Merge pull request #39 from PeptoneLtd/dev

Dev

.gitignore

@@ -30,7 +30,7 @@ Network Trash Folder
 Temporary Items
 .apdisk
 
-# Jupyter chekcpoints & pycache
+# Jupyter checkpoints & pycache
 .ipynb_checkpoints
 __pycache__
 *.pyc
@@ -44,6 +44,12 @@ __pycache__
 # End of https://www.toptal.com/developers/gitignore/api/macos
 *.html
 
+# pytorch files
+*.pt
+
+# onnx files
+*.onnx
+
 .adopt-venv
 .vscode
 build/

Dockerfiles/Dockerfile_adopt_mac_m1

@@ -0,0 +1,18 @@
+FROM sonoisa/deep-learning-coding:pytorch1.12.0_tensorflow2.9.1
+RUN pip install \
+  pandas \
+  fair-esm \
+  biopython \
+  bertviz \
+  skl2onnx \
+  onnxruntime \
+  spacy \
+  plotly \
+  wandb \
+  jupyterlab
+RUN git clone --recurse-submodules https://github.com/PeptoneLtd/ADOPT.git \
+  && cd ADOPT \
+  && python setup.py install \
+  && cd ../
+RUN pip install tables
+

README.md

@@ -80,8 +80,8 @@ MODEL_TYPE = "esm-1b"
 STRATEGY = "train_on_cleared_1325_test_on_117_residue_split"
 
 # Extract residue level representations
-multi_head = MultiHead(MODEL_TYPE, SEQUENCE, PROTID)
-representation, tokens = multi_head.get_representation()
+multi_head = MultiHead(MODEL_TYPE)
+representation, tokens = multi_head.get_representation(SEQUENCE, PROTID)
 
 # Predict the Z score related to each residue in the sequence specified above
 z_score_pred = ZScorePred(STRATEGY, MODEL_TYPE)

adopt/__init__.py

@@ -4,7 +4,7 @@
 # LICENSE file in the root directory of this source tree.
 
 "@generated"
-from . import constants, utils
+from . import constants, utils, inference, embedding
 from .data import CheZod
 from .inference import ZScorePred
 from .training import DisorderPred

adopt/embedding.py

@@ -6,6 +6,7 @@
 import argparse
 import subprocess
 from pathlib import Path
+import time
 
 from adopt import constants, utils
 
@@ -66,3 +67,5 @@ def get_representations(fasta_file, repr_dir, msa):
     parser = create_parser()
     args = parser.parse_args()
     get_representations(args.fasta_path, args.repr_dir, args.msa)
+    print("--- %s seconds ---" % (time.time() - start_time))
+

adopt/inference.py

@@ -8,6 +8,7 @@
 import sys
 import subprocess
 from pathlib import Path
+import time
 
 import numpy as np
 import pandas as pd
@@ -164,6 +165,7 @@ def main(args):
         )
         sys.exit(2)
 
+start_time = time.time()
 
 if __name__ == "__main__":
     parser = create_parser()
@@ -173,3 +175,4 @@ def main(args):
     z_score_pred.get_z_score_from_fasta(
         args.fasta_path, args.repr_dir, args.pred_z_scores_path
     )
+    print("--- %s seconds ---" % (time.time() - start_time))

adopt/transformer.py

@@ -43,21 +43,34 @@ def get_attention(self, sequence, brmid):
         return attention, tokens
 
     def get_representation(self, sequence, brmid):
-        results = self.get_results(sequence, brmid)
-
-        if self.model_type in constants.model_types:
-            representation = results[0]["representations"][33]
-        elif self.model_type == 'esm-msa':
-            representation = results[0]["representations"][12][0]
-        elif self.model_type == "combined":
-            representation = torch.cat(
-                (results[0]["representations"][33], results[1]["representations"][33]), -1)
+
+        max_len = 1000
+        if len(sequence) < max_len:
+            print("Extracting representations.")
         else:
-            print("The model types are:")
-            print(*constants.msa_model_types, sep="\n")
-            sys.exit(2)
+            print("Protein sequence longer than context window!")
+            print("Applying sliding windows.")
 
