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save blast file in the working dir
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@Donaim
Donaim committed Jul 21, 2023
1 parent 14f571d commit 2bb83a0
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Showing 8 changed files with 297 additions and 7 deletions.
13 changes: 8 additions & 5 deletions intact/intact.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,16 +169,16 @@ def iterate_blast_rows_from_tsv(file_path):
yield values


def blast_iterate(subtype, input_file):
with tempfile.NamedTemporaryFile() as output_file:
def blast_iterate(subtype, input_file, working_dir):
with open(os.path.join(working_dir, 'blast.tsv'), 'w') as output_file:
db_file = st.alignment_file(subtype)
wrappers.blast(db_file, input_file, output_file.name)
for seq in iterate_blast_rows_from_tsv(output_file.name):
yield seq


def blast_iterate_inf(subtype, input_file):
for seq in blast_iterate(subtype, input_file):
def blast_iterate_inf(subtype, input_file, working_dir):
for seq in blast_iterate(subtype, input_file, working_dir):
yield seq

while True:
Expand Down Expand Up @@ -734,6 +734,7 @@ def with_blast_rows(blast_it, sequence_it):
class OutputWriter:
def __init__(self, working_dir, fmt):
self.fmt = fmt
self.working_dir = working_dir
self.intact_path = os.path.join(working_dir, "intact.fasta")
self.non_intact_path = os.path.join(working_dir, "nonintact.fasta")
self.orf_path = os.path.join(working_dir, f"orfs.{fmt}")
Expand Down Expand Up @@ -777,6 +778,8 @@ def __exit__(self, *args):
log.info('Non-intact sequences written to ' + self.non_intact_path)
log.info('ORFs for all sequences written to ' + self.orf_path)
log.info('Intactness error information written to ' + self.error_path)
if os.path.exists(os.path.join(self.working_dir, 'blast.tsv')):
log.info('Blast output written to ' + os.path.join(self.working_dir, 'blast.tsv'))


def write(self, sequence, is_intact, orfs, errors):
Expand Down Expand Up @@ -847,7 +850,7 @@ def intact( working_dir,

with OutputWriter(working_dir, "csv" if output_csv else "json") as writer:

blast_it = blast_iterate_inf(subtype, input_file) if check_internal_inversion or check_nonhiv or check_scramble else iterate_empty_lists()
blast_it = blast_iterate_inf(subtype, input_file, working_dir) if check_internal_inversion or check_nonhiv or check_scramble else iterate_empty_lists()
for (sequence, blast_rows) in with_blast_rows(blast_it, iterate_sequences(input_file)):
sequence_errors = []

Expand Down
124 changes: 124 additions & 0 deletions tests/expected-results-large-csv/blast.tsv
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124 changes: 124 additions & 0 deletions tests/expected-results-large/blast.tsv
