@datagrok/bio 1.6.0 → 1.7.0

package/files/samples/sample_FASTA_DNA.csv

@@ -0,0 +1,101 @@
+id,sequence
+1,TGTCTCAGCACCATCCAATTTGCGATTCGACCC
+2,TGTCTCTCATCAAATCATCCCTATGGTGGCCCTAATT
+3,ATTTATCAACGATCATCCCAACAAAGCGAAACCGTCAT
+4,CGAGGCCAGCCCTCATCCAATAGAACACCTTCGTG
+5,TGGGTCACCCTTCATCCCCCACTCCTACTAGGA
+6,TTTATTCATCGGTCATCCACGTGCGTATACATATG
+7,GACCTCAACTGTCCTCCGGGAGACATGCCCGAAAT
+8,CTGCATCAGCTGTCATCCCCTGGTGAGGTTTCTTGTG
+9,TATTTTCACCTATCATCGTTAATGGCTAACCGGCAT
+10,CGCCTTCAGCGGACATCCTATACAGTCGGCCCACTT
+11,ACGCTTCACCCCTCATCCATAACTTTTCGTAGTC
+12,AATCCTCAACATTCATCGCGAAGTAAAGGTCCTTTA
+13,TCGCTTTCAGCGCTCATCCCCAAATCTTCCCAAAAAG
+14,CCATGTTCATCGATCATCCGTAACGTCATACTTAGT
+15,CAAACTCATCATTTATCTATAGTCTTCCGCGAT
+16,CGTTCTCAGCCTCATCCTATGTTCAGCCGGCGT
+17,GTTAGTCATCGCTCATCCTGTCGGCAACTCCTTAC
+18,GGTCGTCACCGTTCATCCTTCAGATCAGCAATGTGTAC
+19,AGACATCAACTCTCAGCCTGCAATGATTACCGATA
+20,TGTATTCATCCTCATCCCAGGTAATGTGACTATCT
+21,ATGGTCAGCGTCCATCAGGAGAATTTTACATACG
+22,TATCTTCAGCGGACATCCTATGTCGCGCACAGACAT
+23,CCATACTCAGCTAGCATCCCAGACCGATCTCATCTC
+24,TCCCTTCAGCTTTCATCCAGACGACTGTTCAAAAA
+25,TCCGTTCAACACGCATCCTCTGACGAGACTCAAGA
+26,CGCATCAGCGATCCTCCGGCAGTGTGGCCCGCTGA
+27,TGCGCTCAACTTTCATCCTGGCGTCCAGGCGAG
+28,TTTCTTCAGCGCTCATCAAAAGGTCCCAGCCATA
+29,TCACGTCACCCATCATCCATCGGACAGACCCCCC
+30,GATTGTTCAACCCTTATCTGAGCGTTATCCCGGCGAG
+31,GAGCTTCATCCGTCATCCCACGAGAAGTACTGGTA
+32,CCTGTTCATCCTTCATCCTGAGGTACAAACCCCCT
+33,AGACGTCAGCCTTCACCGAGATTCTATTCCACATTA
+34,GTGCGTCAGCAGTCATCCTTCTGAACCGGCGGATC
+35,TTTGGTCAGCGATCATCCGTGCGATTGTTACGTCGG
+36,TTGTTTCAGCTGTCATCCAACAAGCTGGCCTATC
+37,CGGTGTCAGCCATCATTCGAACGAGTAGCCGCGGC
+38,TGGGTTCACTCCTTCATCGGGTACGGACCCCAAGCA
+39,CCTATTCATCCCCTCATCGAACAGATTAGCCGAAAC
+40,GGAGGTCACCCTTCATCCTGGTACTGGCAAGA
+41,GGCACTCAGCTCTCATCACGACTATTCGGCAGAGG
+42,CGGTATCAACGGTCATCTAACTTGATGATTCCCTCA
+43,GACTTTCACCAATCATCAGAGGGGTAGCACCTCGAA
+44,AGACGTCAACCCGCATCAAACTGGTTGCACACCA
+45,CAGTTCAGCAAATCATCCCTCTTGTACGACCCTAG
+46,CCAAATCACCGATCATCTAAACCCCTAGACAGCGC
+47,TCTGGTAAACCCTCATCCCCGATAAAGCAGCTATAA
+48,ACTATTCAACCTCATCCGAGAGCCCGCTACGT
+49,TACAAGTCAGCGGCCATCCGCCGATGTGCACTCAGC
+50,TTTAGGTTCAGCAGTTTATCCTCCAAGTTTTTCCTCA
+51,TCTATCTCAGCCTTCATCCAGAACGGTAGTCCTTGTT
+52,GGGAGCTCAGCTCTCATCAAGATAGATCACCGATT
+53,TGACTTCATCACTCATCCGACAGATCACCACTAA
+54,GCTATCAGCCCTCATCAACTAAGGCGAGCGGAAA
+55,TTTAATCAGCGGTCATCAACCCAGCGCGCACACACCG
+56,TGGCATTCATCCGTCATCCAAACGTCCGCGACCATCA
+57,TATGGTCAGCAGTCATCCGCAGCAGCAAACATGGA
+58,AAGCTCATCGGTCAGCCGACGGTAAATACTAAAG
+59,CCGTTCAGCCGACAACCGGGATTCCGCACAGCCT
+60,TTAGTCATCGATCATCCGGGATCTTACGCGTTAT
+61,GGTATCAGCATTCATCCCACAAACCAATAGCCCTCTA
+62,TACCATCAGCTGTCATCGCGTGTAGGCAGACCACCTC
+63,AGTTGTCAACCTCATCCAGACCTCCCTTCCTGAGA
+64,ACCAGTCAGCGATCATCCGCATCTGTTCCCCCGCC
+65,CTGGACCAGCTCACACCCTAGCGAGCAGGCAGGGAG
+66,CTATCGTTCAGCGATCATCCACTGGCGGATCCTTGGG
+67,AGATATCAGCGATCATCGCCGTGTCACACCTAGAC
+68,GCGGTTCAGCATCATCCGTAAGTCGATTCCGACT
+69,CCGCTTCATCGCTCATCCCTGGGGGGACGCAGAAT
+70,GATTTCAACGATCATCCTCATCGACGTTGCCAGA
+71,TGCCCTCAGCGATCATCCGATGGTGCAGGCCTCGG
+72,CGTTATCAGGCCGTCATCCACGCTGGCTACGAGCCT
+73,GCTGTTCACCGCTCATCCGATGGGTGATACATCGC
+74,TGCCCTCAGCACCCATCCCAACGGTTAGTCCGGA
+75,TGTCATCAGCGTTCATCTTTCGACCCGTACCAAAGC
+76,GGTCCCAGCATTCATCTATTTCAGGCGTACTCGG
+77,CCCTGTCAGCGGTCATCCCAGGGACGATCCGTACA
+78,CGGGTTCAGCACTCATCCTGTTGGTTTACCGACTTA
+79,TACAATCAGCGTTCATCCCGGGTTTTTCTCCTGCT
+80,CGGCATCAGCTTCATCCATTGGGTTTGTCTTGA
+81,CTCAATCAGGCTGTCATCCTCTGGGTTAGCCAATGG
+82,TGCAATCAACGATTCATCCGGCTTCCTCCTCGGAT
+83,AGGCTTCAGCTTTCATTAGGCAGACATTGCCATCCGA
+84,CCTAGTCAGTAATTCATCACAAATGAAAGAACAGTC
+85,TTCATTCAGCCCTCATCAGCCATGCCCCTCCGTC
+86,GTCATCAACTCTCATCACTAACATCAAGCGAAT
+87,GGTCTTCAACCATCATCCTGGGGATACACCTACT
+88,TCGTCTCAGCCCTCATCCCACAGTCGATACCCCCC
+89,AGAACTCAACCCTCAACCGGACAGGACCACTC
+90,AGCCGTCAGCTATCATCCTCCTTATTTGTCATAGC
+91,CGTTCAACGGTCATCCGTACCTGATCTCCTTGA
+92,CGTTCTTCATCCCTCATCCGACATGGTAGACTGGGCC
+93,TAGATTCAACGGTCATCCAGACCTACGTTCCCGACA
+94,TCTGTCAGCCATCATCCGAGTCACCATCCTTGT
+95,GGTTCTCAGCGTTCAGCCTGCCTGAGCCCGCGGCCA
+96,AGTGTTCAGCATCATCCGAATAAGGCTGCAACTT
+97,TTCGATCATCGGGCATCGCGGGGATTGTCCGACTG
+98,TTTCATCAGCGTTCATCGAGGTGTGTACCCCAACTC
+99,GTGCTTCAGCTCTCATCAGACGAAAGGGACGAGG
+100,TCCGTTCATCAGTCATCTAGCGGCGCTATCGTAGTG