+        sequence_chunks = [sequence[i:i + max_len] for i in range(0, len(sequence), max_len)]
+
+        chunks_representation = []
+        for seq in sequence_chunks:
+            results = self.get_results(seq, brmid)
+            if self.model_type in constants.model_types:
+                representation = results[0]["representations"][33]
+            elif self.model_type == 'esm-msa':
+                representation = results[0]["representations"][12][0]
+            elif self.model_type == "combined":
+                representation = torch.cat(
+                    (results[0]["representations"][33], results[1]["representations"][33]), -1)
+            else:
+                print("The model types are:")
+                print(*constants.msa_model_types, sep="\n")
+                sys.exit(2)
+            # remove first and last token (<cls> and <sep>)
+            representation = representation[:, 1:-1, :]
+            chunks_representation.append(representation)
+
+        representation = torch.cat(chunks_representation, 1)
         tokens = list(sequence)
-        # remove first and last token (<cls> and <sep>)
-        representation = representation[:, 1:-1, :]
         return representation, tokens

datasets/chezod_117_all_rand_1.fasta

@@ -0,0 +1,234 @@
+>4307
+GQGGGTHNQWNKPSKPKTNMKHMANAAAAGAVVGGLGGYMLGSAMSRPMMHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDIKIMERVVEQMCTTQYQKESQAYYDGRRS
+>15768
+MSTNPKPQRKTLRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRTWAQPGYPHHHHHH
+>15397
+GTQNRPLLRNSLDDKVGPPSNLEGQSDERALLDQLHTLLSNTDATGLEEIDRALGIPELVNQGQALEPKQD
+>15123
+GESGERWARQVSGGHFVTLHGAERLEEETNDEDVSDIERRIAMRLAERRYEDSATHGDE
+>6047
+MKLAPYILELLTSVNRTGGTADLLVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIGYGLTLRETSYVFEIDDRRLYAWCALDTLIFPALIGRTARVSSHCAATGAPVSLTVSPSEIQAVEPAGMAVSLVLPQEAADVRQSFCCHVHFFASVPTAEDWASKHQGLEGLAIVSVHEAFGLGQEFNRHLLQTMSSRTP
+>17290
+MGSSHHHHHHSSGLVPRGSHMYRKDKRRQEPLRQPSPQRGAWAPELGAAPEEELAALQLGPTHHECEASPPHDTLRLTALPDYYLTLRRSPDDIPLMTPNTITMIPNSLVGLQTLHPYNTFAAGFNSTGLPHSHSTTRV
+>16876
+MAEEIKNVPEQEVPKVATEESSAEVTDRGLFDFLGKKKDETKPEETPIASEFEQKVHISEPEPEVKHESLLEKLHRSDSSSSSSSEEEGSDGEKRKKYKEKKKPTTEVEVKEEEKKGFMEKLKEKLPGHKKPEDGSAVAAAPVVVPPPVEEAHPVEKKGILEKIKEKLPGYHPKTTVEEEKKDKE
+>15736