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3 changes: 3 additions & 0 deletions tests/expected-results-single-csv/blast.tsv
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MN692145 9689 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 9689 1 9840 0.0 11812 9863 92.203 9094 23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA153TC12AG13AC29-N-N-N-N-N-N8AG39A-T-TNTNTA63AG9AG6GA36CA27AG3AG11TC27AT7AC32TC25AG51TGGA19AT5TC23GA6GA8AC1AG21AC7CT3-N-N-N-N-N-N-N-N-N30CA1TC5CG11CT42AG28AG62TC41AG107CT65CT41GA8TC17TC17AG3TC10TC17CT14TC8CT48TG1AG20CT19GCAG38GA17AG8CT67GA6GA32GA5TC1TC81AG23AG12CT7GA8AG5CT11GA2-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-N35TC5AT16TC14TC3CT2GA12T-C-C-7GA10AG106AG47TC24TCCT30GT56AG8TC11CT8TC8AG84AGCT15AG65TC17CT41AG11TC20GA11AC74GA2TC114TA127AGTC26TC109AC23AG11TG26TCGC7CT7AGAG14TC5GA3GA64GA6TC91GA48GA56GA4TA37GAGATC1AG11AG65CT65TC18TG4TC2AG33GA1CT11GA9TA44CT19AG66AC34AG11CA14CTTC58TC3AG7TC2AG38AT14CT47GA7GA84GA95AG14CT5CT41AT11TC8TCAG2AG4AG4AG21GA11GA5CA80CT17AG26TC147GA28TC26GA8CT34TC3AG119AG32AC27TCGA64TC40GA24CTAG1CA14GA20TC11AC13GATG3AT10TC8TC5TG41GA9TC24GA2GT6CA15GA1AG2GA45CA10TC1TCCA1GT62GT32CA18AG43CT2TC2-T6GA10AG16AG3TC3CA9AG15AG37CT8GA12TACA30TC5CT8GA57TCCA3AGGA18TC32TC1AC1CATC2TA3AC4TGCT13AT17CA19TC6TA40TC15AC3GT36GA1ANTNCNANGNGNANANGN2CA5AG2-C-T-T-G-T1CG1CGTA1AG-G-G-G-G48GA3GACA2TA38AG46GA66GAAGGT5AT21TC7GA4CGCAAC29TC35GA2GA14CT1CG6TG12GAGAAGCA1GT2GT-N-N-N-N-N-N-N-N-N-N-N-N-A-C-T1GA8AG2AG2TG1AGCGAGGA3GTTG3-A-T-G11AG2GA21TACG1TA6AT1GA2AG6GT3TG13CT16GA2GA9GA4AG3A-G-A-3A-T-G-G-T-A-A-T-T-A-T-T-1TC7GA5TC9TC29AG5AC22TA15GT1AT12GA6GA4AGCAACAG41GA50TC34CT43CAAC14CA13GAGATC10TG2GA1GA1GAGA1TC1AGCT2GC-C-A-G-A-G-A10AGGA6TGAT1GA2GAGT2CG2TA2CT1-N-N-N3GA4AG3AC12TA5AG2AG12CT1GATC7GA2TA1GA3TC1GACGAC8TA2GA6AG1GA-A-A-T13AT5CATG3CT28AG39AT5AC20-T-T-T3GNCNAN1CGATC-2AT1-G2TG2AC2GATAAGCGTG1GCGA3GA1TC5GA4AG1-G-A-C-A-C-A45GA34AT20CA12TC23ANANGNANCNTN2CTGAAGGC1GA3CTAGCACGAT10TC23AG40GA15GA66CT44AG1GC2GA3GA2TC40AG20AG17AG3TC23GA20GA8CG35TA36AC38GA3AG6GA1GTAC3TC18AC9GA1TC18TC2AT1TC6AGCA9GA1TA3AG6CA8AC7GA8GA13AG16GAGA9CT11CT6AT4TC20AG59CT22GA1TC5GA31CA36GACT2CG9AC4TC3AG13TA6AG50ATAG42TC9CT1TG5GA17CGAT72AG11TG5AG3TC2TG9CT1TG3TC2CA4CG18TG6GACT16GT21TG2GA12AC19-N-N-N-N-N-N-N-N-N-N-N-N21GA12TC10TC6GA21TC9AG3AC8AC22AG11-N-N-N118AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT13-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-N10TG31G-21GA1AT22GC20CT-T56GA134 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692145 9689 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 9074 9689 1 634 0.0 752 635 91.811 583 23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA134 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692145 9689 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 616 9181 9840 0.0 720 661 88.654 586 24AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT13-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-N10TG31G-21GA1AT22GC18-T2CT56GA134 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
