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Issue 80 (#84)
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* WIP

* WIP

* fixed examples and minor problem with SingleInputSelector
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@manulera
manulera authored Jan 31, 2024
1 parent 3d98f4f commit 46d1910
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138 changes: 138 additions & 0 deletions public/examples/ase1.gb
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LOCUS CU329670 4538 bp DNA UNK 01-JAN-1980
DEFINITION .
ACCESSION SPAPB1A10.09
VERSION SPAPB1A10.09
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
3'UTR 394..676
/systematic_id="SPAPB1A10.08"
/db_xref="PMID:21511999"
5'UTR 1001..1173
/systematic_id="SPAPB1A10.09"
/db_xref="PMID:30566651"
/feature_source="evidence=ECO:0000309; source=SO:0001238;
condition=FYECO:0000126; during=GO:0072690; score=146.757;
db_xref=PMID:30566651"
CDS join(1174..1597,1645..3416)
/colour="2"
/primary_name="ase1"
/product="antiparallel microtubule cross-linking factor
Ase1"
/systematic_id="SPAPB1A10.09"
/controlled_curation="term=modification, phosphorylated;
db_xref=PMID:19547744; evidence=IDA; cv=pt_mod;
date=20100606"
/controlled_curation="term=orthologous to S. cerevisiae
YOR058C; date=19700101"
/controlled_curation="term=species distribution, conserved
in eukaryotes; date=20081110"
/controlled_curation="term=species distribution, conserved
in metazoa; date=20081110"
/controlled_curation="term=species distribution, conserved
in vertebrates; date=20081110"
/controlled_curation="term=species distribution,
predominantly single copy (one to one); date=20081110"
/controlled_curation="term=species distribution, conserved
in fungi; date=20081110"
/controlled_curation="term=species distribution, conserved
in eukaryotes only; date=20081110"
/translation="MQTVMMDDIQSTDSIAEKDNHSNNESNFTWKAFREQVEKHFSKIE
RLHQVLGTDGDNSSLFELFTTAMNAQLHEMEQCQKKLEDDCQQRIDSIRFLVSSLKLTD
DTSSLKIESPLIQCLNRLSMVEGQYMAQYDQKLSTIKEMYHKLESYCNRLGSPFVLPDF
ENSFLSDVSDAFTESLRGRINEAEKEIDARLEVINSFEEEILGLWSELGVEPADVPQYE
QLLESHTNRPNDVYVTQELIDQLCKQKEVFSAEKEKRSDHLKSIQSEVSNLWNKLQVSP
NEQSQFGDSSNINQENISLWETELEKLHQLKKEHLPIFLEDCRQQILQLWDSLFYSEEQ
RKSFTPMYEDIITEQVLTAHENYIKQLEAEVSANKSFLSLINRYASLIEGKKELEASSN
DASRLTQRGRRDPGLLLREEKIRKRLSRELPKVQSLLIPEITAWEERNGRTFLFYDEPL
LKICQEATQPKSLYRSASAAANRPKTATTTDSVNRTPSQRGRVAVPSTPSVRSASRAMT
SPRTPLPRVKNTQNPSRSISAEPPSATSTANRRHPTANRIDINARLNSASRSRSANMIR
QGANGSDSNMSSSPVSGNSNTPFNKFPNSVSRNTHFESKSPHPNYSRTPHETYSKASSK
NVPLSPPKQRVVNEHALNIMSEKLQRTNLKEQTPEMDIENSSQNLPFSPMKISPIRASP
VKTIPSSPSPTTNIFSAPLNNITNCTPMEDEWGEEGF*"
3'UTR 3417..3538
/systematic_id="SPAPB1A10.09"
/db_xref="PMID:21511999"
3'UTR complement(3510..3690)
/systematic_id="SPAPB1A10.10c"
/db_xref="PMID:21511999"
ORIGIN
1 atcatcagac gtgtatttca caagccagaa gtgcatttgg atccaagtgc ctccatttta
61 aatctctcat cttcgcatgg cgaaagcaac ctgacaaatg gtttgctttg tcaaaatttc
121 aagctttttc aggatgattg gttgatggag gattgtgcgc cagatgccaa tttcactttg
181 tacaccccgc ttcaaccctg ggaaaagcga agtgtgaaac ctgaaatcag acgtcctcga
241 ttaaatccta attttttccg agtatttgtt ttagaagctc aaatgcgacg agctggaaag
301 ctatcagcaa acactgctgg ccgagcccag ttaatttacc tcccaaagcc tgccgttacc
361 ttctccacta gccctttgca tgttgaattg taaaaattta acgcatgact tatatacatt
421 tgcattcttc caagctggtt atatttattt tcattttttt ctcacccaat acttttttat
481 ccctactgtc tttatggaca atcgactcac aattgtttct ttttgttgta tatgattttt
541 tttttaaagg aaatgggttt cgcgatactg ggttgaatcc caattgcggt taatattaca