package/files/samples/sample_FASTA_PT.csv

@@ -0,0 +1,101 @@
+id,sequence
+1,MFITMFCMFWLFIFILMMLIFFMEAMIKPML
+2,AQMTMFCIMFFLMLMFIIMIMFMILEAMKKMLNAI
+3,ILMTMFCICWMIMIFFLLLIMFMLMAMMKMLIFL
+4,FQMTMICMLFFLMMFMFDLIILFIMMEAMMKPDLMFI
+5,LLMTMFCFFMMLLMFFMFMIMFMYFEAMKKFFILF
+6,AMMTMFCFMLIMMFILLFIDIIMEAMLKLDNFI
+7,LLMTMFCMILISMIMILMMIMFLMEAMKKIFFAV
+8,LIMTMFCMLILIFMLMDFMIIMIFFEAMFKMLFLMF
+9,FQMTMFCLMIFMWIFMMMMILDIFIEAMIKFINLFM
+10,FLMTMFCILINIMIIWMIIMLMFEAMFKLDIIF
+11,FFMTMFCMMIFLLLIMIIIMIMDMIMEAMKKMMDIII
+12,IMMTMFCICLLFWLLFMLLIMDMMFEAMLKFIMMI
+13,MQMTMFCFMLLLMFFMDIMIIMLLDEAMLKLDLIL
+14,LQMTMFCIFWMLFMLFMLFIFFLFLEAMLKFINLI
+15,IIMTMFCMIMIISIFFIIMIMLFIFEAMIKLDIIAM
+16,FLMTMLCMCFILFFFLFMFIMLSFFLEALIKILILI
+17,FQMTMFCMMIFLFIMWMIIFIIFFIFEAMKMLLLL
+18,MFMTMFCMCIMFWIFDIIIIILFLIEAMLKLFFIIV
+19,IMLMTMFCMFFFMWIFMFMLIIFSLILEAMMKPDIII
+20,AFLTMFCFMWLLMLMFLFLIMIIIDEAMIKLFFL
+21,FQMTMFCFLLMSFLMIIMIFILMFFDEAMFKILNFI
+22,MIMTMFCMLMNLLMFFMLIILILMIEAMLKLMMAI
+23,MIMTMFCMIILMFHMMMFLIFILYEAMKKLFNMIV
+24,LFTMFCMCWMIMIFWIIILMIMIFLAMKKPMFLF
+25,AFLMTMFCICWFLFFLFMILIMLMFFEAMKKFFLV
+26,LLMTMFCMCMNMMMFMLIMMILMSYIEAMFKFFLI
+27,LQLTMFCFILLIFLMILLILMILFEAMMKMFFAL
+28,IQMTMFCMMMMFLMLFFIDIMFLMMEMMFKMDLMFF
+29,MMTMFCIWIFMMILDMMFFIIMIIAMMMFLLIIV
+30,FQMTMFCMMLFMFILWDIFIMISMLEAMMKLDIIM
+31,LFMTMFCMMMNFMIFWLILIFFSLFEAMKKLILAM
+32,AFMTMFCMFLWFILHLWIFFIMMLIMIEAMIKIDIAV
+33,LLTMFCMILIFWHFMFMDIMMMMIFEAMLMIFIMI
+34,IMMTMFCFCFLIFHMMIFDIMISMIEAMKKIIMLL
+35,FMMTMFCMMMLFIIMFLIMMIDILLFIDEAMMKDFIL
+36,IMMTMFCMIILFMFMFMMIIIMLFFMLEAMFKMMFF
+37,LLMTMFCMLWMMLFIFFIMLIFISLFEAMKKIFIIM
+38,FIMTMFCMMLLLFFFIILDIMLMFIEAMKKLLLL
+39,IMMTMFCFMMMSMMFFFLIIIILFMFDMAMKILLI
+40,MFMTMFCMFILILLLWIIDIMFMLDEAMKKPDFL
+41,LIMTMFCMCMFLILWMMFIMLIIIEAMKKPIILI
+42,AFMTMFCFMMMFMHFMLIFIFMIFMEAMKKFFLFLM
+43,AFIQMTMLCMCMLLMFFLDIFIIIIFLDEAMMKPLMLL
+44,LQMTMFCMFMIILFDMIMMMMMEAMLKIMIF
+45,ALMTMFCFIWNSIFIFIFDILMILLIEAMFKMDNII
+46,LMMTMFCLMLFSWLMWLMIIFIIMMILEAMLKPLFAFV
+47,FFMTMFCMFFIMFLIFFLLLIMLFMMEAMLKIFL
+48,LMMMTMFCIFMLLFFFFMFIMMMFDEAMFKMDMIL
+49,QITMFCIFFMFIIMWLFFFLFFLFEAMLKMIMAL
