| """Built-in example sequences for the LLPSense demo. |
| |
| Shared by app.py (UI + on-the-fly extraction fallback) and |
| preprocess/extract_example_feat.py (offline pre-computation), so both stay |
| in sync on which sequences have a cached ProtT5 feature under assets/. |
| |
| To add another example, just append a dict with a unique "id" here, then |
| run `python preprocess/extract_example_feat.py` to populate its cached |
| feature in assets/ before deploying. |
| """ |
|
|
| from pathlib import Path |
|
|
| ASSETS_DIR = Path(__file__).parent / "assets" |
|
|
| EXAMPLES = [ |
| { |
| "id": "synuclein", |
| "name": "α-Synuclein", |
| "seq": ( |
| "MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTK" |
| "EQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDP" |
| "DNEAYEMPSEEGYQDYEPEA" |
| ), |
| }, |
| { |
| "id": "ubqln4", |
| "name": "UBQLN4", |
| "seq": ( |
| "MAEPSGAETRPPIRVTVKTPKDKEEIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKI" |
| "LKDGDTLNQHGIKDGLTVHLVIKTPQKAQDPAAATASSPSTPDPASAPSTTPASPATPAQ" |
| "PSTSGSASSDAGSGSRRSSGGGPSPGAGEGSPSATASILSGFGGILGLGSLGLGSANFME" |
| "LQQQMQRQLMSNPEMLSQIMENPLVQDMMSNPDLMRHMIMANPQMQQLMERNPEISHMLN" |
| "NPELMRQTMELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQEPMFSAAREQ" |
| "FGNNPFSSLAGNSDSSSSQPLRTENREPLPNPWSPSPPTSQAPGSGGEGTGGSGTSQVHP" |
| "TVSNPFGINAASLGSGMFNSPEMQALLQQISENPQLMQNVISAPYMRSMMQTLAQNPDFA" |
| "AQMMVNVPLFAGNPQLQEQLRLQLPVFLQQMQNPESLSILTNPRAMQALLQIQQGLQTLQ" |
| "TEAPGLVPSLGSFGISRTPAPSAGSNAGSTPEAPTSSPATPATSSPTGASSAQQQLMQQM" |
| "IQLLAGSGNSQVQTPEVRFQQQLEQLNSMGFINREANLQALIATGGDINAAIERLLGSQL" |
| "S" |
| ), |
| }, |
| { |
| "id": 'ascl1', |
| "name": 'ASCL1', |
| "seq": ( |
| "MESSAKMESGGAGQQPQPQPQQPFLPPAACFFATAAAAAAAAAAAAAQSAQQQQQQQQQQ" |
| "QQAPQLRPAADGQPSGGGHKSAPKQVKRQRSSSPELMRCKRRLNFSGFGYSLPQQQPAAV" |
| "ARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDAV" |
| "SAAFQAGVLSPTISPNYSNDLNSMAGSPVSSYSSDEGSYDPLSPEEQELLDFTNWF" |
| ), |
| }, |
| { |
| "id": 'atn1', |
| "name": 'ATN1', |
| "seq": ( |
| "MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTAKKARVE" |
| "EASTPKVNKQGRSEEISESESEETNAPKKTKTEQELPRPQSPSDLDSLDGRSLNDDGSSD" |
| "PRDIDQDNRSTSPSIYSPGSVENDSDSSSGLSQGPARPYHPPPLFPPSPQPPDSTPRQPE" |
| "ASFEPHPSVTPTGYHAPMEPPTSRMFQAPPGAPPPHPQLYPGGTGGVLSGPPMGPKGGGA" |
