testthat::test_that("make_nmers", {
# load test data
dt <- structure(list(var_uuid = c("723c3b52-7c95-11e7-a700-12577141430a",
"f02510f8-fc34-4309-978a-b059640bb367", "a39bf028-dfef-41b5-9198-1192a1a74825",
"723c3b52-7c95-11e7-a700-12577141430a", "f02510f8-fc34-4309-978a-b059640bb367",
"a39bf028-dfef-41b5-9198-1192a1a74825"),
pep_type = c("wt", "wt", "wt",
"mutnfs", "mutnfs", "mutnfs"),
pep_base = c("MAEFSQKQRKQSGSEGLGSVVDFLLANARLVLGVGGAAVLGIATLAVKRLIDRATSPPDEDDTKGDSWKELSLLRATSPQKPQPPPAAFSQPLATGSPSPSVPVEPTPIHSPTTPKFSTIAPLCLTFQERLLAFERKHVITPEAHVTLAKQLAGDIALELQAYLRSKFPELPFGALVPGGPLYDGLQAGTAEHVRLLAPLELEPGLWSLVPGVDTVAREPRCWAVRRTQLEFHPRGCSPWDRFLVGGYLSSRVLLELLRKALSASVNWPAIGSLLGCLIWPDVASEELLLKVQHECLEFTLAVLMVVPGASTDDRLLLAWPLEGLASNLWLQDLYPVETARLRALDDQDAGTRRRLLLLLCGICRGHPALVRLGWSHLTQVVLHLGEEEVAWTEEALGERFLQALEFLVGSLEQASLPCHFNPSVNLLGNFREEEIDDIGYVLYSGLQVPESLF",
"MAAASGYTDLREKLKSMTSRDNYKAGSREAAAAAAAAVAAAAAAAAAAEPYPASGTTKRKYQEDSDPERSDYEEHQLQKEEEARKVKSGIRQIRLFSQDECSKIEARIDEVVSRAEKGLYNEHTVDRAPLRNKYFFGEGYTYGAQLQKRGPGQERLYPPGDVDEIPDWVHQLVIQKLVEHRVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFQFKPIRVSEPVLSLPVRRGSVTVLSGYAADEITHCIRPQDIKERRAVIILRKTRLDAPRLETKSLSSSTLPPSYASDRLSGNTRDPALKPKRSHRKADPDAAHRPRILEMDKEENRRSVLLPTHRRRGSFSSENYWRKSYESSEDCPEAASSPTRKVKMRRH",
"MALGGALALALALALAVLGPLSLRVLAGDCKGQRQVLREAPGFVTDGAGNYSVNGNCEWLIEAPSPQHRILLDFLFLDTECTYDYLFVYDGDSPQGPLLASLSGSTRPPPIEASSGKMLLHLFSDANYNLLGFNASFRFSLCPGGCQNHGQCKSPGVCVCEPGWGGPDCGLQECSAYCGSHGTCASTLGPCRCEPGFLGRACDLHLWENQGAGWWHSVSAGDPAFSARIGAAGAFLSPPGLLAVFGGQDLNKALGDLVLYNFSTNTWESWDLTPAPAARHSHVAVAWAGLLVLMGGELANGLLTNDVWAFSPLGGGHWELLAPPASSSSGPPGLAGHAAALVDDIWLYVSGGRTQHDLFSSGLFRFRLDHTSRGYWEQVIPAGGRPPAATGHSMVFHAPSRTLLVHGGHRPSTARFSVRVNSTELFHVERRVWTTLKGRDGLQGPRERAFHTASVLGNYMVVYGGNVHTHYQEEKCYEDGIFFYHLGCHQWVSGAELAPPGTPEGRAAPPSGRYSHVAAVLGGSVLLVAGGYSGRPRGDLMAYKVPPFVFQAPALDYHLDYCSMYTDHSVCSRDPECSWCQGACQAAPPPGTPSGACPAASCLGLGRLLSDCQACLAFSSPTAPPRGPGALGWCVHNESCLPRPEQARCRGEQISGTVGWWGPAPVFVTSLEACVTQSFLPGLHLLTFQQPPNASQPDKVSIVRSTTITLTPSPETDVSLVYRGFIHPLLPGGPGGPGAEDVAVWARAQRLHVLARMARGPDTENMEEVGRWVAQQEKETRRLQRPGSDRLFPLPGRGNKYAVEIRGQLNGSAGPGHSELTLLWDRTGVPGGSEISFFFLEPYRSSACTSYSSCLGCLADQGCGWCLNSATCHLRQGRAHCEDDGSGESLLVLVPALCPLCEEHRDCHACTQDPFCEWHQSTNRKGDAACSRRGRGRGALKNPEECPPLCSQRLTCEDCLANSSQCAWCQSTHTCFLFAAYLARYPHGGCRGWDDSVHSEPRCRSCGGFLTCHECLQSHECGWCGNEDNPTLGRCLQGDFSGPLGGGNCSLWVGEGLGLPVALPARWAYARCPDVDECRLGLARCHPRATCLNTPLSYECHCQRGYQGDGITHCNRTCLEDCGHGVCSGPPDFTCVCDLGWTSDLPPPTPAPGPPAPRCSRDCGCSFHSHCRRRGPGYCDECQDWTWGEHCERCRPGSFGNATGSGGCRPCQCNGHGDPRRGHCDNLTGLCFCQDHTEGAHCQICSPGYYGDPRAGGSCFRECGGRALLTNVSSVALGSRRFGGLLPPGGGAARAGPGLSYCVWVVSATEALQPCVPGTLCPPLTLTFSPDSSTPCTLSYVLAFDGFPRFLDTGVVQSDRSLIAAFCGQRRDRPLTVQALSGLLVLHWEANGSSSWGFNASVGSARCGSGGPGSCPVPQECVPQDGAAGAGLCRCPQGWAGPHCRMALCPENCNAHTGAGICNQSLGVCICAEGFGGPDCATKLDGGQLVWETLMDSRLSADTASRFLHRLGHTMVEGPDATLWMFGGLGLPQGLLGNLYRYSVSERRWTQMLAGAEDGGPGPSPRSFHAAAYVPAGRGAMYLLGGLTAGGVTRDFWVLNLTTLQWRQEKPPQNMELPAVAGHTLTARRGLSLLLVGGYSPENGFNQQLLEYQLATGTWVSGAQSGTPPTGLYGHSAVYHEATDSLYVFGGFRFHVELAAPSPELYSLHCPDRTWSLLAPSQGAKPRPRLFHASALLGDTMVVLGGRSDPDEFSSDVLLYQVNCNTWLLPALTRPAFVGSPMEESVAHAVAAVGSRLYISGGFGGVALGRLLALTLPPDPCRLLPSPEACNQSGACTWCHGACLSGDQAHRLGCGVPPCSPMPRSPEECRRLRTCSECLARHPRTLQPGDGEASIPRCKWCTNCPEGACIGRNGSCTSENDCRINQREVFWAGNCSEAACGAADCEQCTREGKCMWTRQFKRTGETRRILSVQPTYDWTCFSHSLLNVSPMPVESSPPLPCPTPCHLLPNCTSCLASKGADGGWQHCVWSSSLQQCLSPSYLPLRCMAGGCGRLLRGPESCSLGCAQATQCALCLRRPHCGWCAWGGQDGGGHCMEGGLSGPRDGLTCGRPGASWAFLSCPPEDECANGHHDCNETQNCHDQPHGYECSCKTGYTMDNVTGVCRPVCAQGCVNGSCVEPDHCRCHFGFVGRNCSTECRCNRHSECAGVGAQDHCLLCRNHTKGSHCEQCLPLFVGSALGGGTCRPCHAFCRGNSHVCVSRKELEMARKEPEKYSLDPEEIETWVAEGPSEDEAVCVNCQNNSYGDRCESCLHGYFLLDGKCTKCQCNGHADTCNEQDGTGCPCQNNTETGTCQGSSPSDRRDCYKYQCAKCRESFHGSPLGGQQCYRLISVEQECCLDPTSQTNCFHEPKRRALGPGRTVLFGVQPKFTNVDIRLTLDVTFGAVDLYVSTSYDTFVVRVAPDTGVHTVHIQPPPPPPPPPPPADGVPRVAADLGGLGTGSGSGSPVEPRVREVWPRGLITYVTVTEPSAVLVVRSVRDRLVITYPHEHHALKSSRFYLLLLGVGDPNGPGANGSADSQGLLFFRQDQAHIDLFVFFSVFFSCFFLFLSLCVLLWKAKQALDQRQEQRRHLQEMTKMASRPFAKVTVCFPPDPAGPAPAWKPAGLPPPAFRRSEPFLAPLLLTGAGGPWGPMGGGCCPPALPATTAGLRAGPITLEPTEDGMAGVATLLLQLPGGPHAPNGACLGSALVTLRHRLHEYCGGSGGAGGSGHGGGGGRKGLLSQDNLTSMSL",