+50,IIMTMFCIMLILWIFLFIIIIMILIAMKKLILLL
+51,ILMTMFCMMLIIFFFMLFFILIILDFFFEAMLKIDMMI
+52,FIMTMFCMCWFILLIMMIIIFLIDEAMMKMFLMM
+53,FIMTMFCMLLMFSLMFFMMMILIFYIEAMIKMMLFI
+54,IQMTMFCMCWMFLHMMFLDILFIFLDEAMLKMIIFL
+55,FMMTMFCMLILMMHLFFFIIMDMIEAMLKMDMLV
+56,LMMTMFCMFINSMLLMMFILILMMLFEAMKKPFMIM
+57,MLMTMFCLIMNFFMFLMFMIMMMEAMFKMLM
+58,ILMTMFCLFFFSFFFILIMMIYIEAMLKIMMIL
+59,IIMMTMFCMCLLMLMFWIIMIMISFLMEAMKKFLIAM
+60,IFMTMFCMMFNSFLIFWIILMFFLLILEAMMKPLNLV
+61,IFITMFCMILLSMLFILFDIFFIIMEIMKKFIIAF
+62,IMMTMFCFCMIMFMFILFLILFLDEAMMKMLIL
+63,IFMTMFCMFLMFMIMLLFDIFLSFFEAMKKFFIAV
+64,IQMTMFCMIFFSMMFFMDMDIMIFIIEAMFKMNMLL
+65,LFMTMFCMFLLMFILFFIIMDFYFFEAMKKPMLILL
+66,AMMTMFCMLLMMFHMLDFIFDFFMEAMKKMMML
+67,AIMTMFCMFLNLMLMMFIFMMIDEAMIKFLLFI
+68,MFMTMFCMFIIFLIIMMDLIIMIIMLEAMIFILILLL
+69,IFMTMFFMFMMIIFWLMWDLMIIFSIMIMAMIKLMMAL
+70,ILMTMFCMMLFLLFFFLIIIIFSMMEAMMKPDIMM
+71,FFMTMFCMFFIFLHMIFFDIFLFFYLEAMMKPMFFI
+72,MFMTMFCMLWMFMLHIMFFLIMMMLFEAMFKFMLAF
+73,AIMTMFCMMIMMIMLFFLLILMFLIEAMFKFIFFM
+74,MMMTMFCMLMFWIIFIIFLIFILMIEAMFKMINIV
+75,LLMTMFCMLIMLIMLWLMDIMMMLIEAMKKPLMFFL
+76,LQITMFIMMWILLFMIFIFILFFEAMMKFMLF
+77,ILMTMFCIFFIFFMFMFMFFIMFFLIEAMKKLDIML
+78,MLMTMLCMMMFSLLIFIFLDIIIFILEAMLKFMMI
+79,ILMTMFCMCMMMIMMIIIIMDSFLEAMKKPMMMI
+80,QMTMFCMMFFIIHMMIIFFMDLIMMLAMKKPDMAI
+81,LLMTMICILFFMFMFLMMLIIMFLYFEAMMKMLNII
+82,MMMMFCMFIFFIHFMLILIMLIYMMIMKIMMNML
+83,ALMTMFCMFIFFMLMMMIIIFFFFEAMMKMFIFV
+84,ALMTMFCMWLILMWFMIIILMMDEAMKKLLNIL
+85,LIIMTMFCMMLLLIIMMFLIFIFLLEAMIKFLLFLL
+86,MLMTMFCMLLMFHFLIMMILISYFEAMKKLIFML
+87,FIMTMFCMMIFIFFFMFDIILSMMAMFKIDLIM
+88,FMTMFCMMWLSLFFMFLILFFIFIEAMFKLMNFV
+89,MMMTMMCMLLIMFLFMFIMFIFMLIEAMKKLDLLI
+90,AFMTMFCFMFISWMMIIFMLIMFILFEAMMKMFFFL
+91,LIMTMFCMIWFIMHFLILMLIMILYLEAMFKPLIFF
+92,MIMTMFCMFINLWIFFLLDIFFLIMEAMKLDMIM
+93,LLMTMFCMFIIMLFFLFMFLIMFFIDEAMFKPLFIM
+94,FFMTMFCIFFMSLHLFMLLIIFMFDEAMKKMLLFI
+95,IFFTMFLIFLLFIMMMIDMIIFILLEAMKKPMFII
+96,MFMMTMFCFMIIFFMMMDIMIIMDFILEAMLKIFLIII
+97,IIMTMFCMIINMLFFDLLIIILLEAMLKFDMFF
+98,MLMTMFCMLLIMFMILILMFIFLLYDEAMKKMLMLI
+99,LFMTMFCMLINSLIMIFFDIIIFLEAMFKFFLILL
+100,FLMTMFCMMMFSMMMMFIIFMLLIEAMLKIFNAL

