テンクーでのClojure活用事例

2023/07/13 ClojureエンジニアLT&交流会

Transcript

1. ςϯΫʔͰͷ$MPKVSF׆༻ࣄྫ
   $MPKVSFΤϯδχΞ-5ˍަྲྀձ
   גࣜձࣾςϯΫʔ
   !BUIPT
   

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2. $MPKVSF-5@0965
   ࣗݾ঺հ
   w !BUIPT
   w ೥͔Β$MPKVSFΛ৮Γ࢝ΊΔ
   w ೥ʹςϯΫʔೖࣾ
   w $MPKVSF 4DSJQU
   ίϯτϦϏϡʔλ
   2
   

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3. $MPKVSF-5@0965
   ςϯΫʔͷաڈͷൃද
   3
   $MPKVSFDPOK
   4FRVFODFBOE$PODVSSFOU1SPDFTTJOH
   GPS)VHF(FOPNJD%BUB
   https://youtu.be/ipNru1QSeWc
   4IJCVZBMJTQ5FDI5BML
   
   ςϯΫʔͰͷ$MPKVSFͷ׆༻ࣄྫ
   $MPKVSFͰͷή
   ϊϜղੳͱΤϯδχΞϦϯά
   https://youtu.be/ltdMlYLsb3I?t=2947
   

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4. $MPKVSF-5@0965
   ΞδΣϯμ
   w ςϯΫʔͷ঺հ
   w ςϯΫʔͰͷ$MPKVSFͷ࢖ΘΕํ
   w $MPKVSFΛ࢖͏خ͠͞
   4
   

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5. $MPKVSF-5@0965
   ςϯΫʔͷ঺հ
   

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6. $MPKVSF-5@0965
   ͲΜͳձࣾʁ
   6
   ໊ࣾ גࣜձࣾςϯΫʔ (Xcoo, Inc.)
   ୅දऔక໾ ੢ଜ ๜༟
   ઃཱ 2011೥4݄1೔
   ελοϑ 44໊
   Web https://xcoo.co.jp
   ॴࡏ஍ ౦ژ౎จژ۠ຊڷ2-40-8
   ࢿຊۚ 1ԯԁ
   ೝূ
   ISO/IEC 27001 (ISMS)
   
   ݈߁ܦӦ༏ྑ๏ਓ2021
   ༀࣄ
   ୈҰछҩྍػث੡଄ൢചۀऀ
   
   ҩྍػث੡଄ۀऀ
   
   ߴ౓؅ཧҩྍػث౳ൢചۀ/ି༩ۀऀ
   ৘ใٕज़Ͱҩྍʹߩݙ
   ࣾձ࣮૷΁ͷՍ͚ڮ
   ή
   ϊϜҩྍͷτʔλϧιϦϡʔγϣϯιϑτ΢ΣΞ
   ͕Μή
   ϊϜҩྍͷ৘ใղੳ෦෼ΛτʔλϧͰαϙʔτ
   

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7. $MPKVSF-5@0965
   ͕Μή
   ϊϜҩྍ
   7
   ͕Μࡉ๔ͷή
   ϊϜͷมԽΛಛఆ
   ͦͷή
   ϊϜͷมԽʹ߹Θͤͯ
   

   ࠷దͳ࣏ྍɾ਍அɾ༧๷Λߦ͏
   ۙ೥͸ɺή
   ϊϜͷมԽʹ߹Θͤͨ෼ࢠඪతༀͷొ৔ʹΑΓɺ͕Μͷ࣏ྍ੒੷͕ܶతʹվળ
   T
   A G C
   A T G G G G C A T
   T
   A G C
   A T C A T
   

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8. $MPKVSF-5@0965
   ։ൃνʔϜߏ੒
   8
   Analysis
   Database
   Report
   όΠΦΠϯϑΥϚςΟΫεͷΞϧΰϦζϜܥ
   σʔλͷΞάϦήʔγϣϯ
   

   ߴ଎ͳݕࡧ
   6*΍8FCܥ
   

   ҩֶత஌ݟʹ΋ͱ͍ͮͯ൑ఆϩδοΫ
   Infrastructure
   +
   $ISPWJTΛӡ༻͢ΔͨΊͷ଍ճΓ
   

   ֤πʔϧ΍ϥΠϒϥϦ΋࣮૷
   

   ͦͷଞͷࣾ಺γεςϜ΋։ൃ
   Chrovisͷ։ൃνʔϜ͸ΤϯδχΞ20ਓఔ౓
   

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9. $MPKVSF-5@0965
   ςϯΫʔͰͷ$MPKVSFͷ࢖ΘΕํ
   

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10. $MPKVSF-5@0965
    ։ൃن໛
    10
    ϦϙδτϦ਺
    ιʔείʔυͷϑΝΠϧ਺ DMK DMKT DMKD
    