601 taaaataatt ctcccatagt cctagatcct gtctttgaat atgagcaaat aaaagaattg
661 aacaaatcat gaatgctttt ctctcttaga tgatattttg tatgcataag tctaattata
721 ttgattacga taagacttaa aaagtaagcc tttgtatcct tttaagcagt atttgaattt
781 tcttgtatca tattttaggt agagcaaaag ataccagttt gtagaacttt atgtgcttcc
841 ttacattggt atatttcagg cacataaata ttcttcaact tacaattcta agtattttgt
901 ttatactaaa aggagctgaa taacgtttat acagtgctga cattgaaatc tatttgcttt
961 ctttggaata taagcgcatg ctgagttact ttcgcaggcc aagccatatc caaccaccat
1021 ttttgtgcca agcttttatg caaggttaat tccttgtact gcttgttatg ttataatata
1081 tcaacatctt aacagttttc atatcttcct ttatattcta ttaattgaat ttcaaacatc
1141 gttttattga gctcatttac atcaaccggt tcaatgcaaa cagtaatgat ggatgacatt
1201 caaagcactg attctattgc tgaaaaagat aatcactcta ataatgaatc taactttact
1261 tggaaagcgt ttcgtgaaca agtggaaaag catttttcta aaattgaaag gcttcaccaa
1321 gtccttggaa cagatggaga caattcatca ttatttgagt tgtttacaac ggcaatgaat
1381 gcccagcttc atgaaatgga acagtgccag aaaaaacttg aagatgactg tcagcaaaga
1441 attgattcaa tcagattttt ggtttcctca ttaaagttaa cggatgatac ttctagtctc
1501 aaaattgagt ctcctttaat tcagtgtttg aatcgtttgt caatggtaga aggacaatat
1561 atggcacagt atgatcaaaa gttaagtacg attaaaggta tgtaatcgtc tttaatttag
1621 acttgtgttt taactgatgt atagaaatgt atcacaaatt ggagtcatat tgtaaccgct
1681 taggaagtcc gttcgtttta cctgattttg agaattcatt tttatctgat gtatccgatg
1741 cttttactga atctttgaga ggacgcatca acgaagccga aaaggagatt gatgcgagat
1801 tagaggttat taattccttt gaagaagaaa ttttgggttt gtggtctgaa ctcggtgttg
1861 agcccgctga tgttccacaa tacgaacaat tgcttgaatc ccatactaat cgaccaaatg
1921 atgtttatgt tactcaagaa cttatcgacc aactttgcaa gcaaaaagaa gttttttccg
1981 ctgaaaaaga aaagagaagt gatcatttaa aaagtataca atcagaagtt agcaacttgt
2041 ggaataagct tcaagtttct cccaatgaac aaagtcaatt tggcgattca tcaaacatta
2101 atcaagaaaa tatttcatta tgggaaactg aacttgaaaa acttcatcag ttaaaaaagg
2161 agcatttacc cattttttta gaagactgtc gtcaacaaat tcttcagctt tgggattctc
2221 tgttttattc agaagaacaa agaaagtcct ttacacctat gtatgaagac attattacag
2281 agcaggttct tacggcccat gaaaactata taaagcaact agaggccgaa gtttctgcta
2341 ataagtcctt tttaagctta attaatcgct atgcctcttt aatagaagga aagaaagagc
2401 ttgaagctag ttctaatgat gcctctcgtc taacacaacg gggacgccgg gacccaggtt
2461 tacttctacg tgaagagaaa atccgtaagc gactttctag agaacttcct aaggttcagt
2521 cgctgcttat accagagatt acagcatggg aagaaagaaa tggaaggacg ttcctttttt
2581 atgatgaacc acttctcaag atttgccaag aggccactca accaaaatca ttatatagaa
2641 gtgcaagtgc tgccgcaaac cgcccgaaaa cagcaactac aacggactct gttaatagaa
2701 caccttctca acgagggcgt gtagctgtac cttcaacacc aagtgttagg tccgcttctc
2761 gagctatgac gagtccaagg acaccgcttc ctagagtaaa aaacactcaa aatccaagtc
2821 gttccattag tgcagaaccg ccatcagcaa ccagtaccgc caatagaaga caccccactg
2881 ctaatcgaat tgatataaac gctagattaa acagtgctag tcggtctcga agcgcgaaca
2941 tgataagaca aggggcaaat ggtagtgaca gcaatatgtc ttcttcaccc gtttctggaa
3001 attccaatac cccttttaac aagtttccaa attctgtatc tcgcaataca cattttgaat
3061 ccaagtcacc gcacccaaat tactctcgaa ctcctcatga aacgtattca aaggcttcat
3121 ctaagaacgt cccattaagt cctccaaagc agcgtgtagt taatgaacac gctttaaata
3181 ttatgtcgga aaaattgcaa agaactaatc tgaaagaaca aacacccgag atggacattg
3241 aaaacagctc gcagaacctt cctttttctc ctatgaagat atcccccata agagcatcac
3301 ccgtaaagac aattccatca tcaccgtccc ccactaccaa cattttttct gctccactca
3361 acaatattac aaattgtaca ccgatggagg atgaatgggg agaagaaggc ttttaagctt
3421 cttatttacc taatcgatca aatttaaata tacatatttt tgcatatgaa tacagcatat