+MGSSHHHHHHSSGLVPRGSHMDIDATCTPRRASSNQRGLNQIWNVKKQSVYLMNLRKSGTLGHPGSLDETTYERLAEETLDSLAEFFECLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAYSGKDA
+>25118
+LADGSSDAAREPRPAPAPIRRRSSNYRAYATEPHAKKKSKISASRKLQLKTLLLQIAKQELEREAEERRGFKGRHHHHHH
+>15274
+GSHMSSSSESTGTPSNPDLDAGVSEHSGDWLDQDSVSDQFSVEFEVESLDSEDYSLSEEGQELSDEDDEVYQVTVYQAGESDTDSFERDPEISLADYWK
+>4950
+GKKWSKSSVVGWPAVRERMRRAEPAADGVGAASRDLEKHGAITSSNTAANNAACAWX
+>16505
+MKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGTWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGIGQGGGTHNQWNKPSKPK
+>11454
+GILTNSQGQTPQRVSGLQGSDALNIQQNQTSGGSLQAGQQKEGEQNQQTQQQQILIQPQLVQGGQALQALQAAPLSGQTFTTQAISQETLQNLQLQAVPNSGPIIIRTPTVGPFGQVSWQTLQLQNLQVQNPQAQTITLAPMQGVSLGQTPGGTLEDYKDDDDKGSHHHHHH
+>15131
+ASQKRPSQRSKYLATASTMDHARHGFLPRHRDTGILDSIGRFFSGDRGAPKRGSGKDSHTRTTHYGSLPQKSQHGRTQDENPVVHFFKNIVTPRTNPPSQGKGRGLSLSRFSWGAEGQRPGFGYGGRASDYKSAHKGFKGAYDAQGTLSKIFKLGGRDSRSGSPMARRLEHHHHHH
+>6078
+MNTDQQKVSEIFQSSKEKLQGDAKVVSDAFKKMASQDKDGKTTDADESECHNYQEQYNKLKGAGHKKELEHHHHHH
+>4287
+GSHMSYNNPYQLETPFEESYELDEGSSAIGAEGHDFVGFMNKISQINRDLDKYDHTINQVDSLHKRLLTEVNEEQASHLRHSLDNFVAQATDLQFKLKNEIKSAQRDGIHDTNKQAQAENSRQRFLKLIQDYRIVDSNYKEENKEQAKRQYMIIQPEATEDEMEAAISDVGGQQIFSQALLNANRRGEAKTALAEVQARHQELLKLEKSMAELTQLFNDMEELVIEQQENVDVIDKNVEDAQLDVEQGVGHTDKAVKSARKARKNKIR
+>15086
+MPTKTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGSNHNVQGTCPSAAVSEAEQIRQLKKENALQRARTRHPAESCLEHHHHHH
+>16912
+SIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVKAKKKKAKKAVEEDLDLDEFEEIDEDDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK
+>18177
+MQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMNEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEGGGACSWRPGRRGPSSGGCG
+>18198
+GAMGASGGEDDELKGLLGLPEEETEFDNLTEFNTAHNKRISTLTIEEGNLDIQRPKRKRKNSRVTFSEDDEIINPEDVDPSVGRFRNM
+>15179
+GHMPIKNILKNKTSTTSSMVASAEQPRGNVDEELSKKSQKWDEMNILATYHPADKDYGLMKIDEPSTPYHSMMGDDEDACSDTEATEAMAPDILARKLAAAEGLEPKYRIQEQESSGEEDSDLSPEEREKKRQFEMKRKLHYNEGLNIKLARQLISKDL
+>18248
+ASSHSLLFSSSFLSKPSSFTSSLRRFVYLPTRQFWPRQRHGFSTVFAVATERAISSSGP
+>7279
+MSESSSKSSQPLASKQEKDGTEKRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNKGAAKTRKTTTTPGVKPRGRPKKLEKEEEEGISQESSEEEQ
+>18446
+MGEKTVKLYEDTHFKGYSVELPVGDYNLSSLISRGALNDDLSSARVPSGLRLEVFQHNNFKGVRDFYASDAAELSRDNDASSVRVSKMETTN
+>19650
+SLLDKDDSKAGMEEDHTYEGLDIDQTATYEDIVTLRTGEVKWSVGEHPGTE
+>19224
+GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHNGKCRECFPNHQWVKEETQEDKDCPIKEEKGSPLNAAPYGIESMSQDTEVRSRVVGGSLRGAQAASPAKGEPS
+>5204
+SKKIKDPDAAKPEDWDERAKIDDPTDSKPEDWDKPEHIPDPDAKKPEDWDEEMDGEWEPPVIQNPEAKGEWKPR
+>4686
+SKSMQVPFSRCCFSFAEQEIPLRAILCYRNTSSICSNEGLIFKLKKGKEACALDTVGWVQRHRKMLRHCPSKRK
+>10010
+EAEAYVTQTMKGLDIQKVAGTWYSLAMAASDISLLDCQSAPLRVYVEELKPTPEGDLEILLQKWENDECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLVCQCLVRTPECDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
+>19672
+WVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYGRDGVMFSFEAGRRCPSGPGTFTFQTAQGNDIFQAVETAIHRQKAQG
+>18890
+SLQDGVRQSRDSDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLRRN
+>5545
+SYYHHHHHHDYDIPTTENLYFQGAMGSEPCRRHLDSVLQQLQTEVYRGAQTLYVPNCDHRGFYRKRQCRSSQGQRRGPCWCVDRMGKSLPGSPDGNGSSSCPTGSSG
+>17483
+MSDAGVKGFGEKASEALKPDSQKSYAEQGKEYITDKADKVAGKVQPEDNKGVFQGVHDSAEKGKDNAEGQGESLADQARDYMGAAKSKLNDAVEYVSGRVHGEEDPTKK
+>11019
+GSFTMPGLVDSNPAPPESQEKKPLKPCCACPETKKARDACIIEKGEEHCGHLIEAHKECMRALGKKI
+>15563
+MASNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGERGPSAAFAPAAAEPKLFGGFNSSDTVTSPQRAGPLAGGSAWSHPQFEK
+>18578
+GSKRRELDDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQYTELSNAKIAYKQNKANIAQEQQYGSHEEHLPADLETLQREIRMAQERLDLAIQAYHHWNNPHGPREKKAKVGSKSGSNKSSISSKSGDGKTSVWI
+>17836
+MAYSEKVIDHYENPRNVGSFDNKDENVGSGMVGAPACGDVMKLQIKVNDEGIIEDARFKTYGCGSAIASSSLVTEWVKGKSLDEAQAIKNTDIAEELELPPVKIHCSILAEDAIKAAIADYKSKREAK
+>5076
+MKKVIATKVLGTVKWQNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG
+>5736
+MHHHHHHLEMSFLKSFPPPGSAEGLRQQQPETEAVLNGKGLGTGTLYIAESRLSWLDVSGLGFSLEYPTISLHAVSRDLNAYPREHLYVMVNAKFGEESKESVAEEEDSDDDVEPIAEFRFVPSDKSALEAMFTAMCECQALHPDPEDEDSDDYDGEEYDVEAHEQGQGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRTEDSTRDYEDGMEVDTTPTVAGQFEDADVDH
+>18631
+MAAPGERGRFHGGNLFFLPGGARSEMMDDLATDARGRGAGRRDAAASASTLAQAPTSDSPVAEDASRRRPCRACVDFKTW
+>4286
+GSPEFMSSSTPFDPYALSEHDEERPQNVQSKSRTAELQAEIDDFVGIMRDNINKVAERGERLTSIEDKADNLAVSAQGFKRGANRVRKAMWYKDLKMK
+>19332
+MVRTKADSVPGTYRKVVAARAPRKVLGSSTSATNSTSVSSRKHENKYAGGNPVCVRPTPKWQKGIGEFFRLSPKDSEKENQIPEEAGSSGLGKAKRKACPLQPDHTNDEKE
+>15180
+GHMDEEDGEPPYEPESGCVEIPGLSEEEDPAPSRKIHFSQAPIQVFSTYSNEDYDRRNEDVDPMAASAEYELEKRVERLEL
+>2956
+MKPVTLIDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELIYIPNRVAQQL
+>18927
+ENREIQPPFKPKVSGKGAENFDKFFTRGQPVLTPPDQLVIANIDQSDFEGFWYVNPQFVHPILQSAVX
+>18867
+SLRKRWQNEKLGLDAGDEYEDENLYEGLNLDDCSMYEDISRGLQGTYQWVGSLNIGDVQLEKP
+>4034
+AMPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYKRRLDSENS
+>19482
+NPLEAVVFEERDGNAVLNLLFSLRGTKPSSLSRAVKVFETFEAKIHHLETRPAQRPLAGSPHLEYFVFFEVPSGDLAALLSSVRRVSDDVRSA
+>25093
+MIHSSVKRWGNSPAVRIPATLMQALNLNIDDEVKIDLVDGKLIIEPVRKEPVFTLAELVNDITPENLHENILWGEPKDKEVW
+>15430
+MNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRKFKSKPPKKGVQGFGDDIPGMEGLGTDITVIAPWEAFNHLELHELAQYGII
+>25327
+GSHMADENANRPVNPGEDPNEAFRSTPFEATTSALGDCRECIAYRTGATTGKGSRRHDDTCSREIKGSSATPGGSEKAGTGRQ
+>17048
+ASTASPAKAESSGVIDLFGDAFGSGASETQPAPQRVSSSSASADLLAGFGGSFMAPST
+>16670
+MAWGAWGRLACYLEFLKKEELKEFQLLLANKAHSRSSSGETPAQPEKTSGMEVASYLVAQYGEQRAWDLALHTWEQMGLRSLCAQAQEGAGHSLEHH
+>15162
+NDDKLYRADSRPPDEIKQSGGLMPRGQSDGFDRGTQMNINLYDHARGTQTGFVRHDDGYVSTSISLRSAHLVGQTILSGHSTYYIYVIATAPNMFNVNDVLGAYSPHPDEQDVSALGGIPYSQIVGWYRVHFGVLDEQLHRNRGYRDRYYSNLDIAPAADGYGLAGF
+>15336
+GAAESAERRNSILTETLHRFSLEGDAPVSWTETKKQSFKQTGEFGEKRKNSILNPINSIRKFSIVQKTPLQMNGIEEDSDEPLERRLSLVPDSEQGEAILPRISVISTGPTLQARRRQSVLNLMTHSVNQGQNIHRKTTASTRKVSLAPQANLTELDIYSRRLSQETGLEISEEINEEDLKECLFDDME
+>5022
+AFPSPAADYVEQRIDLNQLLIQHPFATYFVKASGDSMIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYSPITISSEDTLDVFGVVIHVVKAMR
+>15855
+GPHMTLEEFSAGEQKTERMDKVGDALEEVLSKALSQRTITVGVYEAAKLLNVDPDNVVLCLLAADEDDDRDVALQIHFTLIQAFCCENDINILRVSNPGRLAELLLLETDAGPAASEGAEQPPDLHCVLVTNPHSSQWKDPALSQLICYCRESRYMDQWVPVINLPER
+>16450
+MAYQQDPCANPTRQTGKTGGQTDQYGNPVHQTEALGAYGAGTGTGMHGGEHQQQPHQQPGVLNRSGSSSSEDDGQGGRRKKGMKEKIKERIPGMGRKDEQKQTSATSTPGQGQQKKGMMEKIKEKLPGAH
+>15766
+AVPVESKPDKPSGKSGMDAALDDLIDTLGGPEETEEENTTYSGPEVSDPMSSTYIEELGKREVTIPPKYRELLAKKEGITGPPADSSKPIGPDDAIDALSSDFTCGSPTAAGKKTEKEESTEVLKAQSAGTVRSAAPPQEK
+>6431
+EAESLTSAQKAKAEERKRRKMSRGLPDKTEEEKSVMAKKLEQKPKGEGIPTTAKLKVDEFESNVNEVKDPYPSADFPGDDEEDEPEIPVSPSPRPLAELQLKEKAVPIPEASSFFIFSPTNKVRVL
+>17926
+MGSSHHHHHHSSGLVPRGSHMAAPEGGISDVVEKLIKEAQETCAGDPVSGECVAAWDEVEELSAAASHARDKKKADGSDPLEEYCKDNPETNECRTYDN
+>4280
+ASASPKQRRSIIRDREPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTVTGRGSGSGC
+>6139
+DEAQFKECYDTCHKECSDKGNGFTFCEMKCDTDYSVKDVKEKLENYKPKN
+>11338