3 changes: 3 additions & 0 deletions tests/expected-results-single/blast.tsv
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MN692145 9689 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 9689 1 9840 0.0 11812 9863 92.203 9094 23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA153TC12AG13AC29-N-N-N-N-N-N8AG39A-T-TNTNTA63AG9AG6GA36CA27AG3AG11TC27AT7AC32TC25AG51TGGA19AT5TC23GA6GA8AC1AG21AC7CT3-N-N-N-N-N-N-N-N-N30CA1TC5CG11CT42AG28AG62TC41AG107CT65CT41GA8TC17TC17AG3TC10TC17CT14TC8CT48TG1AG20CT19GCAG38GA17AG8CT67GA6GA32GA5TC1TC81AG23AG12CT7GA8AG5CT11GA2-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-N35TC5AT16TC14TC3CT2GA12T-C-C-7GA10AG106AG47TC24TCCT30GT56AG8TC11CT8TC8AG84AGCT15AG65TC17CT41AG11TC20GA11AC74GA2TC114TA127AGTC26TC109AC23AG11TG26TCGC7CT7AGAG14TC5GA3GA64GA6TC91GA48GA56GA4TA37GAGATC1AG11AG65CT65TC18TG4TC2AG33GA1CT11GA9TA44CT19AG66AC34AG11CA14CTTC58TC3AG7TC2AG38AT14CT47GA7GA84GA95AG14CT5CT41AT11TC8TCAG2AG4AG4AG21GA11GA5CA80CT17AG26TC147GA28TC26GA8CT34TC3AG119AG32AC27TCGA64TC40GA24CTAG1CA14GA20TC11AC13GATG3AT10TC8TC5TG41GA9TC24GA2GT6CA15GA1AG2GA45CA10TC1TCCA1GT62GT32CA18AG43CT2TC2-T6GA10AG16AG3TC3CA9AG15AG37CT8GA12TACA30TC5CT8GA57TCCA3AGGA18TC32TC1AC1CATC2TA3AC4TGCT13AT17CA19TC6TA40TC15AC3GT36GA1ANTNCNANGNGNANANGN2CA5AG2-C-T-T-G-T1CG1CGTA1AG-G-G-G-G48GA3GACA2TA38AG46GA66GAAGGT5AT21TC7GA4CGCAAC29TC35GA2GA14CT1CG6TG12GAGAAGCA1GT2GT-N-N-N-N-N-N-N-N-N-N-N-N-A-C-T1GA8AG2AG2TG1AGCGAGGA3GTTG3-A-T-G11AG2GA21TACG1TA6AT1GA2AG6GT3TG13CT16GA2GA9GA4AG3A-G-A-3A-T-G-G-T-A-A-T-T-A-T-T-1TC7GA5TC9TC29AG5AC22TA15GT1AT12GA6GA4AGCAACAG41GA50TC34CT43CAAC14CA13GAGATC10TG2GA1GA1GAGA1TC1AGCT2GC-C-A-G-A-G-A10AGGA6TGAT1GA2GAGT2CG2TA2CT1-N-N-N3GA4AG3AC12TA5AG2AG12CT1GATC7GA2TA1GA3TC1GACGAC8TA2GA6AG1GA-A-A-T13AT5CATG3CT28AG39AT5AC20-T-T-T3GNCNAN1CGATC-2AT1-G2TG2AC2GATAAGCGTG1GCGA3GA1TC5GA4AG1-G-A-C-A-C-A45GA34AT20CA12TC23ANANGNANCNTN2CTGAAGGC1GA3CTAGCACGAT10TC23AG40GA15GA66CT44AG1GC2GA3GA2TC40AG20AG17AG3TC23GA20GA8CG35TA36AC38GA3AG6GA1GTAC3TC18AC9GA1TC18TC2AT1TC6AGCA9GA1TA3AG6CA8AC7GA8GA13AG16GAGA9CT11CT6AT4TC20AG59CT22GA1TC5GA31CA36GACT2CG9AC4TC3AG13TA6AG50ATAG42TC9CT1TG5GA17CGAT72AG11TG5AG3TC2TG9CT1TG3TC2CA4CG18TG6GACT16GT21TG2GA12AC19-N-N-N-N-N-N-N-N-N-N-N-N21GA12TC10TC6GA21TC9AG3AC8AC22AG11-N-N-N118AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT13-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-N10TG31G-21GA1AT22GC20CT-T56GA134 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692145 9689 