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Running on Zero
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62a01bd a9bb355 62a01bd a9bb355 62a01bd a9bb355 62a01bd a9bb355 62a01bd | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 | """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
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