    ιʔείʔυߦ਺ DMK DMKT DMKD
    
    ϓϧϦΫΤετ਺ Ҏ߱
    
    ˞ݱࡏ
    

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11. $MPKVSF-5@0965
    ςϯΫʔ͕։ൃ͢Δ044
    w $ISPWJTؔ࿈ͷ044͸IUUQTHJUIVCDPNDISPWJTͰެ։͞Ε͍ͯΔ
    DMKBNή
    ϊϜղੳͰΑ͘࢖ΘΕΔϑΝΠϧܗࣜͷೖग़ྗ΍ΞϧΰϦζϜͷ࣮૷
    WBSJUZมҟͷදهܗࣜ )(74˱7$'
    ؒͷม׵౳
    DMKIHWT)(74ه๏ͷύʔαɾϑΥʔϚολ
    DMKEFDPOTUSVDUTJHTมҟύλʔϯ͔Βͷมҟγάωνϟͷಉఆ
    EVYIVOE%69༥߹Ҩ఻ࢠͷݕग़
    FUDFUD
    11
    

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12. $MPKVSF-5@0965
    Α͘࢖ΘΕΔϑΝΠϧܗࣜ
    w '"452
    Ԙج഑ྻͱͦͷΫΦϦςΟ ֤Ԙج͕Ͳͷఔ౓ͷ͔֬Β͠͞ͰಡΊ͔ͨ
    ͷ৘ใΛه࿥
    w 4".#".
    ֤഑ྻΛϦϑΝϨϯε഑ྻʹରͯ͠ΞϥΠϝϯτ ҐஔΛಉఆ
    ͨ݁͠ՌΛه࿥
    w 7$'#$'
    มҟίʔϧʹΑͬͯಉఆ͞ΕͨมҟΛه࿥
    12
    '"452
    4".
    #".
    7$'
    #$'
    ΞϥΠϯϝϯτ มҟίʔϧ
    

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13. $MPKVSF-5@0965
    DMKBNͷར༻ྫ
    13
    (require '[cljam.io.sam :as sam])
    (with-open [r (sam/reader "in.bam")
    w (sam/writer "out.bam")]
    (sam/write-header w (sam/read-header r))
    (sam/write-refs w (sam/read-refs r)
    (->> (sam/read-alignments r)
    (sam/write-alignments w)))
    (require '[cljam.io.vcf :as vcf])
    (with-open [r (vcf/reader "in.vcf")
    w (vcf/writer "out.vcf")]
    (->> (vcf/read-variants r)
    (vcf/write-variants w)))
    4".#".ͷಡΈॻ͖
    7$'#$'ͷಡΈॻ͖
    (…
    {:qname "HWI-ST216_0147:5:48:13963:160437#0/1",
    :flag 0,
    :rname "chr1",
    :pos 23000088,
    :end 23000123,
    :mapq 255,
    :seq "TATAGGATTTGTTTGTTGTGTTTAGGTGGGTATAGT",
    :qual "HFHHHHEHHHHFHHHHEHFHHHHBHGBFFE>EGCFC",
    :cigar "36M",
    …}
    …)
    (…
    {:chr "19",
    :pos 111,
    :ref "A",
    :alt ["C"],
    :qual 9.6,
    :filter nil,
    :FORMAT (:GT :HQ),
    :NA00001 {:GT "0|0", :HQ (10 10)},
    :NA00002 {:GT "0|0", :HQ (10 10)},
    …}
    …)
    

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14. $MPKVSF-5@0965
    ࣮ࡍͷγεςϜͰ࢖ΘΕΔπʔϧɾϥΠϒϥϦ܈
    14
    GSPN4FRVFODFBOE$PODVSSFOU1SPDFTTJOHGPS)VHF(FOPNJD%BUB
    
    

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15. $MPKVSF-5@0965
    $MPKVSFΛ࢖͏خ͠͞
    

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16. $MPKVSF-5@0965
    γʔέϯεʹΑΔσʔλදݱ
    w ή
    ϊϜղੳͰ࢖ΘΕΔϑΝΠϧ͸αΠζ͕େ͖͘ͳΓ͕ͪ
    ώτͷή
    ϊϜ഑ྻ͸ԯԘج
    ϑΝΠϧͰ਺ेʙ਺ඦ(#ΦʔμʔʹͳΔ͜ͱ΋
    ϑΝΠϧશମͷ಺༰͸ϝϞϦ্ʹࡌΒͳ͍
    w ͜ΕΒͷେ͖ͳσʔλΛ஗Ԇγʔέϯεͱͯ͠දݱ͢Δ͜ͱͰɺ$MPKVSFͰ
    ࣗવʹॲཧͰ͖Δ
    16
    