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 9074 9689 1 634 0.0 752 635 91.811 583 23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA134 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692145 9689 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 616 9181 9840 0.0 720 661 88.654 586 24AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT13-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-N10TG31G-21GA1AT22GC18-T2CT56GA134 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
17 changes: 17 additions & 0 deletions tests/expected-results-small-csv/blast.tsv
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KX505501.1 1997 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 1746 455 2249 0.0 2116 1796 91.537 1644 255-A-N-N-N-N-N-N6GA1AG35GA3ANTNTA68GA3AC17CT10AG5TG4GA7CT25AG33CT46GAAT1TC3AC21AGGA2TA2GA9AG5GATC12AG7AGAG5TGGA1GA17CT14AG16TG2GA4CA11AG1CA7-A-C-A5ACGATC4GA4-N-N-N-N-N-N-N-N-N8CA9GA10T-3-C15TC8CA1GA5AT27AG4GA2AG20AG44CT17TC47TC27TG99CG36GA23AG2GA30GATC36TC32CT11AG5CTAT7AG35GA20AG17AG8AG2CT26CT8GA9AG7AG30AG1GA14ACGA12AG24AG1CT9CT25TC24AG25GA9TC11CT24GT7AG12CT13GA8CT7AG6-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-N20CA14TC5AT7CA5 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
KX505501.1 1997 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1747 1997 301 550 6.53e-87 312 251 93.625 235 2AC15AT4GA10CTTC6TGTCCT30T-AG1GA42GC21CT9GTAG46GA49 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
KX505501.1 1997 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1783 1997 9543 9756 9.85e-76 275 215 94.884 204 6TGTCCT30T-AG1GA42GC21CT9GTAG46GA49 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
KX505501.1 1997 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 180 9661 9840 5.28e-71 259 180 100.000 180 180 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN691959 9493 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 9493 151 9753 0.0 12961 9606 97.345 9351 13TG3GT7GA5TC56TG51GA129GC68TC84AG135-N-N-N-N-N-N24AC23-N-N336GC71CT3-N-N-N-N-N-N-N-N-NAG41GA79AG256YCWAYC2WA103AG146WA2AG38GA142TC72GT83-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-N58TC52AG298TC8AG101AG125AG539AG65GA7GA4TC55GA2AG131GA13CT66TC25GA9AG38AG38CT11TC53TC50GA11CT1AG12GA6CA8AG263AG349AT21AG12AG313GA254ACAC26TC108GA105TC119AG229-T41AG5AG81CA45GA54CG3CA3AGGA18TC32TC11AC2-T-A-G49AG41GA67-N-N-N-N-N-N-N-N-N2GA1GA51AG114GA215GAGA5CA1ANCNTNANANTNANCNCNANANTN1GCT-A-G-22GAAG6GA54AGAG24CT18GA30CA231TG16CT9AG33CAAC48TA51-N-N-N48GACA172-N-N-N53AC21TA17GA34CT57-N-N-N-N-N-N4AG8GA207GC122AG68CT81AC3TC290AC4GA85AG143AG14GA38TC52AG125-N-N-N-N-N-N-N-N-N-N-N-N21GA110-N-N-N175GA25AG11TC47GA58AG11TG93-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-N88GC68TC57 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN691959 