Help with generation of paired MSA. NameError: name 'MSABlockDeletion' is not defined

[hqdream]

Thank you for releasing RF-Lite. It's truly a fantastic tool.

I've attempted to generate paired MSA files for use with RF2-Lite, but encountered some difficulties in the process. Specifically, I tried using MSA files generated by RosettaFold2 or Colabfold with two protein sequences as input. However, RF2-Lite appears unable to process these MSA files properly. The error message I received was:

NameError: name 'MSABlockDeletion' is not defined.

Could you please advise if there's a method to generate paired MSA files from individual a3m files for each protein?

Your guidance on this matter would be greatly appreciated. Many thanks in advance for your support.

Best regards,
Qi

[hqdream]

Here is the partial content of paired MSA file P77499_P77689.fas provided in the example folder.

_>query
MLSIKDLHVSVEDKAILRGLSLDVHPGEVHAIMGPNGSGKSTLSATLAGREDYEVTGGTVEFKGKDLLALSPEDRAGEGIFMAFQYPVEIPGVSNQFFLQTALNAVRSYRGQETLDRFDFQDLMEEKIALLKMPEDLLTRSVNVGFSGGEKKRNDILQMAVLEPELCILDESDSGLDIDALKVVADGVNSLRDGKRSFIIVTHYQRILDYIKPDYVHVLYQGRIVKSGDFTLVKQLEEQGYGWLTEQQMAGLPNSSNALQQWHHLFEAEGTKRSPQAQQHLQQLLRTGLPTRKHENWKYTPLEGLINSQFVSIAGEISPQQRDALALTLDSVRLVFVDGRYVPALSDATEGSGYEVSINDDRQGLPDAIQAEVFLHLTESLAQSVTHIAVKRGQRPAKPLLLMHITQGVAGEEVNTAHYRHHLDLAEGAEATVIEHFVSLNDARHFTGARFTINVAANAHLQHIKLAFENPLSHHFAHNDLLLAEDATAFSHSFLLGGAVLRHNTSTQLNGENSTLRINSLAMPVKNEVCDTRTWLEHNKGFCNSRQLHKTIVSDKGRAVFNGLINVAQHAIKTDGQMTNNNLLMGKLAEVDTKPQLEIYADDVKCSHGATVGRIDDEQIFYLRSRGINQQDAQQMIIYAFAAELTEALRDEGLKQQVLARIGQRLPGGAR