+GSSGSSGMTDYGEEQRNELEALESIYPDSFTVLSENPPSFTITVTSEAGENDETVQTTLKFTYSEKYPDEAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIWTLVTAVQEKLNEIVDQIKTR
+>18889
+SLKNRKAKAKPVTRLAGAGGRQRGQNKERPPPVPNPDYEPIRKGQRDLYSGLNQRRI
+>19485
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+>15174
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+>6974
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+>19796
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+>5956
+MADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQQDIDDLKRQNALLEQQVNALEGSGC
+>7292
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+>19037
+LLQEALSAYFDSMKIPSGQPETADVSREQVDKELDRASNSLISGLSQDEEDPPLPPTPMNSLVDECPLDQGLPKLSAEAVFEKCSQISLSNSTTASLSKK
+>1128
+VVYTDCTESGQNLCLCEGSNVCGQGNKCIPGSDGEKNQCVTGEGTPKPQSHNDGDFEEIPEEYLQ
+>4272
+MSATAATAPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVVEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLKMM
+>15136
+MSQKQEEENPAEETGEEKQDTQEKEGILPERAEEAKLKAKYPSLGQKPGGSDFLMKRLQKGQKYFDSGDYNMAKAKMKNKQLPSAYPDKNLVTGDHIPTPQDLPQRKSSLVTSKLAGGQVE
+>11388
+GSSGSSGEAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRMWTKIATKMGFAPGKAVGSHIRGHYERILNPYNLFLSGDSLRCLQKPNLTSDTKDKEY
+>6968
+MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQHGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA
+>6498
+MASVLEELQKDLEEVKVLLEKSTRFRLRDTLTSEKSKIETELKNKMQQKSQKKPELDNEKPAAVVAPLTTGYTVKIS
+>6212
+NKELDPVQKLFVDKIREYRTKRQTSGGPVDAGPEYQQRLDRELFKLKQMYGKADMNTFPNFTFEDPKFEVVEKPQS
+>19521
+GHSMSQSNRELVVDFLSYKLSQKGYSWSQFSDVEENRTEAPEGTESEMETPSAIEGNPSWHLADSPAVNGATGHSSSLDAREVIPMAAVKQALREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIAAWMATYLNDHLEPWIQENGGWDTFVELYGNNAAAESRKGQER
+>6970
+MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALHQRGLKTVFDEAIRAVLSPPPVK
+>5313
+GPLGSPSKDCGSPKYAYFNGCSSPTAPLSPMSPPGYKLVTGDRNNSSCRNYNKQASEQNWANYSAEQNRMGQAGSTISNSHAQPFDFPDDNQNAKKVAAGHELQPLAIVDQRTSSRASSRASSRPRPDDLEI
+>6846
+HLMYTLGPDGKRIYTLKKCTESGEITKSAHPARFSPDDKYSRQRVTLKKRFGLVPGQHHHHHH
+>19135
+MADERKDEGKAPHWTSASLTEAAAHPHSPEMKDQGGSGEGLSRSANGFPYREEEEGAFGEHGSQGTYSDTKENGINGELTSADRETAEEVSARIVQVVTAEAVAVLKGEQEKEAQHKDQPAALPLAAEETVNLPPSPPPSPASEQTAALEEATSGESAQAPSAFKQAKDKVTDGITKSPEKRSSLPRPSSILPPRRGVSGDREENSFSLNSSISSARRTTRSEPIRRAGKSGTSTPTTPGSTAITPGTPPSYSSRTPGTPGTPSYPRTPGTPKSGILVPSEKKVAIIREPPKSPATPKQLRLINQPLPDLKNVKSKIGSTDNIKYQPKGGQVQIVTKKIDLSHVTSKCGSLKNIRHRPGGGRVKIESVKLDFKEKAQAKVGSLDNAHHVPGGGNVKIDSQKLNFREHAKARVDHGAEIITQSPSRSSVASPRRLSNVSSSGSINLLESPQLATLAEDVTAALAKQGL