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17. $MPKVSF-5@0965
    ฒྻԽ
    w σʔλ͕େ͖͍ͱॲཧ࣌ؒ΋௕͘ͳΓ͕ͪ
    σʔλαΠζʹΑͬͯ͸ύΠϓϥΠϯશମͷ࣮ߦͰ೔Ҏ্͔͔Δ͜ͱ΋
    ఆ਺ഒͷߴ଎Խ͕ޮՌతͳέʔε͸গͳ͘ͳ͍
    w $MPKVSFͰ͸جຊతͳσʔλܕ΍ϩʔΧϧଋറ͕Πϛϡʔλϒϧͳ͜ͱͰɺ
    ϚϧνεϨουʹΑΔฒྻԽ͕༰қ
    w ςϯΫʔͰ͸ɺฒྻ౓ͷ੍ޚͷ͠΍͢͞౳͔ΒεϨουϓʔϧϥΠϒϥϦ
    $MBZQPPMF͕Α͘࢖ΘΕΔ
    17
    

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18. $MPKVSF-5@0965
    3&1-Ͱͷ୳ࡧ
    w ίʔυʹखΛண͚Δલͷ3&1-Ͱͷࢼߦࡨޡ
    "OBMZTJTνʔϜͷϓϩμΫτ։ൃ͸ʮԿΛͲ͏࡞Δ͔ ௚͔͢
    ʯ͕࣮ࡍͷσʔλΛ
    ݟͳ͕Βܾ·Δݚڀ։ൃతͳଆ໘Λ΋ͭ͜ͱ΋͋Δ
    w Ͳ͜Ͱ΋σόοά؀ڥΛ࡞ΕΔ
    VCFSKBS͑͋͞Ε͹ɺαʔό্΍%PDLFSίϯςφ಺౳ͷ؀ڥͰ΋$MPKVSFͷ3&1-Λ
    ্ཱͪ͛ͯΞϓϦέʔγϣϯͷ؀ڥΛ੔͑ΒΕΔ
    ιέοτ3&1-Λ࢖͑͹ϦϞʔτσόοά΋༰қ
    18
    

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19. $MPKVSF-5@0965
    σʔλ෼ੳʹ͓͚ΔڧΈ
    w DG$MPKVSFGPS%BUB4DJFODFJOUIF3FBM8PSMEGSPN$MPKVSFDPOK
    w +7.͕े෼ߴ଎Ͱɺ+BWBͷϥΠϒϥϦ΋๛෋
    w 5FDI"TDFOU΍4DJ$MPKΛத৺ʹ$MPKVSFͷσʔλ෼ੳɾ౷ܭղੳɾػցֶश
    ϥΠϒϥϦ͕׆ൃʹ։ൃ͞Ε͍ͯΔ
    w 3&1-Ͱࢼߦࡨޡ͠΍͍͢
    w ·ͱ΋ͳύοέʔδ؅ཧγεςϜ͕͋Δ😎
    19
    

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20. $MPKVSF-5@0965
    ͍Ζ͍ΖͳϓϥοτϑΥʔϜͰ࢖͑Δ
    w ςϯΫʔͰͷར༻ྫ
    $MPKVSF PO+7.
    ղੳπʔϧɺ8FCαʔϏε όοΫΤϯυ
    
    $MPKVSF4DSJQU8FCαʔϏε ϑϩϯτΤϯυ
    
    #BCBTILB$-*πʔϧɺεΫϦϓςΟϯά
    w #BCBTILBBTCFUUFSγΣϧεΫϦϓτ
    #BCBTILB͸ଞͷίϚϯυͱ૊Έ߹Θͤͯ࢖͍΍͘͢ɺେྔͷϑΝΠϧ͕ੜ੒͞Ε
    Δॲཧͷूܭ౳ʹศར
    $MPKVSFͷศརͳίϨΫγϣϯΛඋ͑ɺͦͷؾʹͳΕ͹εϨου΋࢖͑Δɺ࢖͍ग़
    ͕͋ΔεΫϦϓτݴޠͱͯ͠׆༻Ͱ͖Δ
    20
    

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21. $MPKVSF-5@0965
    ·ͱΊ
    w ςϯΫʔͰ͸$ISPWJTΛ͸͡Ίͱͨ͠γεςϜͷେ෦෼Λ$MPKVSFΛ࢖ͬͯ
    ։ൃ͍ͯ͠Δ
    w $MPKVSFͷγʔέϯεॲཧɾฒྻԽͷ༰қ͞͸ή
    ϊϜղੳͷڊେͳσʔλΛ
    ѻ͏ͷʹద͠ɺ3&1-ʹΑΔߴ଎ͳϑΟʔυόοΫ͸ݚڀ։ൃతͳࢼߦࡨޡ
    ͷ͠΍͢͞ʹߩݙ͍ͯ͠Δ
    w ΞϧΰϦζϜدΓ͔ΒXFCدΓͷ࢓ࣄ·Ͱ͍Ζ͍Ζ͋Γָ͍͠ʂ✌ Т
    ✌
    w ڵຯ͕͋Δํ͸ͥͻ͓੠ֻ͚Λʂ
    21
    

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