9493 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 8947 9493 1 547 0.0 752 547 97.989 536 23AC57GA37TC43TG3GT7GA5TC56TG51GA129GC68TC57 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN691959 9493 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 484 9331 9840 0.0 636 510 93.725 478 17GA58AG11TG93-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-N88GC68TC84AG59 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692074 4178 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 4082 1 4129 0.0 5408 4129 95.931 3961 14TCGAGC5GAACAG56GA21GA4CT5TA23TA18TG9GT7GA5TCGACA11AC16AG1AG11GA5GT10AG10AGTA5AG56AT6TC7TA7ATTG77GC79GA48TC103TC12AG43-N-N-N-N-N-N48-N-N57TC1CG12CTACAG44GA154AG27AG7GA25GC3GA31GA27AC3AG2GACT3-N-N-N-N-N-N-N-N-N122AG138TG4CT41GA92CT18AC22GA8TC59TC107GA17CG6TC31GA17AG14GT46AG20AG2GA2AT35TC29GA88CT22CT14-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-N35TC5AT16GC41GA10AG33GA68AG195TC8AG101AG181GA33GT27AG4AC2TC5AG20CT4GT96TC29AC29AG14TC22TC12AG20AG6TC34CT110AG65GA21AG2GA11AG13GA17GA2AG26AG53TC61AG105AG11AG12GA52CT128CT21TA31AG12CT86 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692074 4178 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 634 9181 9840 0.0 773 660 91.061 601 14TCGAGC5GA1AG56GA21GA3AGCT5TA23TA18TG5GT3GA14GACA11AC16AG1AG17GT10AG10AGTA5AG28AG27AT6TC6-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-N1TA7ATTG77GC79GA48TC84 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692074 4178 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 4087 4178 403 494 5.54e-32 131 92 98.913 91 18GC73 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692074 4178 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 4087 4178 9609 9700 5.54e-32 131 92 98.913 91 18GC73 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692145 9689 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 9689 1 9840 0.0 11812 9863 92.203 9094 23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA153TC12AG13AC29-N-N-N-N-N-N8AG39A-T-TNTNTA63AG9AG6GA36CA27AG3AG11TC27AT7AC32TC25AG51TGGA19AT5TC23GA6GA8AC1AG21AC7CT3-N-N-N-N-N-N-N-N-N30CA1TC5CG11CT42AG28AG62TC41AG107CT65CT41GA8TC17TC17AG3TC10TC17CT14TC8CT48TG1AG20CT19GCAG38GA17AG8CT67GA6GA32GA5TC1TC81AG23AG12CT7GA8AG5CT11GA2-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-N35TC5AT16TC14TC3CT2GA12T-C-C-7GA10AG106AG47TC24TCCT30GT56AG8TC11CT8TC8AG84AGCT15AG65TC17CT41AG11TC20GA11AC74GA2TC114TA127AGTC26TC109AC23AG11TG26TCGC7CT7AGAG14TC5GA3GA64GA6TC91GA48GA56GA4TA37GAGATC1AG11AG65CT65TC18TG4TC2AG33GA1CT11GA9TA44CT19AG66AC34AG11CA14CTTC58TC3AG7TC2AG38AT14CT47GA7GA84GA95AG14CT5CT41AT11TC8TCAG2AG4AG4AG21GA11GA5CA80CT17AG26TC147GA28TC26GA8CT34TC3AG119AG32AC27TCGA64TC40GA24CTAG1CA14GA20TC11AC13GATG3AT10TC8TC5TG41GA9TC24GA2GT6CA15GA1AG2GA45CA10TC1TCCA1GT62GT32CA18AG43CT2TC2-T6GA10AG16AG3TC3CA9AG15AG37CT8GA12TACA30TC5CT8GA57TCCA3AGGA18TC32TC1AC1CATC2TA3AC4TGCT13AT17CA19TC6TA40TC15AC3GT36GA1ANTNCNANGNGNANANGN2CA5AG2-C-T-T-G-T1CG1CGTA1AG-G-G-G-G48GA3GACA2TA38AG46GA66GAAGGT5AT21TC7GA4CGCAAC29TC35GA2GA14CT1CG6TG12GAGAAGCA1GT2GT-N-N-N-N-N-N-N-N-N-N-N-N-A-C-T1GA8AG2AG2TG1AGCGAGGA3GTTG3-A-T-G11AG2GA21TACG1TA6AT1GA2AG6GT3TG13CT16GA2GA9GA4AG3A-G-A-3A-T-G-G-T-A-A-T-T-A-T-T-1TC7GA5TC9TC29AG5AC22TA15GT1AT12GA6GA4AGCAACAG41GA50TC34CT43CAAC14CA13GAGATC10TG2GA1GA1GAGA1TC1AGCT2GC-C-A-G-A-G-A10AGGA6TGAT1GA2GAGT2CG2TA2CT1-N-N-N3GA4AG3AC12TA5AG2AG12CT1GATC7GA2TA1GA3TC1GACGAC8TA2GA6AG1GA-A-A-T13AT5CATG3CT28AG39AT5AC20-T-T-T3GNCNAN1CGATC-2AT1-G2TG2AC2GATAAGCGTG1GCGA3GA1TC5GA4AG1-G-A-C-A-C-A45GA34AT20CA12TC23ANANGNANCNTN2CTGAAGGC1GA3CTAGCACGAT10TC23AG40GA15GA66CT44AG1GC2GA3GA2TC40AG20AG17AG3TC23GA20GA8CG35TA36AC38GA3AG6GA1GTAC3TC18AC9GA1TC18TC2AT1TC6AGCA9GA1TA3AG6CA8AC7GA8GA13AG16GAGA9CT11CT6AT4TC20AG59CT22GA1TC5GA31CA36GACT2CG9AC4TC3AG13TA6AG50ATAG42TC9CT1TG5GA17CGAT72AG11TG5AG3TC2TG9CT1TG3TC2CA4CG18TG6GACT16GT21TG2GA12AC19-N-N-N-N-N-N-N-N-N-N-N-N21GA12TC10TC6GA21TC9AG3AC8AC22AG11-N-N-N118AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT13-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-N10TG31G-21GA1AT22GC20CT-T56GA134 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692145 9689 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 9074 9689 1 634 0.0 752 635 91.811 583 23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA134 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN692145 9689 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 1 616 9181 9840 0.0 720 661 88.654 586 24AG12TC8AG34GA56TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT13-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-N10TG31G-21GA1AT22GC18-T2CT56GA134 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN090335 9069 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 666 9069 1340 9794 0.0 9541 8485 89.582 7601 18GA5TC17TG5CT8TC18GATC31TG1AG108CA25GA20TC6CT38TC9AGGA5GA45TC17AT7AG35GA5AG2TC11AG17AG8AG38GA2GA14AG31CT4GAGA1AT4CT1AC4CA35CACT6AG28TC5AG44GA18GA5CT29AG11TCCT19CT4CT7CA4ANGNANANANTNTNCNCNTNCNANGNANGNCNANGNANCNCNANGNANGNCNCNANANCN2CACG3CA7TA19TC5AT2-A-G-A11TC14AC1AG2GA8GA5T-C-C-4CT13AG20AC38TC34GA2CA2AGGAAG11AG51AG5AT3GA3CT9TCAT1CT5CT17GA51CA11CT13CT11AG32CT8GA17AG41AG59GA20TCGA1CT53AC9AG10TA11TC6CT19CA45AG13AG59TC14AG44GA3CT1GA14GAACCA69AG12GA7AG5GA9AT11TC19GA2CT11CT17GT15AG25AG11GA2AC2TC32AG5AG20TCGC13GA1AG12GA8GA12TC11GA43GA14TA2GA10CTAG12GT4GA15CA13AGGC4TC2GA47GA13CT12TC14GA27TA10TC16GA14GA1TC1AG11AG26TG20CT17CT2CT35AG12AG37TC5TG1AC5CT22GA16GA9AC3AC18AG5AG8CA3CT7CT14GACT28GA11GA21