3481 agataattca taaaagttta ttaactgagg tcataattaa aagactattt acacctaaaa
3541 aaaaacgtgt atcaatagag ggaaaagaga agaattaaga acagaaagta accatagttt
3601 tgttaaaata gcaatgtaaa aaaatattat gaaaagaaaa cgtatagcac attttgaaat
3661 gtaaaagaat ctgagagagc gtgtgaatat ctagcaatta caagaagatg tattattcaa
3721 aggctttgaa agaagcaaag gttcagagaa gtcattaaca aagtcatctc tcgagctttc
3781 attttctaaa gctaaacgac tgactgtttc gaaaaggtca gtaacgtttg tattttcttt
3841 tgcactagct tcaaaatgaa tcatatttga tccatgtttg gatttgcaat agtcaagagc
3901 tcgatgaaga gatacggctc gtttagacgc gtctttgtcg atttgatttc caacgataat
3961 gaaagggaat gcacattcat cttgtgaagt ttgatataaa aattcttgcc tccagttttc
4021 tactgagtca aaagacttcg agttattcac attataaaca attacacaac aatcggcccc
4081 tctgtaaaaa gccattccca ggctttgaaa tcgttcttga ccagcagtat cccaaagctg
4141 tttataatta gcaaacgaat ttagatgggc ggaacttata ttggaactta cctgtaatgt
4201 gaccaatttg tcgtcaacca caacgtcctt ggttaaaaaa tcagcaccga tggtagcttt
4261 atattcgcga ctaaactttt gattgacgaa ctaaaatgac gatgttaaca aattgccaaa
4321 gcaatactca tagagaagct gatgtaaaga tcgttaacca tatttgagct agtatttaat
4381 aacaaagtga ataaatttta aaagcaatca ccttgtagcg acaaataaca acttatcgac
4441 ataaaatcaa tgggaaattg cagtattgga ttttacagct caatacaaaa accaaaaaga
4501 aaaatatact gaacgtataa aatttaacgc ttcaattg
//
33 changes: 32 additions & 1 deletion public/examples/gibson_assembly.json
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{"sequences":[{"id":3,"kind":"entity","sequence":{"type":"file","file_extension":"gb","file_content":"LOCUS first 21 bp DNA linear UNK 01-JAN-1980\nDEFINITION first.\nACCESSION first\nVERSION first\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nFEATURES Location/Qualifiers\nORIGIN\n 1 ttttacgata atgctccccc c\n//","overhang_crick_3prime":0,"overhang_watson_3prime":0}},{"id":5,"kind":"entity","sequence":{"type":"file","file_extension":"gb","file_content":"LOCUS second 12 bp DNA linear UNK 01-JAN-1980\nDEFINITION second.\nACCESSION second\nVERSION second\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nFEATURES Location/Qualifiers\nORIGIN\n 1 cccctcatgg gg\n//","overhang_crick_3prime":0,"overhang_watson_3prime":0}},{"id":7,"kind":"entity","sequence":{"type":"file","file_extension":"gb","file_content":"LOCUS third 13 bp DNA linear UNK 01-JAN-1980\nDEFINITION third.\nACCESSION third\nVERSION third\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nFEATURES Location/Qualifiers\nORIGIN\n 1 ggggatatat ttt\n//","overhang_crick_3prime":0,"overhang_watson_3prime":0}},{"id":9,"kind":"entity","sequence":{"type":"file","file_extension":"gb","file_content":"LOCUS name 38 bp DNA linear UNK 01-JAN-1980\nDEFINITION description.\nACCESSION id\nVERSION id\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nFEATURES Location/Qualifiers\nORIGIN\n 1 cccctcatgg ggggagcatt atcgtaaaat atatcccc\n//","overhang_crick_3prime":0,"overhang_watson_3prime":0}}],"sources":[{"id":1,"input":[],"output":3,"type":"file","kind":"source","info":{},"file_name":"gibson_assembly_fragments.fasta","file_format":"fasta","index_in_file":0},{"id":4,"input":[],"output":5,"type":"file","kind":"source","info":{},"file_name":"gibson_assembly_fragments.fasta","file_format":"fasta","index_in_file":1},{"id":6,"input":[],"output":7,"type":"file","kind":"source","info":{},"file_name":"gibson_assembly_fragments.fasta","file_format":"fasta","index_in_file":2},{"id":8,"input":[3,5,7],"output":9,"type":"gibson_assembly","kind":"source","info":{},"assembly":[[2,-1,"complement(9..12)","complement(1..4)"],[-1,-3,"complement(18..21)","complement(1..4)"]],"circular":false}],"description":"","primers":[{"id":1,"name":"fwd","sequence":"gatctcgccataaaagacag"},{"id":2,"name":"rvs","sequence":"ttaacaaagcgactataagt"}]}
