tests/testthat/test-make_nmers.R

In andrewrech/antigen.garnish: Tumor neoantigen prediction

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)

    })