| "ASSVGGPNGGKQHPPPTTPISVSSSGASGAPPTKPPTTPVGGGNLPSAPPPANFPHVTPN" |
| "LPPPPALRPLNNASASPPGLGAQPLPGHLPSPHAMGQGMGGLPPGPEKGPTLAPSPHSLP" |
| "PASSSAPAPPMRFPYSSSSSSSAAASSSSSSSSSSASPFPASQALPSYPHSFPPPTSLSV" |
| "SNQPPKYTQPSLPSQAVWSQGPPPPPPYGRLLANSNAHPGPFPPSTGAQSTAHPPVSTHH" |
| "HHHQQQQQQQQQQQQQQQQQQQHHGNSGPPPPGAFPHPLEGGSSHHAHPYAMSPSLGSLR" |
| "PYPPGPAHLPPPHSQVSYSQAGPNGPPVSSSSNSSSSTSQGSYPCSHPSPSQGPQGAPYP" |
| "FPPVPTVTTSSATLSTVIATVASSPAGYKTASPPGPPPYGKRAPSPGAYKTATPPGYKPG" |
| "SPPSFRTGTPPGYRGTSPPAGPGTFKPGSPTVGPGPLPPAGPSGLPSLPPPPAAPASGPP" |
| "LSATQIKQEPAEEYETPESPVPPARSPSPPPKVVDVPSHASQSARFNKHLDRGFNSCARS" |
| "DLYFVPLEGSKLAKKRADLVEKVRREAEQRAREEKEREREREREKEREREKERELERSVK" |
| "LAQEGRAPVECPSLGPVPHRPPFEPGSAVATVPPYLGPDTPALRTLSEYARPHVMSPGNR" |
| "NHPFYVPLGAVDPGLLGYNVPALYSSDPAAREREREARERDLRDRLKPGFEVKPSELEPL" |
| "HGVPGPGLDPFPRHGGLALQPGPPGLHPFPFHPSLGPLERERLALAAGPALRPDMSYAER" |
| "LAAERQHAERVAALGNDPLARLQMLNVTPHHHQHSHIHSHLHLHQQDAIHAASASVHPLI" |
| "DPLASGSHLTRIPYPAGTLPNPLLPHPLHENEVLRHQLFAAPYRDLPASLSAPMSAAHQL" |
| "QAMHAQSAELQRLALEQQQWLHAHHPLHSVPLPAQEDYYSHLKKESDKPL" |
| ), |
| }, |
| { |
| "id": 'fbll1', |
| "name": 'FBLL1', |
| "seq": ( |
| "MKSAASSRGGGGGGRGGGGWGSWGGGRGGGGGAGKGGGGDGGGQGGKGGFGARARGFGGG" |
| "GRGRGRGGGDGKDRGGGGQRRGGVAKSKSRRRKGAMVVSVEPHRHEGVFIYRGAEDALVT" |
| "LNMVPGQSVYGERRVTVTEGGVKQEYRTWNPFRSKLAAAILGGVDQIHIKPKSKVLYLGA" |
| "ASGTTVSHVSDIIGPDGLVYAVEFSHRAGRDLVNVAKKRTNIIPVLEDARHPLKYRMLIG" |
| "MVDVIFADVAQPDQSRIVALNAHTFLRNGGHFLISIKANCIDSTASAEAVFASEVRKLQQ" |
| "ENLKPQEQLTLEPYERDHAVVVGVYRPLPKSSSK" |
| ), |
| }, |
| { |
| "id": 'foxp2', |
| "name": 'FOXP2', |
| "seq": ( |
| "MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA" |
| "ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVITPQQMQQILQQQVLSPQQLQA" |
| "LLQQQQAVMLQQQQLQEFYKKQQEQLHLQLLQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ" |
| "QQQQQQQQQQQHPGKQAKEQQQQQQQQQQLAAQQLVFQQQLLQMQQLQQQQHLLSLQRQG" |
| "LISIPPGQAALPVQSLPQAGLSPAEIQQLWKEVTGVHSMEDNGIKHGGLDLTTNNSSSTT" |
| "SSNTSKASPPITHHSIVNGQSSVLSARRDSSSHEETGASHTLYGHGVCKWPGCESICEDF" |
| "GQFLKHLNNEHALDDRSTAQCRVQMQVVQQLEIQLSKERERLQAMMTHLHMRPSEPKPSP" |
| "KPLNLVSSVTMSKNMLETSPQSLPQTPTTPTAPVTPITQGPSVITPASVPNVGAIRRRHS" |
| "DKYNIPMSSEIAPNYEFYKNADVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFAY" |
| "FRRNAATWKNAVRHNLSLHKCFVRVENVKGAVWTVDEVEYQKRRSQKITGSPTLVKNIPT" |