{
"sequences": [
{ "id": 3, "kind": "entity", "sequence": { "type": "file", "file_extension": "gb", "file_content": "LOCUS first 21 bp DNA linear UNK 01-JAN-1980\nDEFINITION first.\nACCESSION first\nVERSION first\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nFEATURES Location/Qualifiers\nORIGIN\n 1 ttttacgata atgctccccc c\n//", "overhang_crick_3prime": 0, "overhang_watson_3prime": 0 } },
{ "id": 5, "kind": "entity", "sequence": { "type": "file", "file_extension": "gb", "file_content": "LOCUS second 12 bp DNA linear UNK 01-JAN-1980\nDEFINITION second.\nACCESSION second\nVERSION second\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nFEATURES Location/Qualifiers\nORIGIN\n 1 cccctcatgg gg\n//", "overhang_crick_3prime": 0, "overhang_watson_3prime": 0 } },
{ "id": 7, "kind": "entity", "sequence": { "type": "file", "file_extension": "gb", "file_content": "LOCUS third 13 bp DNA linear UNK 01-JAN-1980\nDEFINITION third.\nACCESSION third\nVERSION third\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nFEATURES Location/Qualifiers\nORIGIN\n 1 ggggatatat ttt\n//", "overhang_crick_3prime": 0, "overhang_watson_3prime": 0 } },
{ "id": 12, "kind": "entity", "sequence": { "type": "file", "file_extension": "gb", "file_content": "LOCUS name 34 bp DNA circular UNK 01-JAN-1980\nDEFINITION description.\nACCESSION id\nVERSION id\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nFEATURES Location/Qualifiers\nORIGIN\n 1 ttttacgata atgctccccc ctcatgggga tata\n//", "overhang_crick_3prime": 0, "overhang_watson_3prime": 0 } }
],
"sources": [
{ "id": 1, "input": [], "output": 3, "type": "file", "kind": "source", "info": {}, "file_name": "gibson_assembly_fragments.fasta", "file_format": "fasta", "index_in_file": 0 },
{ "id": 4, "input": [], "output": 5, "type": "file", "kind": "source", "info": {}, "file_name": "gibson_assembly_fragments.fasta", "file_format": "fasta", "index_in_file": 1 },
{ "id": 6, "input": [], "output": 7, "type": "file", "kind": "source", "info": {}, "file_name": "gibson_assembly_fragments.fasta", "file_format": "fasta", "index_in_file": 2 },
{
"id": 11,
"input": [3, 5, 7],
"output": 12,
"type": "gibson_assembly",
"kind": "source",
"info": {},
"assembly": [
[1, 2, "18..21", "1..4"],
[2, 3, "9..12", "1..4"],
[3, 1, "10..13", "1..4"]
],
"circular": true
}
],
"description": "",
"primers": [
{ "id": 1, "name": "fwd", "sequence": "gatctcgccataaaagacag" },
{ "id": 2, "name": "rvs", "sequence": "ttaacaaagcgactataagt" }
]
}
36 changes: 36 additions & 0 deletions public/examples/golden_gate.json
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{
"sequences": [
{ "id": 3, "kind": "entity", "sequence": { "type": "file", "file_extension": "gb", "file_content": "LOCUS pj5_00001 27 bp DNA linear SYN 15-JAN-2024\nDEFINITION .\nACCESSION pj5_00001\nVERSION pj5_00001\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nCOMMENT teselagen_unique_id: 5adf735aa1811801e17d8aac\nFEATURES Location/Qualifiers\n misc_feature 10..17\n /label=\"A\"\nORIGIN\n 1 ggtctcaatt aaaaaattaa agagacc\n//", "overhang_crick_3prime": 0, "overhang_watson_3prime": 0 } },
