examples.py

"""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