package/files/samples/sample_FASTA_RNA.csv

@@ -0,0 +1,101 @@
+id,sequence
+1,AAGGCCAGCAAAGUCUUCACGAGAGCGCGGAAACUU
+2,AGGCCAUACGACUAAUUCUGAAUCUGCGGAAAUCA
+3,GUGCCCGCAUCUUCAGUGGUGUAAUUUGCGGAUGCUCG
+4,GGGCCAGAAUACAUAGCUAAGCAGCUGCGAACGGUA
+5,CUGCCAGCCUUGAAAAGGCGGUCGCGCGGAGCUAA
+6,AGGCCAGCUUCUCACUGUCUCGUUCGCGGAUAGCA
+7,UAGCCAGCAAUAUUAGUAGGAAUAGCGGAGGCCA
+8,ACGCCAGUACCGCGCAUAGGAGCAGCGUACCCUA
+9,AUGCCAGCUCAUCACCAUAGCCCUGCGGAUGGCCG
+10,ACGCCAGCAAUAGCACCUAGUCCCUUGCGGACAUCA
+11,CGGCCAGCUGCUCUCGGGGACUAGCGAAUGGGG
+12,CUCCCAGCCAGACAUGCGUGAGUCUAGCGUAACAC
+13,GGGCCAGCCUGAUUUGGCGCGAACGAGCGGAACGA
+14,CUGUCCAGCAUUUGGGAGCAGUUCUAGCGCACGGCG
+15,GCGCCAGCUCGUUUUGCGGUGUGCGUGCGGAACUA
+16,UCGCCGGCCGUUGUUACCGGACAUGCGGCAAGUCU
+17,GGGCCAGCGGUAACCGGAGGCGUGUGCGUAUGCUA
+18,UGGCCAGUGUUAUCAUUGAUGGGCGCACAAAA
+19,GGGCCAGCAAAUCGUAGGAAGUAAAUGCGCAUCCCA
+20,GGGCCAGGAAUCAAUAAGUGCAGGAGCGUAACAU
+21,UAUGCCAGCGGGCGAUGUGAAUAAUUCGCGGACCGGU
+22,GUACCAGAAUAGAAUGCUAGAUACGGCGAAUUGCA
+23,CGGCCAGCCCGCGGCAGCGCGUUAGCGGACGCGU
+24,GUGCCAGCUCUGUUCCUCCGCUUAGGCGAAUCUG
+25,GUGCCAGCGCAAUUCGCGAGCCAUGUGCGCAGCACG
+26,AAGCCAGCCACGCCUGAGAGGCAUCCUCGCGGACGCC
+27,UGCCUGUCGACGGCCGAGCGGCGGCGUACGAGC
+28,CGGCCAGCGAUCUUUUUGUGGGGGGGCGCACAAAU
+29,CAAGCCAGCAAGCUACAUAGGGUGUGCGGAGGUA
+30,CGGCCAGCCCCACUUACGUAGUGUAGCGCAUUCUA
+31,GGCCCAGCAACGUUCGAAUGCACCGGCGUAACCGC
+32,UAGCCAGCUUCUUAACACAUGCACGAGCGAAGAACG
+33,GAGGUAGCCUAACAAGGAUUAGUUUGGGCGGAUGACU
+34,UGGCCUGACGUAACCAUUCGAACAGCGGACGCGG
+35,GGCCAGCUUGUCUUAACCGAAUGAGCGAAAGUUU
+36,GUGCCAGCGCGCGGCGACGCAACAGCGGUAGCGU
+37,UUGCCAGCGUGUGGAGCCGAUUUGCGCAAUGUA
+38,GACGCCAGCUCGGAGAUAGUGAUGAUGCGGAUAGGG
+39,CAGCCAGAUCAUCGUAAGAGAGUGCGGAACCA
+40,UUGCCAGGUAGCAUUCGCUGAGGGGCGGAGAGAA
+41,CGGCCGGCGUGAGUAAGGUGCACUUGCGGAGUUGG
+42,UGACCAGCCAGGCCCUGAUGAAUGCGGCGGAAUCUU
+43,CAGCCAGCCCCGGCAAGGUAGCGUCAGCGGAUUGGA
+44,AGGCCAGCAAGAAGCGCAGCACGCCGGGGACCAC
+45,UCGCCAGCUAGUUGACAUAGAAUACGCGGACAAGUA
+46,GUGCCUGCUUCAAAAGAGGGUCCGCGCACCCGG
+47,GAGCCAGAUGGGCCAGGUGUAGUUGAGGACCCG
+48,UGGCCUGCGGGCAUGUCAAGGUCAAGCGGAUAUA
+49,GCGCCAGUGACCGUCUUAUGACUUAACGGGCUCA