| "SLGYGAALNASLQAALAESSLPLLSNPGLINNASSGLLQAVHEDLNGSLDHIDSNGNSSP" |
| "GCSPQPHIHSIHVKEEPVIAEDEDCPMSLVTTANHSPELEDDREIEEEPLSEDLE" |
| ), |
| }, |
| { |
| "id": 'semg2', |
| "name": 'SEMG2', |
| "seq": ( |
| "MKSIILFVLSLLLILEKQAAVMGQKGGSKGQLPSGSSQFPHGQKGQHYFGQKDQQHTKSK" |
| "GSFSIQHTYHVDINDHDWTRKSQQYDLNALHKATKSKQHLGGSQQLLNYKQEGRDHDKSK" |
| "GHFHMIVIHHKGGQAHHGTQNPSQDQGNSPSGKGLSSQCSNTEKRLWVHGLSKEQASASG" |
| "AQKGRTQGGSQSSYVLQTEELVVNKQQRETKNSHQNKGHYQNVVDVREEHSSKLQTSLHP" |
| "AHQDRLQHGPKDIFTTQDELLVYNKNQHQTKNLSQDQEHGRKAHKISYPSSRTEERQLHH" |
| "GEKSVQKDVSKGSISIQTEEKIHGKSQNQVTIHSQDQEHGHKENKISYQSSSTEERHLNC" |
| "GEKGIQKGVSKGSISIQTEEQIHGKSQNQVRIPSQAQEYGHKENKISYQSSSTEERRLNS" |
| "GEKDVQKGVSKGSISIQTEEKIHGKSQNQVTIPSQDQEHGHKENKMSYQSSSTEERRLNY" |
| "GGKSTQKDVSQSSISFQIEKLVEGKSQIQTPNPNQDQWSGQNAKGKSGQSADSKQDLLSH" |
| "EQKGRYKQESSESHNIVITEHEVAQDDHLTQQYNEDRNPIST" |
| ), |
| }, |
| { |
| "id": 'sgta', |
| "name": 'SGTA', |
| "seq": ( |
| "MDNKKRLAYAIIQFLHDQLRHGGLSSDAQESLEVAIQCLETAFGVTVEDSDLALPQTLPE" |
| "IFEAAATGKEMPQDLRSPARTPPSEEDSAEAERLKTEGNEQMKVENFEAAVHFYGKAIEL" |
| "NPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLALSSLNKHVEAVA" |
| "YYKKALELDPDNETYKSNLKIAELKLREAPSPTGGVGSFDIAGLLNNPGFMSMASNLMNN" |
| "PQIQQLMSGMISGGNNPLGTPGTSPSQNDLASLIQAGQQFAQQMQQQNPELIEQLRSQIR" |
| "SRTPSASNDDQQE" |
| ), |
| }, |
| { |
| "id": 'ss18', |
| "name": 'SS18', |
| "seq": ( |
| "MSVAFAAPRQRGKGEITPAAIQKMLDDNNHLIQCIMDSQNKGKTSECSQYQQMLHTNLVY" |
| "LATIADSNQNMQSLLPAPPTQNMPMGPGGMNQSGPPPPPRSHNMPSDGMVGGGPPAPHMQ" |
| "NQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQSMPVQNQMT" |
| "MSQGQPMGNYGPRPNMSMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQ" |
| "GNHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDGHNDYGY" |
| "QQPSYPEQGYDRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPG" |
| "QQQGYGPSQGGPGPQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQGQYGNYQQ" |
| ), |
| }, |
| { |
| "id": 'ubqln4_mut10', |
| "name": 'UBQLN4-mut10', |
| "seq": ( |
| "MAEPSGAETRPPIRVTVKTPKDKEEIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKI" |
| "LKDGDTLNQHGIKDGLTVHLVIKTPQKAQDPAAATASSPSTPDPASAPSTTPASPATPAQ" |
| "PSTSGSASSDAGSGSRRSSGGGPSPGAGEGSPSATASILSGFGGILGLGSLGLGSANFME" |
| "LQQQMQRQLMSNPEMLSQICENPLVQDMMSNPDLMRHCCMANPQYQQLCERNPEISHMLN" |
| "NPELMRQTMELARNPAMMQEMMRNQDRALSNCESIPGGYNALRRMYTDIQEPMFSAAREQ" |