+>4716
+GPLGSPEFSMPHSSPQNRPNYNVSFSSMPGGQNERGKAAANLEGKQKAADFEDLLSGQGFNAHKDKKGPRTIAEMRKEEMAKEMDPEKLKIVEWIEGKERNIRALLSTMHTVLWAGETKWKPVGMADLVTPEQVKKVYRKAVLVVHPDKATGQPYEQYAKMIFMELNDAWSEFENQGQKPLY
+>6521
+GSHMNNTSSSPQPKKKPLDGEHFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
+>26549
+GHMASGSLRGGEPEPDVTVLTSMLTDPSHITAETAKRRLARGSPPSLASSSASQLSAPSLKATCTTHHDSPDADLIEANLLWRQEMGGNITRVESENKVVILDSFEPLHADGDEREISVAAEILRKSRKFPSALPIWARPDYNPPLLESWKDPDYVPPVVHGCPLPPTKAPPIPPPRRKRTVVLTESNVSSALAELATKTFGSSGSSAVDSGTATALPDQASDDGDKGSDVESYSSMPHLEGEPGDPDLSDGSWSTVSEEASEDVVCC
+>11526
+MNIVPQDTFKSQVSTDQDKSVLSSAVPSLPDTLRQQEGGAVPLSTQLNDRHPLESTLKNWETTQRQRQMEQYRQIFGIAEPMKRTMEMEIVNRTDFNPLSTNGSIHRDILLNKECSIDWEDVYPGTGLQASTMVGDDVHSKIEKQLGY
+>19364
+MDGSHHHHHHGSATFPPATSAPQQPPGPEDEDSSLDESDLYSLAHSYLGGGGRKGRTKREAAANTNRPSPGGHERKLVTKLQNSERKKRGARR
+>15719
+AKTKGNKVNVGVKYAEKQERRFEPEKLREGRNIIGFQMGINKFASQQGMTAYGTRRHLYDPKLGTDQPLDQATISLQMGTNKGASQAGMTAPGTKRQI
+>4985
+ATPAPAAEMPGITIISASQTGNARRVAEALRDDLLAAKLNVKLVNAGDYKFKQIASEKLLIVVTSTQGEGEPPEEAVALHKFLFSKKAPKLENTAFAVFSLGDTSYEFFCQSGKDFDSKLAELGGERLLDRVDADVEYQAAASEWRKRVVDALKSRAPVAAPSQSVA
+>15506
+GSNGADNAHNNAFGGGKNPGIGNTSGAGSNGSASSNRGNSNDWSWSNKPHKNDGFHSDGSYHITFHGDNNSKPKPGGNSGNRGNNGDGAS
+>6112
+GSHMEHPKPSACRNLFGPLDHEELTRDLEKHCRDMEEASQRKWNFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQE
+>15398
+PNRSISPSALQDLLRTLKSPSSPQQQQQVLNILKSNPQLMAAFIKQRHAKYVANQPGMQ
+>19357
+MEANIRGQGGLAYPGVRTHGTLESVNGPKAGSRGLTSLADTFEHMIEELLDEDQKVRPNEENNKDADLYTGRVMLSSQVPLEPPLLFLLEEY
+>15141
+MKAKRSHQAIIMSTSLRVSPSIHGYHFDTASRKKAVGNIFENTDQESLERLFRNSGDKKAEERAKIIFAIDQDVEEKTHALMALKKRTKDKLFQFLKLRKYSIKVH
+>15711
+ATKAVAVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEEEDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSEDHAIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
+>16296
+PGPEEQEEEPQPRKPGTRRERTLGAPASSERSAAGGRGPRGHKRKLNEEDAASESSREKSNEDEGSSSEADEMAKALEAELNDLM
+>17760
+MEEPQSDPSVEPPLSQETFSDLWKDLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPL
+>19507
+MAEMKTDAATLAQEMGNFERISGDLKTQIDQVESTAGSLQGQWRGAAGTAAQAAVVRFQEAANKQKQELDEISTNIRQAGVQYSRADEEQQQALSSQMGFKLAAALEHHHHHH
+>4922