+50,GGCCAGAUGUCACGGUUUGCUGAGGCGGACGGA
+51,ACGCCAGAUAUUCACGACCCGGGGCCGCGGAAGGUU
+52,CUGCCAGCUUUUAUAAGCAGGUAUGUGCGCAUCAAUG
+53,ACGCCAGUUACUGCAAAACGCACAGCGCACCCAC
+54,GCGCCAGACUCGUAGGCUCGCUGGGUGCGGAUGUAA
+55,GAGCCAGCAGUAGCGAUAGGUUGCCGCGGAGCCGG
+56,AGGCCUGCUUGCCCCGGGAAUGGGCCUGCGUAGCUG
+57,UAGCCAAGUGACAACUGUAGGUCGCGCGAAUGCCC
+58,CAGCCAGCUGUUCUCAGCGUGGGAGCGGAAGCAG
+59,CCUCCAGGUAUAUGGACGGCAGCUGCGGAUAUGA
+60,CCGCCAGCGAACUAAAAAGGACGGCAGCGAAAUCUG
+61,ACGCCAGCAAAAAACGGGUGUGUGUGCGGAUUUGA
+62,GGACCAGUUAUGAUGUAGAGGAAGAGCAGAACAAUA
+63,GGGCCAGCCGGUUCACCGGACGGUGCGGAAGGC
+64,GGACCAGCGGCAGACCGACGCCUGUGCGUAUUAAA
+65,GUGCCAGCGGUCUCCGCCAGUAUCGGCGUAUCUCA
+66,UAGCCAGCUAAAUACUCACGGGUUUGCGGAACCCG
+67,GUGCCAGCGCGGUUACAGGGCAGCAGGCGGACGACA
+68,UGGCCAGCAGCCGACUCGCCAGUGCGGACUAC
+69,GGCCACCGAGCACGGGUUGUACGUGCGGAUGAGCG
+70,UAGCCAGCCCUAGUCAGACGAGAACGCGAAUAUGUGG
+71,UUGGCCAGCGCAGCGUCAUCGCCGCGCGCAUGUG
+72,CAGCCAGCCGCUCAUGAAAGCUGAGCGUAUUAA
+73,CGGCCAGCUGUGAACACGCAGUAGCUGCGCAGUCC
+74,AAGCCAGGUUUCGUCGCCCUGCUGGAUCGCAUCGCAG
+75,UAGCCAGCUAGCUUUAGCGAAGGCAAGCGGCCGGAAC
+76,GAGCCGGUAAAUGCCGCCGAGCAGCACCGGAUUAGC
+77,CCAGCCAGCCAUGAUCACGCGUUCUCAGCGGAUGCGA
+78,GGGCCAGCCUUUUACGCGUCCCCGCGUAGAAA
+79,GGGCCAGCUUCACGAUGUACGACCCGGGGGAACCUG
+80,GACCGUUGGCCGGUGAAGCAUCUGCGGAUGCAA
+81,AGGCCAGGAAAUUCCUGAGAGAUAUCCGGACGCCC
+82,AGGCCAGCCAUCAUACCCCUGUUGAAAAGGCGGAUAUGA
+83,CAGCCAGGUGUCAUAAGCGGCCUCCGCGAAAGGA
+84,GCGCCGGCGGUUGCAUCGGACCUAGCGCAUGCGC
+85,GGGCCAGCGUGUUAAUUGUGAUCACGCGUAAAGUGU
+86,UAGCCAGCUAUGGGACAAGUAAGGCGAACGCAU
+87,GUGCCAGCAAUAAUACCUAAGAUUCAGCGGAGGAU
+88,AGCCCCAGAUUUGUACCUCAGUCUGCGGCGGAGUGA
+89,UGGCCAGUCUCAACGCAUGAGCACGCGAACGACA
+90,AAGCCAGCCUUCGCUGGAUGGAUUUGCGCAACCUA
+91,GUGCCAGUGAUUAACGGAUUCUGCUGCGGACUCCC
+92,GGGCCGGAUACUCUGAUGCUGCAGAAGCGAAGUGAU
+93,UUCGCCAGGAGAUAUCCUAUGGGUGGUGCGCAACAA
+94,UAGCCACCUCAAUAUGCAAUGGUGCAGCGGAGGCGA
+95,GCGCCAGCUAUUCUGGUGGGUCUCUGCGGAUACUG
+96,GAGCCAGGGUACCUCAUUCGCCGCACGCGUAGCCUGA
+97,GAGCCAGGAGGUUCGUUAGGAAUCUGCGGAAGGGA
+98,AAACCAGGAUCAAUAACAAGAAGACGCGCACAGCGC
+99,GAGCCAGCGGGUUUUUGAGGAGAUCUGCGGACGUUC
+100,GAGCCAGCUACCGAAAGGGCACAGCGGACUUUACG