AC21GA12AG26CT11GA5CA26GA9CT46AT2AG8AT2CA27AG22AG6AG55TC8GA20TA8GA22AG4AG49GT11GA8AG11CT3AC8CT34AT9CA11AG2AGAC3AG2GT1AG39TA17GA29TA110AG41AC5GA34CA31GA28TC38CT35AG91TC11AG5AGAG6CT1AGAGAGAG4GTCT9CT2TC2CT4CG1AC28TC16AC42GA17CT23AG4GA27CATC10TA9GC2CT4TC5TC11AC14TG3AT10TC1GT67AG5GT13GA26AT1AC53AG6TC28AG10GAAT17CT5AGCACTAT5AC2AT1AG1CT4AG3TC29AG35AC10TC2-T17AGCA15AG2GATC2TGGA2AG2AG26AC38GAGA3CG46GT5TC3CAAC43AC8TG3CA3AGGA18TC1CT5CT14AG9TC4TC2TA2GCACGA3TG26GACT22AT8GAGT39TC1AGAGAT5AG5AC3GT30CT5GA1ANTNCNANGNGNANANGN2TA1GA11-G-G-A-G-A-T-G-G-G6AG9GC33GA1GA5TA37GAAG2TA4ACTC11CT32AG44TC8TA7AT4AGAT21TC12AG7GA2CA22AG29CT6GA16CG6TG11AG1GAAG6-N-N-NANCNTNGNTNANGNGNAN1AC1CA1AT2AC3CATGCT1CG1-A-G-C-G-G2AG1CA1AG2A-C-3AGCG2GAGA1AG4AG2GA1CA20CG4GAAGGC7AG3AG4GAAG6CT5CT17GA1CA2GA10GAGT4AC3AC2TC4CAAG4TC2AG3CT2TC33AT7AG21AG1TC2AG11AG8GA5GTGA2GA3TC23ACGA35AG8GA11AG11TC2CT9AG5AG5CA9ATAC8AG7GC5ACTC14AG2TC1GC4AG3TA39-A-A-T-C-C-G3-C-C-AAG2TA1TG1GC11AT2TGAT1GA3CT3GACA1GA3ANTNAN3GA4AG20CT3-A3A-2GA1TA6GA9GACAAC1AG4TC1GAAGAC8GA3AC10ATGA19TG5AC12ACTCGA7AT42CTAT6GA19-T-T-T-A-A-T-N-N-N-A-G-T-A-C-T-T-G-G3-AGC1TG2TG2-T-C2CA2GA2TCATAG1CA4CG1AG1AC1ACTA5AC5GA25GT7GA28TC8GAACTA6GA2CT17AG2AGAC20ANCNANANANTN5TC1CAACGA1GT3AT1GC4CT15GA3AG6AG30CT17GA27CA32AG1AG3G-C-G-TA8AT7CT38GC3CA16AG29AG12CT29AC28AG15GA5TG17CA56AG14AG10CT9TCATCG2TAACCACG2CT3GA2AC3TC10CG17CA1AC9GA1GCATAT4TC2ATAC4CA4GA10TA3AG2GA12AC1GA8AG3CT5CA9AG17GATC8AT18AT25AG10AG4AG11TC31CT11AG2GT7TA21AC46GA7GAGTATAC9CATC4TC3AGCG4CT11CT31AG24GACATC5CT4CG2GC9AG12GAAGTC6GA2CT7GA6GA10TG37AG3TC3TC2CA14AG17GA4GT4AG2AGTC1GT1CT6TA3TG15GA11AC2AG6GACT5AT4AG21GA2TA2AG2GACT28G-A-A-3A-T-T-G-A-T-C-C-A-A-G-G-C-C-T-G-C-T-GNCNANANGNGNANGNGNGNANAN1AG17CA1GA4AG18TC8TC26TG2AG4TC41-G-N-NAN2AG2CT10GC33AG6TG1GA48TCGAGC5GA11AT9TC5GA1TC14AC13GA3AG14AG13TA23TA18TG5CTCA1AGGA4GAAG8GA12AC1TA5CT8AG19AT3TC1AG3GA11AGTA5AG10AC4GA2GA8TCAGGTAG8AG1ATAG13AT3AGGA8-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-N2CTTC5ATTG37TC16CT22GC21CT24GA120 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
MN090335 9069 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 46 669 1343 700 0.0 762 644 91.770 591 33TC20TC68TG1GT16AT7AG3GATC-N-N-N-N-N-N-N-N-N3GACTCTTG4TG15CT11CT31CT9CA19CTAC6TC7TC14GT63TC3AG3CT3TC8CT43TC30CT37CT7TG18CT53AT-N-N-T-T-T45-N-N-N-N-N-N11 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 minus
MN090335 9069 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 0 9840 8482 9069 1 588 0.0 673 588 89.966 529 14TCGAGC5GAAC10AT9TC5GA1TC14AC13GA3AG14AG6GA6TA23TA18TG5CGCA1AGGT4GAAG1GA5TCGA12AC1TA5CT8AG13GA5AT3TC1AG3GA11AGTA5AG10AC4GA2GA8TC1GTAG8AG1ATAG13AT3AGGA10CTTC5ATTG37TC16CT22GC21CT24GA120 Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 plus
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