{ "id": 5, "kind": "entity", "sequence": { "type": "file", "file_extension": "gb", "file_content": "LOCUS pj5_00001 27 bp DNA linear SYN 15-JAN-2024\nDEFINITION .\nACCESSION pj5_00001\nVERSION pj5_00001\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nCOMMENT teselagen_unique_id: 5adf735aa1811801e17d8aac\nFEATURES Location/Qualifiers\n misc_feature complement(10..17)\n /label=\"B\"\nORIGIN\n 1 ggtctcatta acccccatat agagacc\n//", "overhang_crick_3prime": 0, "overhang_watson_3prime": 0 } },
{ "id": 7, "kind": "entity", "sequence": { "type": "file", "file_extension": "gb", "file_content": "LOCUS pj5_00001 27 bp DNA linear SYN 15-JAN-2024\nDEFINITION .\nACCESSION pj5_00001\nVERSION pj5_00001\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nCOMMENT teselagen_unique_id: 5adf735aa1811801e17d8aac\nFEATURES Location/Qualifiers\n misc_feature 10..17\n /label=\"C\"\nORIGIN\n 1 ggtctcaata tgggggccgg agagacc\n//", "overhang_crick_3prime": 0, "overhang_watson_3prime": 0 } },
{ "id": 15, "kind": "entity", "sequence": { "type": "file", "file_extension": "gb", "file_content": "LOCUS pj5_00001 35 bp DNA circular SYN 15-JAN-2024\nDEFINITION .\nACCESSION pj5_00001\nVERSION pj5_00001\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nCOMMENT teselagen_unique_id: 5adf735aa1811801e17d8aac\nFEATURES Location/Qualifiers\n misc_feature 11..25\n /label=\"VectorOUT\"\n misc_feature 32..36\n /label=\"VectorIN\"\nORIGIN\n 1 ttttattaag agaccttttt ggtctcaccg gtttt\n//", "overhang_crick_3prime": 0, "overhang_watson_3prime": 0 } },
{ "id": 19, "kind": "entity", "sequence": { "type": "file", "file_extension": "gb", "file_content": "LOCUS name 39 bp DNA circular UNK 01-JAN-1980\nDEFINITION description.\nACCESSION id\nVERSION id\nKEYWORDS .\nSOURCE .\n ORGANISM .\n .\nFEATURES Location/Qualifiers\n misc_feature 3..10\n /label=\"A\"\n misc_feature complement(12..19)\n /label=\"B\"\n misc_feature 21..28\n /label=\"C\"\n misc_feature 32..36\n /label=\"VectorIN\"\nORIGIN\n 1 attaaaaaat taacccccat atgggggccg gtttttttt\n//", "overhang_crick_3prime": 0, "overhang_watson_3prime": 0 } }
],
"sources": [
{ "id": 1, "input": [], "output": 3, "type": "file", "kind": "source", "info": {}, "file_name": "golden_gate.gb", "file_format": "genbank", "index_in_file": 0 },
{ "id": 4, "input": [], "output": 5, "type": "file", "kind": "source", "info": {}, "file_name": "golden_gate.gb", "file_format": "genbank", "index_in_file": 1 },
{ "id": 6, "input": [], "output": 7, "type": "file", "kind": "source", "info": {}, "file_name": "golden_gate.gb", "file_format": "genbank", "index_in_file": 2 },
{ "id": 14, "input": [], "output": 15, "type": "file", "kind": "source", "info": {}, "file_name": "golden_gate.gb", "file_format": "genbank", "index_in_file": 3 },
{
"id": 18,
"input": [3, 5, 7, 15],
"output": 19,
"type": "restriction_and_ligation",
"kind": "source",
"info": {},
"assembly": [
[1, 2, "17..20", "8..11"],
[2, 3, "17..20", "8..11"],
[3, 4, "17..20", "28..31"],
[4, 1, "5..8", "8..11"]
],
"circular": true,
"restriction_enzymes": ["BsaI"]
}
],
"description": "",
"primers": [
{ "id": 1, "name": "fwd", "sequence": "gatctcgccataaaagacag" },
{ "id": 2, "name": "rvs", "sequence": "ttaacaaagcgactataagt" }
]
}
60 changes: 59 additions & 1 deletion public/examples/history.json
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56 changes: 55 additions & 1 deletion public/examples/homologous_recombination.json
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