package/package.json

@@ -2,7 +2,7 @@
   "name": "@datagrok/bio",
   "beta": false,
   "friendlyName": "Bio",
-  "version": "1.6.0",
+  "version": "1.7.0",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",

package/scripts/generate_fasta_csv_for_alphabets.R

@@ -0,0 +1,70 @@
+require(tidyverse)
+library(random)
+
+alphabetDna <- c('A','C','G','T')
+alphabetRna <- c('A','C','G','U')
+alphabetPt <- c('G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',
+                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',)
+
+toAlphabet <- function(v, a;ph){
+  paste(sapply(v, function(ci){ alph[ci]; }), collapse = '')
+}
+
+mutateString <- function(s, p){
+
+}
+
+seq <- toAlphabet(sample.int(4, 35, replace=TRUE), alphabet);
+seqPt <- toAlphabet(sample.int(20, 35, replace=TRUE), alphabetPt);
+seqDna <- toAlphabet(sample.int(4, 35, replace=TRUE), alphabetDna);
+seqRna <- toAlphabet(sample.int(4, 35, replace=TRUE), alphabetRna);
+# probability to mutate
+seq_p1 <- c(100,  100,  100, 100, 100,   5,  2,  2,  50, 3,
+           100,  100,   7,  2,  2,   7,  2,  33,  100, 100,
+           100,  100,  100, 100, 100, 100, 100, 100, 100, 2,
+           100,  100,  100, 100, 100)
+seq_p2 <- c(100,  100,   7,  2,  2,   7,  2,  33,  100, 100,
+           100,  100,  100, 100, 100, 100, 100, 100, 100, 2,
+           100,  100,  100, 100, 100,   5,  2,  2,  50, 3,
+           100,  100,  100, 100, 100)
+
+# mutate string s with probability p and alphabet
+seq_mutate <- function(s, p, alphabet){
+  # s <- seqDna
+  # p <- seq_p
+  # alphabet <- alphabetDna
+  res_s <- s
+  res_p <- p
+  for (i in 1:(str_length(res_s)*2)) {
+    pos <- sample.int(str_length(res_s), 1)
+    if (sample.int(100, 1) < res_p[pos]) {
+      cast <- sample.int(100, 1) # mutation type probabilty
+      if (0 < cast && cast <= 2 ) {
+        #insertion
+        res_s <- paste(substr(res_s, 1, pos), alphabet[sample.int(4, 1)], substr(res_s, pos+1, str_length(res_s)), collapse='', sep='')
+        res_p <- c(res_p[1:pos], c(100), res_p[(pos+1):length(res_p)])
+        #cat('insertion');
+      } else if (2 < cast && cast <= 4 ) {
+        # deletion
+        res_s <- paste(substr(res_s, 1, pos-1), substr(res_s, pos+1, str_length(res_s)), collapse = '', sep='')
+        res_p <- c(res_p[1: (pos-1)], res_p[(pos+1):length(res_p)])
+        #cat('deletion');
+      } else {
+        # replace
+        res_s <- paste(substr(res_s, 1, pos-1), alphabet[sample.int(4, 1)], substr(res_s, pos+1, str_length(res_s)), collapse='', sep='')
+        #cat('replace')
+      }
+      #cat(res, '\n')
+    }
+  }
+  res_s;
+}
+
+fastaDna_df <- data.frame(id = 1:100, sequence = sapply(1:100, function(id){ seq_mutate(seqDna, seq_p1, alphabetDna)}));
+write_csv(fastaDna_df, 'D:/HOME/atanas/Datagrok/projs/public/packages/Bio/files/samples/sample_FASTA_DNA.csv');
+
+fastaRna_df <- data.frame(id = 1:100, sequence = sapply(1:100, function(id){ seq_mutate(seqRna, seq_p2, alphabetRna)}));
+write_csv(fastaRna_df, 'D:/HOME/atanas/Datagrok/projs/public/packages/Bio/files/samples/sample_FASTA_RNA.csv');
+
+fastaPt_df <- data.frame(id = 1:100, sequence = sapply(1:100, function(id){ seq_mutate(seqPt, seq_p2, alphabetPt)}));
+write_csv(fastaPt_df, 'D:/HOME/atanas/Datagrok/projs/public/packages/Bio/files/samples/sample_FASTA_PT.csv');