"MAEFSQKQRKQSGSEGLGSVVDFLLANARLVLGVGGAAVLGIATLAVKRLIDRATSPPDEDDTKGDSWKELSLLRATSPQKPQPPPAAFSQPLATGSPSPSVPVEPTPIHSPTTPKFSTIAPLCLTFQERLLAFERKHVITPEAHVTLAKQLAGDIALELQAYLRSKFPELPFGALVPGGPLYDGLQAGTAEHVRLLAPLELEPGLWSLVPGVDTVAREPRCWAVRRTQLEFHPRGCSPRDRFLVGGYLSSRVLLELLRKALSASVNWPAIGSLLGCLIWPDVASEELLLKVQHECLEFTLAVLMVVPGASTDDRLLLAWPLEGLASNLWLQDLYPVETARLRALDDQDAGTRRRLLLLLCGICRGHPALVRLGWSHLTQVVLHLGEEEVAWTEEALGERFLQALEFLVGSLEQASLPCHFNPSVNLLGNFREEEIDDIGYVLYSGLQVPESLF",
"MAAASGYTDLREKLKSMTSRDNYKAGSREAAAAAAAAVAAAAAAAAAAEPYPASGTTKRKYQEDSDPERSDYEEHQLQKEEEARKVKSGIRQIRLFSQDECSKIEARIDEVVSRAEKGLYNEHTVDRAPLRNKYFFGEGYTYGAQLQKRGPGQERLYPPGDVDEIPDWVHQLVIQKLVEHRVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFQFKPIRVSEPVLSLPVRRGSVTVLSGYAADEITHCIRPQDIKERRAVIILRKTRLDAPRLETKSLSSSTLPPSYASDRLSGNTRDPALKPKRSHRKADPDAAHRPRILEMDKEENRRSVLLPTHRRRGSFSSENYWRKAYESSEDCPEAASSPTRKVKMRRH",
"MALGGALALALALALAVLGPLSLRVLAGDCKGQRQVLREAPGFVTDGAGNYSVNGNCEWLIEAPSPQHRILLDFLFLDTECTYDYLFVYDGDSPQGPLLASLSGSTRPPPIEASSGKMLLHLFSDANYNLLGFNASFRFSLCPGGCQNHGQCKSPGVCVCEPGWGGPDCGLQECSAYCGSHGTCASTLGPCRCEPGFLGRACDLHLWENQGAGWWHSVSAGDPAFSARIGAAGAFLSPPGLLAVFGGQDLNKALGDLVLYNFSTNTWESWDLTPAPAARHSHVAVAWAGLLVLMGGELANGLLTNDVWAFSPLGGGHWELLAPPASSSSGPPGLAGHAAALVDDIWLYVSGGRTQHDLFSSGLFRFRLDHTSRGYWEQVIPAGGRPPAATGHSMVFHAPSRTLLVHGGHRPSTARFSVRVNSTELFHVERRVWTTLKGRDGLQGPRERAFHTASVLGNYMVVYGGNVHTHYQEEKCYEDGIFFYHLGCHQWVSGAELAPPGTPEGRAAPPSGRYSHVAAVLGGSVLLVAGGYSGRPRGDLMAYKVPPFVFQAPALDYHLDYCSMYTDHSVCSRDPECSWCQGACQAAPPPGTPSGACPAASCLGLGRLLSDCQACLAFSSPTAPPRGPGALGWCVHNESCLPRPEQARCRGEQISGTVGWWGPAPVFVTSLEACVTQSFLPGLHLLTFQQPPNASQPDKVSIVRSTTITLTPSPETDVSLVYRGFIHPLLPGGPGGPGAEDVAVWARAQRLHVLARMARGPDTENMEEVGRWVAQQEKETRRLQRPGSDRLFPLPGRGNKYAVEIRGQLNGSAGPGHSELTLLWDRTGVPGGSEISFFFLEPYRSSACTSYSSCLGCLADQGCGWCLNSATCHLRQGRAHCEDDGSGESLLVLVPALCPLCEEHRDCHACTQDPFCEWHQSTNRKGDAACSRRGRGRGALKNPEECPPLCSQRLTCEDCLANSSQCAWCQSTHTCFLFAAYLARYPHGGCRGWDDSVHSEPRCRSCGGFLTCHECLQSHECGWCGNEDNPTLGRCLQGDFSGPLGGGNCSLWVGEGLGLPVALPARWAYARCPDVDECRLGLARCHPRATCLNTPLSYECHCQRGYQGDGITHCNRTCLEDCGHGVCSGPPDFTCVCDLGWTSDLPPPTPAPGPPAPRCSRDCGCSFHSHCRRRGPGYCDECQDWTWGEHCERCRPGSFGNATGSGGCRPCQCNGHGDPRRGHCDNLTGLCFCQDHTEGAHCQICSPGYYGDPRAGGSCFRECGGRALLTNVSSVALGSRRFGGLLPPGGGAARAGPGLSYCVWVVSATEALQPCVPGTLCPPLTLTFSPDSSTPCTLSYVLAFDGFPRFLDTGVVQSDRSLIAAFCGQRRDRPLTVQALSGLLVLHWEANGSSSWGFNASVGSARCGSGGPGSCPVPQECVPQDGAAGAGLCRCPQGWAGPHCRMALCPENCNAHTGAGICNQSLGVCICAEGFGGPDCATKLDGGQLVWETLMDSRLSADTASRFLHRLGHTMVEGPDATLWMFGGLGLPQGLLGNLYRYSVSERRWTQMLAGAEDGGPGPSPRSFHAAAYVPAGRGAMYLLGGLTAGGVTRDFWVLNLTTLQWRQEKPPQNMELPAVAGHTLTARRGLSLLLVGGYSPENGFNQQLLEYQLATGTWVSGVQSGTPPTGLYGHSAVYHEATDSLYVFGGFRFHVELAAPSPELYSLHCPDRTWSLLAPSQGAKPRPRLFHASALLGDTMVVLGGRSDPDEFSSDVLLYQVNCNTWLLPALTRPAFVGSPMEESVAHAVAAVGSRLYISGGFGGVALGRLLALTLPPDPCRLLPSPEACNQSGACTWCHGACLSGDQAHRLGCGVPPCSPMPRSPEECRRLRTCSECLARHPRTLQPGDGEASIPRCKWCTNCPEGACIGRNGSCTSENDCRINQREVFWAGNCSEAACGAADCEQCTREGKCMWTRQFKRTGETRRILSVQPTYDWTCFSHSLLNVSPMPVESSPPLPCPTPCHLLPNCTSCLASKGADGGWQHCVWSSSLQQCLSPSYLPLRCMAGGCGRLLRGPESCSLGCAQATQCALCLRRPHCGWCAWGGQDGGGHCMEGGLSGPRDGLTCGRPGASWAFLSCPPEDECANGHHDCNETQNCHDQPHGYECSCKTGYTMDNVTGVCRPVCAQGCVNGSCVEPDHCRCHFGFVGRNCSTECRCNRHSECAGVGAQDHCLLCRNHTKGSHCEQCLPLFVGSALGGGTCRPCHAFCRGNSHVCVSRKELEMARKEPEKYSLDPEEIETWVAEGPSEDEAVCVNCQNNSYGDRCESCLHGYFLLDGKCTKCQCNGHADTCNEQDGTGCPCQNNTETGTCQGSSPSDRRDCYKYQCAKCRESFHGSPLGGQQCYRLISVEQECCLDPTSQTNCFHEPKRRALGPGRTVLFGVQPKFTNVDIRLTLDVTFGAVDLYVSTSYDTFVVRVAPDTGVHTVHIQPPPPPPPPPPPADGVPRVAADLGGLGTGSGSGSPVEPRVREVWPRGLITYVTVTEPSAVLVVRSVRDRLVITYPHEHHALKSSRFYLLLLGVGDPNGPGANGSADSQGLLFFRQDQAHIDLFVFFSVFFSCFFLFLSLCVLLWKAKQALDQRQEQRRHLQEMTKMASRPFAKVTVCFPPDPAGPAPAWKPAGLPPPAFRRSEPFLAPLLLTGAGGPWGPMGGGCCPPALPATTAGLRAGPITLEPTEDGMAGVATLLLQLPGGPHAPNGACLGSALVTLRHRLHEYCGGSGGAGGSGHGGGGGRKGLLSQDNLTSMSL"),
mutant_index = c(240, 372, 1663, 240, 372, 1663)),
class = c("data.table", "data.frame"),
row.names = c(NA, -6L), .Names = c("var_uuid",
"pep_type", "pep_base", "mutant_index"))
# run test
dto <- antigen.garnish:::make_nmers(dt)
testthat::expect_equal(dto %>% nrow, 552)
})
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