| "FGNNPFSSLAGNSDSSSSQPLRTENREPLPNPWSPSPPTSQAPGSGGEGTGGSGTSQVHP" |
| "TVSNPFGINAASLGSGMCNSPEMQALLQQISENCQLMQNVISAPYMRSMMQTLAQNPDFA" |
| "AQMMVNVPLFAGNPQLQEQLRLQLPVFLQQCQNPESLSILTNPRAMQALLQIQQGLQTLQ" |
| "TEAPGLVPSLGSFGISRTPAPSAGSNAGSTPEAPTSSPATPATSSPTGASSAQQQLMQQM" |
| "IQLLAGSGNSQVQTPEVRFQQQLEQLNSCGFINREANLQALIATGGDINAAIERLLGSQL" |
| "S" |
| ), |
| }, |
| { |
| "id": 'ubqln4_mut20', |
| "name": 'UBQLN4-mut20', |
| "seq": ( |
| "MAEPSGAETNPNIRVTVKTPKDKEEIVICDIASVKEFKEEISRRFKAQQDQLVLIFAGKD" |
| "LKDGDTLNQHGIKDGETYHLVIKTPQKAQDPAAATASSPSTPDPASAPSTTPASPATPAQ" |
| "PSTSGSASSDAGSGSRRSSGGGPSPGAGEGSPSATASILSGFGGILGLGSLGLGSANFME" |
| "LQQQMQRQLMSNPEMLSQICENPLVQDMMSNPDLMRHCCMANPQYQQLCERNPEISHMLN" |
| "NPELMRQTMELARNPAMMQEMMRNQDRALSNCESIPGGYNALRRMYTDIQEPMFSAAREQ" |
| "FGNNPDSSLAGNSDSSSSQPLRTENREPLPNPWSPSPPTSQAPGSGGEGTGGSGTSQVHP" |
| "TVSNPFGINAASLGSGMCNSPEMQALLQQISENCQLMQNVISAPKMRSMMQTLAQNPDFA" |
| "AQMMVNVPLFAGNPQLQEQLRLQLPVFLQQCQNPESLSIDTNPRAMQALLQIQQGLQTLQ" |
| "TEAPGLVPSLGSFGISRTPAPSAGSNAGSTPEAPTSSPATPATSSPTGASSAQQQLKQQM" |
| "IQLLAGSGNSQVQTPEVRFQQQLEQLNSCGFINREANLQALIATGGDINAAIERLLGSQL" |
| "S" |
| ), |
| }, |
| { |
| "id": 'ubqln4_mut30', |
| "name": 'UBQLN4-mut30', |
| "seq": ( |
| "MAEPSGAETNPNIRVTVKTPKDKEEIVICDIASVKEFKEEISRRFKAQQDQLVLIFAGKD" |
| "DKDGDTDNQHGIKDGETYHLVIKTPQKAQDPAAATASSPSTPDPASAPSTTPASPATPAQ" |
| "PSTSGSASSDAGSGSRRSSGGGPSPGAGEGSPSATASILSGFGGILGLGSLGLGSANFME" |
| "LQQQMQRQLMSNPEMLSQPCENLLVQDMMSNPDLMRHCCMANPQYQQLCERNPEISHMLN" |
| "NPELMRQPMELARNPAMMQEMMRNQDRALSNCESIPGGYNADRRDYTDIQEPMFSAAREQ" |
| "FGNNPDSSLAGNSDSSSSQPLRTENREPLPNPWSPSPPTSQAPGSGGEGTGGSGTSQVHP" |
| "TVSNPFGINAASLGSGMCNSPEMQALLQQISENCQLMQNVISAPKMRSMMQTLAQNPDFA" |
| "AQMMVNVPLFAGNPQLQEQLRLQLPVFLQQCQNPESLSIDTNPRAMQALLQIQQGLQTLQ" |
| "TEAPGLVPSLGSFGISRTPAPSAGSNAGSTPEAPTSSPATPATSSPTGASSAQQQLKQQM" |
| "IQLLAGSGNSQVQTPEVRFQQQLEQLNSCGPINREANLQALPATGGDINADIERLLGSQL" |
| "S" |
| ), |
| }, |
| ] |
|
|
|
|
| def feature_path(example_id: str) -> Path: |
| return ASSETS_DIR / f"{example_id}.h5" |
|
|
|
|
| def find_example_by_seq(seq: str): |
| """Return the EXAMPLES entry whose sequence matches `seq`, or None.""" |
| norm = seq.strip().upper() |
| for example in EXAMPLES: |
| if example["seq"].strip().upper() == norm: |
| return example |
| return None |
|
|