package/src/package.ts

@@ -21,6 +21,8 @@ import {getMacroMol} from './utils/atomic-works';
 import {MacromoleculeSequenceCellRenderer} from './utils/cell-renderer';
 import {Column} from 'datagrok-api/dg';
 import {SEM_TYPES} from './utils/constants';
+import { delay } from '@datagrok-libraries/utils/src/test';
+import { TableView } from 'datagrok-api/dg';
 
 //tags: init
 export async function initBio(): Promise<void> {
@@ -173,6 +175,21 @@ export async function toAtomicLevel(df: DG.DataFrame, macroMolecule: DG.Column):
   if (!checkInputColumn(macroMolecule, 'To Atomic Level'))
     return;
 
+  let currentView: TableView;
+  for (let view of grok.shell.tableViews) {
+    if (df.name === view.name) {
+      currentView = view;
+    }
+  }
+  const file = await _package.files.readAsText('samples/sar-small.csv');
+  const df2 = DG.DataFrame.fromCsv(file);
+  const v = grok.shell.addTableView(df2);
+  setTimeout(()=> {
+    grok.shell.closeTable(df2);
+    v.close();
+    grok.shell.v = currentView;
+  }, 100);
+  
   const monomersLibFile = await _package.files.readAsText(HELM_CORE_LIB_FILENAME);
   const monomersLibObject: any[] = JSON.parse(monomersLibFile);
   const atomicCodes = getMolfilesFromSeq(macroMolecule, monomersLibObject);
@@ -181,7 +198,8 @@ export async function toAtomicLevel(df: DG.DataFrame, macroMolecule: DG.Column):
   const col = DG.Column.fromStrings('regenerated', result);
   col.semType = DG.SEMTYPE.MOLECULE;
   col.tags[DG.TAGS.UNITS] = 'molblock';
-  df.columns.add(col);
+  df.columns.add(col, true);
+
 }
 
 

package/src/tests/detectors-test.ts

@@ -104,6 +104,7 @@ MWRSWY-CKHP
     peptidesComplex = 'peptidesComplex',
     fastaCsv = 'fastaCsv',
     fastaFasta = 'fastaFasta',
+    fastaPtCsv = 'fastaPtCsv',
     msaComplex = 'msaComplex',
     helmCsv = 'helmCsv',
     testDemogCsv = 'testDemogCsv',
@@ -117,6 +118,7 @@ MWRSWY-CKHP
     'peptidesComplex': 'System:AppData/Bio/samples/peptides_complex_msa.csv',
     'fastaCsv': 'System:AppData/Bio/samples/sample_FASTA.csv',
     'fastaFasta': 'System:AppData/Bio/samples/sample_FASTA.fasta',
+    'fastaPtCsv': 'System:AppData/Bio/samples/sample_FASTA_PT.csv',
     'msaComplex': 'System:AppData/Bio/samples/sample_MSA.csv',
     'helmCsv': 'System:AppData/Bio/samples/sample_HELM.csv',
     'testDemogCsv': 'System:AppData/Bio/samples/testDemog.csv',
@@ -294,6 +296,10 @@ MWRSWY-CKHP
   test('samplesTestSmiles2NegativeSmiles', async () => {
     await _testNeg(readSamples(Samples.testSmiles2Csv), 'SMILES');
   });
+
+  test('samplesFastaPtPosSequence', async () => {
+    await (_testPos(readSamples(Samples.fastaPtCsv), 'sequence', 'fasta:SEQ:PT'));
+  });
 });
 
 export async function _testNeg(readDf: DfReaderFunc, colName: string) {

package/src/utils/cell-renderer.ts

@@ -1,32 +1,36 @@
-import * as C from "./constants";
+import * as C from './constants';
 import * as DG from 'datagrok-api/dg';
-import {AminoacidsPalettes} from "@datagrok-libraries/bio/src/aminoacids";
-import {NucleotidesPalettes} from "@datagrok-libraries/bio/src/nucleotides";
-import {UnknownSeqPalettes} from "@datagrok-libraries/bio/src/unknown";
-import {SplitterFunc, WebLogo} from "@datagrok-libraries/bio/src/viewers/web-logo";
-import {SeqPalette} from "@datagrok-libraries/bio/src/seq-palettes";
+import {AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';
+import {NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
+import {UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
+import {SplitterFunc, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 import * as ui from 'datagrok-api/ui';
 
 const lru = new DG.LruCache<any, any>();
-const undefinedColor =  'rgb(100,100,100)';
+const undefinedColor = 'rgb(100,100,100)';
 
