA36CA27AG3AG11TC27AT7AC32TC25AG51TGGA19AT5TC23GA6GA8AC1AG21AC7CT33CA1TC5CG11CT42AG28AG62TC41AG107CT65CT41GA8TC17TC17AG3TC10TC17CT14TC8CT48TG1AG20CT19GCAG38GA17AG8CT67GA6GA32GA5TC1TC81AG23AG12CT7GA8AG5CT11GA37TC5AT16TC14TC3CT2GA12T-C-C-7GA10AG106AG47TC24TCCT30GT56AG8TC11CT8TC8AG84AGCT15AG65TC17CT41AG11TC20GA11AC74GA2TC114TA127AGTC26TC109AC23AG11TG26TCGC7CT7AGAG14TC5GA3GA64GA6TC91GA48GA56GA4TA37GAGATC1AG11AG65CT65TC18TG4TC2AG33GA1CT11GA9TA44CT19AG66AC34AG11CA14CTTC58TC3AG7TC2AG38AT14CT47GA7GA84GA95AG14CT5CT41AT11TC8TCAG2AG4AG4AG21GA11GA5CA80CT17AG26TC147GA28TC26GA8CT34TC3AG119AG32AC27TCGA64TC40GA24CTAG1CA14GA20TC11AC13GATG3AT10TC8TC5TG41GA9TC24GA2GT6CA15GA1AG2GA45CA10TC1TCCA1GT62GT32CA18AG43CT2TC2-T6GA10AG16AG3TC3CA9AG15AG37CT8GA12TACA30TC5CT8GA57TCCA3AGGA18TC32TC1AC1CATC2TA3AC4TGCT13AT17CA19TC6TA40TC15AC3GT36GA2TACAATGAGTAC2AC3A-1CGATAGCG2CAATCGTGTGAG-G48GA3GACA2TA38AG46GA66GAAGGT5AT21TC7GA4CGCAAC29TC35GA2GA14CT1CG6TG12GAGAAGCA1GT2GT1GC-T-A-A8AG2AG2TG1AGCGAGGA3GTTG3-A-T-G11AG2GA21TACG1TA6AT1GA2AG6GT3TG13CT16GA2GA9GA4AG3A-G-A-3A-T-G-G-T-A-A-T-T-A-T-T-1TC7GA5TC9TC29AG5AC22TA15GT1AT12GA6GA4AGCAACAG41GA50TC34CT43CAAC14CA13GAGATC10TG2GA1GA1GAGA1TC1AGCT2GC-C-A-G-A-G-A10AGGA6TGAT1GA2GAGT2CG2TA2CT4GA4AG3AC12TA5AG2AG12CT1GATC7GA2TA1GA3TC1GACGAC8TA2GA6AG1GA-A-A-T13AT5CATG3CT28AG39AT5AC20ATAT1G-C-2CT1CG-T2AT1-G2TG2AC2GATAAGCGTG1GCGA3GA1TC5GA4AG1-G-A-C-A-C-A45GA34AT20CA12TC25GT1CGTC3GA1-T3CTA-A-C-A-C-C-A-10TC23AG40GA15GA66CT44AG1GC2GA3GA2TC40AG20AG17AG3TC23GA20GA8CG35TA36AC38GA3AG6GA1GTAC3TC18AC9GA1TC18TC2AT1TC6AGCA9GA1TA3AG6CA8AC7GA8GA13AG16GAGA9CT11CT6AT4TC20AG59CT22GA1TC5GA31CA36GACT2CG9AC4TC3AG13TA6AG50ATAG42TC9CT1TG5GA17CGAT72AG11TG5AG3TC2TG9CT1TG3TC2CA4CG18TG6GACT16GT21TG2GA12AC40GA12TC10TC6GA21TC9AG3AC8AC22AG129AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT23TG31G-21GA1AT22GC20CT-T56GA134
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,9719,635,1,616,9086,9719,0.0,760,92.283,586,plus,24AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT23TG31G-21GA1AT22GC18-T2CT56GA134
MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,9719,635,9074,9689,1,634,0.0,752,91.811,583,plus,23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA134
5 changes: 0 additions & 5 deletions tests/expected-results-single/errors.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,6 @@
"sequence_name": "MN692145",
"error": "InsertionInOrf",
"message": "Smaller ORF nef at 8796-9417 can have maximum insertions 90, got 231"
},
{
"sequence_name": "MN692145",
"error": "Scramble",
"message": "Sequence is plus-scrambled."
}
]
}
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