+IDVLLGADDGSLAFVPSEFSISPGEKIVFKNNAGFPHNIVFDEDSIPSGVDASKIDMSEEDLLNAKGETFEVALSNKGEYSFYCSPHQGAGMVGKVTVN
+>17325
+GPMELSVSSDSDSSQAGSNAGNQPMLWPAWVYCTRYSDRPSSGPRSRKPKKKNPNKEDKRPRTAFTAEQLQRLKAEFQTNRYLTNQRRQSLAQELGLNESQIKIWFQNKRAKIKKAT
+>15672
+PALTPSLGAKPKPQVLSDSGGPLIDLLTEDPPPYRDPRPPPSDRDGNGGEATPAGEAPDPSPMASRLRGRREPPVADSTTSQAFPLIAGGNGQLQYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLITHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGDDGRPTQLPNEVDAAFPLERPDWDYTTQAGRNHLVHYRQLLLAGLQNAGRSHHHHHHHH
+>15176
+GHMDPKGRKKIQFSVPAPPSQLDPRQVEMIRRRRPTPALLFRVSEHSSPEEESSPHQRTSGEGHHPKSKRPNPSAYTPPSLKAVQRIAEFHLQTISNLSENQASEEEDELGELRELGYPQ
+>17205
+MTETDKKQEQENHAECEDKPKPCCVCKFEKEERDTCILFNGQDSEKCKEFIEKYKECMKGYGFEVPSAN
+>4914
+LGASWHRPDKCCLGYQKRPLGQVLLSSWYPTSQLCSKPGVIFLTKRGRQVCADKSKDWVKKLMQQLPVTAR
+>hmbdi
+MKHDHHIGHTHSGKGHACHHEHNSPKTQQASSKMEGPIVYTCPMHPEIRQSAPGHCPLCGMALEPETVTVSEVVSPEYLDMRRR
+>15097
+PRLFECSNKTGRFLATEIVDFTQDDLDENDVYLLDTWDQIFFWIGKGANESEKEAAAETAQEYLRSHPGSRDLDTPIIVVKQGFEPPTFTGWFMAWDPLCWSDRKSYDELKAELGDNASIGQLVSGLTSKNEVFTATTTLVPTKLETFPLDVLVNTAAEDLPRGVDPSRKENHLSDEDFKAVFGMTRSAVANLPLWKQQNLKKEKGLF
+>19478
+GPDSMDCQAVLTTLLSRTDLDPRVLSNTGWGQTQIKQDTVWDIEEVPRPEGKSDKGTEGWESAATQTKNSGGWGDAPSQSNQMKSGWGEL
+>6580
+LKTFSSKSEYQLVVNAVRKHQESGFYWSAVTGGEANLLLSAEPAGTFLIRDSSDQRHFFTLSVKTQSGTKNLRIQCEGGSFSLQSDPRSTQPVPRFDCVLKLVHHYMPPPGTPSFSLPPTEPSSEVPEQPPAQALPGSTPKRAYYIYSGGEKIPLVLSRPLSSN
+>16160
+GHMKMADAKQKRNEQLKRWIGSETDLEPPVVKRKKTKVKFDDGAVFLAACSSGDTEEVLRLLERGADINYANVDGLTALHQASIDDNVDMVKFLVEAGAN
+>5070
+ALFSGDIANLTAAEITQGFKDVPSFVHEGGDVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRLEGRFTVIRRGKKKYYLIRYALEHHHHHH
+>15409
+GSLRVKFSRSADAPAYQQGQNQLLNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQEGLYNELQKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR
+>19171
+MHHHHHHSSGLVPRGSEFDEWTPGTAVITSPVLVPGCPSKAVDPGLPSVKQEPPDPEEDKEENKDDSASKLAPEEEAGGAGTPVITEIFSLGGTRFRDTAVWLPRSKDLKKPGARKQ
+>15441
+SHHHHHHSMANSAGSSNTQTPDASLQATYNGQSGGKKQPLNLSVYNVQATNIPPKETLVYTKQTQTTSTGGGNGD
+>19114
+MPLGSPEFMSSSAGSGHQPSQSRAIPTRTVAISDAAQLPHDYCTTPGGTLFSTTPGGTRIIYDRKFLLDRRNSPMAQTPPCHLPNIPGVTSPGTLIEDSKVEVNNLDNLDNHDRKHAVGDDAQFEMHI
+>7358
+GNHSGKRELSANKASKDGEIHRGEAGKKRSVGKLSQTASEDSDVFGEADAIQNNGTSAEDTAVTDSKHTADPKNNWQGAHPADPGNRPHLIRLFSRDAPGREDNTFKDRPSESDELQTIQEDPTAASGGLDVMASQKRPSQRSKYLATASTMDHARHGFLPRHRDTGILDSIGRFFSGDRGAPKRGSGKVSLEHHHHHH