-function getPalleteByType(paletteType: string): SeqPalette  {
+function getPalleteByType(paletteType: string): SeqPalette {
   switch (paletteType) {
-    case 'PT':
-      return  AminoacidsPalettes.GrokGroups;
-    case 'NT':
-      return  NucleotidesPalettes.Chromatogram
-      // other
-    default:
-      return UnknownSeqPalettes.Color;
+  case 'PT':
+    return AminoacidsPalettes.GrokGroups;
+  case 'NT':
+    return NucleotidesPalettes.Chromatogram;
+  case 'DNA':
+    return NucleotidesPalettes.Chromatogram;
+  case 'RNA':
+    return NucleotidesPalettes.Chromatogram;
+    // other
+  default:
+    return UnknownSeqPalettes.Color;
   }
 }
 
 export function processSequence(subParts: string[]): [string[], boolean] {
   const simplified = !subParts.some((amino, index) =>
-      amino.length > 1 &&
-      index != 0 &&
-      index != subParts.length - 1);
+    amino.length > 1 &&
+    index != 0 &&
+    index != subParts.length - 1);
 
   const text: string[] = [];
   const gap = simplified ? '' : ' ';
@@ -38,6 +42,7 @@ export function processSequence(subParts: string[]): [string[], boolean] {
   });
   return [text, simplified];
 }
+
 /**
  * A function that prints a string aligned to left or centered.
  *
@@ -55,10 +60,10 @@ export function processSequence(subParts: string[]): [string[], boolean] {
  * @return {number} x coordinate to start printing at.
  */
 function printLeftOrCentered(
-    x: number, y: number, w: number, h: number,
-    g: CanvasRenderingContext2D, s: string, color = undefinedColor,
-    pivot: number = 0, left = false, hideMod = false, transparencyRate: number = 1.0,
-    separator: string = '', last:boolean = false): number {
+  x: number, y: number, w: number, h: number,
+  g: CanvasRenderingContext2D, s: string, color = undefinedColor,
+  pivot: number = 0, left = false, hideMod = false, transparencyRate: number = 1.0,
+  separator: string = '', last: boolean = false): number {
   g.textAlign = 'start';
   let colorPart = s.substring(0);
   let grayPart = separator;
@@ -113,19 +118,19 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
    * @memberof AlignedSequenceCellRenderer
    */
   render(
-      g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
-      cellStyle: DG.GridCellStyle,
+    g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
+    cellStyle: DG.GridCellStyle,
   ): void {
     const grid = gridCell.grid;
     const cell = gridCell.cell;
     const tag = gridCell.cell.column.getTag(DG.TAGS.UNITS);
     if (tag === 'HELM') {
-      let host = ui.div([], { style: { width: `${w}px`, height: `${h}px`}});
+      let host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
       host.setAttribute('dataformat', 'helm');
       host.setAttribute('data', gridCell.cell.value);
       gridCell.element = host;
       //@ts-ignore
-      var canvas = new JSDraw2.Editor(host, { width: w, height: h, skin: "w8", viewonly: true });
+      var canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
       var formula = canvas.getFormula(true);
       if (!formula) {
         gridCell.element = ui.divText(gridCell.cell.value, {style: {color: 'red'}});
@@ -138,7 +143,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         lru.set(gridCell.cell.value, result);
       }
     } else {
-      const [type, subtype, paletteType] =  gridCell.cell.column.getTag(DG.TAGS.UNITS).split(":");
+      const [type, subtype, paletteType] = gridCell.cell.column.getTag(DG.TAGS.UNITS).split(':');
       w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
       g.save();
       g.beginPath();
@@ -154,9 +159,9 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       const palette = getPalleteByType(paletteType);
 
       const separator = gridCell.cell.column.getTag('separator') ?? '';
-      const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, gridCell.cell.column.getTag('separator') );// splitter,
+      const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, gridCell.cell.column.getTag('separator'));// splitter,
 
-      const subParts:string[] =  splitterFunc(cell.value);
+      const subParts: string[] = splitterFunc(cell.value);
       // console.log(subParts);
 
       const textSize = g.measureText(subParts.join(''));

package/{test-Bio-34f75e5127b8-95c6fae9.html → test-Bio-34f75e5127b8-7af21e5d.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 95c6fae9.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 7af21e5d.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 95c6fae9.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-12 11:55:44</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">112.789s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">100.002s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 7af21e5d.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-12 16:48:34</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">113.338s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">100.002s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
 Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long-running test."
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:22:1)
     at Runtime._execModule (/home/runner/work/public/public/packages/Bio/node_modules/jest-runtime/build/index.js:1646:24)