1737490_GCF_002157225.1
MLSINNLQAQVEDKPILKGLNFTVNPGEVHAIMGPNGSGKSTLGHVLSGREGYEVTGGSVEFCGKDLLAMETEERAREGLFLAFQYPVEIPGVSNMEFLKASVDAVREHRGLPALDAIAFMKQAREMCKAVNLEQSFLKRGVNEGFSGGEKKRNEIMQMMLLEPRLAILDETDSGLDIDALQVVAEGVNSLRAEDRSFIVVTHYQRLLNYIEPDFVHVLAGGQIVKSGDKSLALELEEKGYGWLES--------------------------------------QQASFPHRKTEHWKYTNLKALEQGEFFQSTHTLDEKALERLAIPLDTIDLIFINGVFQQHLSTAANDEGLNVTRFAASSQQQDVIQEHLFVTLNNSHLADGVFVSVDKNTQASKPIRIVQLTSAQAQN--FAVAPRLLVVLEEGAEACVIEHFASDDKQTSFVNAVCEIEVKDNAKLEHYRLHLEHESNLHIGGMHVNLRRDAVLDSFHLALGSVLKRIDVVVNHLGKGAHSNLNGVYLPSNKQHVDYHTCIEHAVPHCTSNEVFRGIISDNAKAVFNGRIHIHKDAQKTLAQLSNKNLLTSNKAEIDTKPELEIYADDVQCAHGATVAQLDDNAMHYLMTRGVSKDDARVMMSFGFINELINQINHEALANYLRPKMAQLFSG---
331104_GCA_000022605.2
MLSIKNLHVSIEDKRVLQGINLEIKTGETHVIMGPNGSGKSTLASIIAGKKEYHITEGEIYFLNKNLVNFSPEERAHLGIFLSFQHPIEIPGISIINFIKTAINSIRKERNLNKMSAKEILFKIKNTSSRLNIENDFIYRSLNEGFSGGEKKRNEIFQMMMLNPLLSILDEVDSGLDIDALRVVSQGINAFRNKKNSILIITHYKRLLDHILSDYVHILYNGKIIQSGDKKLSEKLEKEGYDWIAK--------------------------ISFLQQKHINLFKKKGFPSSENEEWKNTDINPIINQDYHEKIKHIEYKKIKEFLFLKESFLFIFIDGKYNSFLSQLFGVKNHVINISQKENEIKNSYQYDVFYTLNTLFSKDGVYIYIPDNIVLERPIEILHISTGLESGRIM-LNSRNLIVVGERSDVKIIEHHKSLKKHLAFINSVSEIYASNYSRIDYYKVQDNSDETFIIDNTFLKQKKHSQCSVWTFSFQGNFIRNNLKFYSRGEKTSSYLYGISLLSEKQLVDHHTLIDHFYSNAYSYQLYKNILFDQSKGIFNGKIIVNECIKGINAFQRNSNILLSDEACMYTKPQLEIYSEDVKCSHGCTIGNLQEEELFYLQSRGISERNGKILLLFSFLEEILNFIHIFELKKLIYQKMKKKLNQ---
1123256_GCF_000382285.1
LLQIENLHAEVAGKEILKGLDLVVNAGEVHAIMGPNGAGKSTLSKVLAGAEDYVVTAGTIRYQGRDLAELSAEQRAAHGIFMGFQYPVEIPGVSNMMFLKAALNAQRKERGEPELDAGDFLAWVRHRVKQMKMDPAMLSRGVNQGFSGGEKKRNEILQMLVLEPRLMVLDETDSGLDIDALKIVADGINAMRSPERATILVTHYQRLLDHVQPDAVHVLAAGRIVKSGGPDLARELEEKGYGWLQQ----------------------------------FDTFAQRGLPDDGIERWHYTNLQPFAAQPVQLAPAAAGTPDLSAWRLE-DCDEHVWINGRALN--------------AAAAPAPLPSLDAHAGLAGLHRAFATPGLQLTVPRDVRLDRPLHVLSVSDAREAGEM--FHLAHRIRLERGAQALLIVQNLGLPGATRFSTQSLSIELAEGAQLTLVRVQDEARGTTHWLQTTAEVGHDARL-------GGTLIRSDWRVKLAAPGAHAELSGLFGADGRVHLDNQYEIDHAAPHGTSRQWFRGLGFGPSRAILNGRVVVQRGAQKTDSEQRIANLMLAKGAEIDAKPELEIYADDVKCAHGASCGQLDDAAVFYLRSRGVPEAQARALLIYSFINDVLARVPHVALRLRLARRITARLGA---
240016_GCF_000172155.1
-LLIQDLHACIPDREILKGFSLEVKPGEVHAIMGPNGSGKSTLSKVLCGHEDYEVTSGSVTLDGEDLLAMEVDARSRAGLFLAFQYPFEIPGVSNANFIRAALQARL-PK-GEELDAVAYYKKLYSRMDELEMSRSFTARSVNEGFSGGEKKRNEILQLMMLEPKYSILDETDSGLDIDALKVVSQGVNSMRSPERGFLVITHYQRLLDYIKPDIVHVMVEGRIIRSGGPELALELEAKGYEL------------------------------QSRARAAWEEFQALPMPGLRDEHWRYSQSKNLSLDGLHLAGETTEAEKQAAKGLSHVAARLIFLNDRLIHSQTDGLEHGVVVLPFAEALRTHGDVLQQYLMKRKADLGSEKFAALHLAHVRAPKNAVLKAPIEIFHWVSGVNSLVFPHTLIVADHAQVTVLDHHASLRDEVAQSVAVADFVAGNGSHITYVNSQ-ELADSARALHSSTTVARDAQVKALQLQLGASFARSESVSDLAGEGSRSDMLGVSLPFSSQIVDMRTLQNHLAPRTYSDLLYKNALYDKTRTIFSGLINVADGAHYTDAYQKCRNLLNSADSEAVSMPGLEINADQVKCSHGATSAPISEDELFYLKARGIPDQESRQLIAIGFVEDVISRLGHEELIESLDRRIEEKFARQ--_

Below is the partial content of a paired MSA file modifed from the paired MSA file generated by RosettaFold2 which removes the dash and gaps:

_>query
MLSIKDLHVSVEDKAILRGLSLDVHPGEVHAIMGPNGSGKSTLSATLAGREDYEVTGGTVEFKGKDLLALSPEDRAGEGIFMAFQYPVEIPGVSNQFFLQTALNAVRSYRGQETLDRFDFQDLMEEKIALLKMPEDLLTRSVNVGFSGGEKKRNDILQMAVLEPELCILDESDSGLDIDALKVVADGVNSLRDGKRSFIIVTHYQRILDYIKPDYVHVLYQGRIVKSGDFTLVKQLEEQGYGWLTEQQMAGLPNSSNALQQWHHLFEAEGTKRSPQAQQHLQQLLRTGLPTRKHENWKYTPLEGLINSQFVSIAGEISPQQRDALALTLDSVRLVFVDGRYVPALSDATEGSGYEVSINDDRQGLPDAIQAEVFLHLTESLAQSVTHIAVKRGQRPAKPLLLMHITQGVAGEEVNTAHYRHHLDLAEGAEATVIEHFVSLNDARHFTGARFTINVAANAHLQHIKLAFENPLSHHFAHNDLLLAEDATAFSHSFLLGGAVLRHNTSTQLNGENSTLRINSLAMPVKNEVCDTRTWLEHNKGFCNSRQLHKTIVSDKGRAVFNGLINVAQHAIKTDGQMTNNNLLMGKLAEVDTKPQLEIYADDVKCSHGATVGRIDDEQIFYLRSRGINQQDAQQMIIYAFAAELTEALRDEGLKQQVLARIGQRLPGGAR

UniRef100_A0A0J8VGC3UniRef100_A0A2T3P884
MLEIKDLHVSVDDKPILQGIHLTIKPGEVHAIMGPNGSGKSTLSSTLAGKEEYQVDKGSMVFNGKELAELESEERAGEGIFLAFQYPVEIPGVSNKLFLKTALNGIRKYRGQDEIDRFDFDDLLEDKAKLLKMPADLLQRAVNEGFSGGEKKRNDILQMAVLSPQLCILDETDSGLDIDALKAVSAGVNALRDDKRSFIMVTHYQRILDYIKPDYVHVLYKGKIVKSGDHSLAKQLEDKGYGWITG--MGGSQVKNnaALMENLEGMVQS--G-KWQ--QQQWRKIAAEGLPINKDDAWKYTSLSGFKQLPLHSAVFQpVENISYESLSLNLDGYRLVFFDGLFSVRCSDwipKITITPLDRLSDVETYELSKSVQPDAFTYLTDATATGGVLIEVDAETVIDKPIYLLHISSGMKG-D--VCSYRHHISLGRLSQCELIEHHISLDQGGGVTLSRMSADVGKGAHFYHTKLIEEAPCQHHFGHNDIVVDRDASVHSHCLMLSGVLCRHQTSSHLQGENGFIEMNSLSMPDDQQTFDSRTYLRHQAPHCRSEQLHKTIARGASNGVFDGMIYVEPSALKTDGQMDSHNLLLSESAQVNCKPQLEIYADDVKCSHGATTGQLDARQVDYMRARGISKDKAQQMLLFAFASEVAFKIRNGCVKQHVCDKLVGSLSQVR-
UniRef100_A0A0X3T6L2UniRef100_A0A0X3T6Y2
LLNVENLHAEVAEggQPILKGLNLQVEPGEVHAIMGPNGAGKSTLSSVLAGRDDYEVTDGSAQFDGEDLLEMDPEERARKGVFLAFQYPVEIPGVSNKLFMQTAVNAVREERGQAPLDMFDFDEYAQSKMSTLNMRPDLLERSVNVGFSGGEKKRNDMYQMALLEPKLCIMDETDSGLDIDALKVVAKGVNALRSPERSFLVVTHYQRLLDYIKPDVVHVLYDGKIVKSGGFELVEKLENEGYDQIIQ--MPPNARALlEAlEQESQALNQRDQAdParekLVARRIAAAEQLRQTGWPTRKHENWHYTGLTPLFESSFSLaatpnndqdpaDVAGLSDAALTPYLPPFETIRLVFVDGVFSESLSGglDAIDDDLSIEMADADaiQSmtLADlrryqgvqdgtrnaarpvapsdaPSVDDVFVHINEMCLDQGLTIRLAPNKVLARPLQILQL-VTQ-N-D-ALVNLRVRFELGHHAQMSWLNQCACLDDaARSWVNRLQQVSLADGAVARQVDWQGLNDQSFLSSMTYVDQAPHSQWQNHALALGARWSRQQSYVCLNGEGADAEQNTLAWVRGQQLTDARTETQHGAAHCTSRQLHKFVVQDQGRGVFNGMIGVAKAAQKTDGQMDNKNLLLSPKAKMDTKPQLEIYADDVACSHGCASGEIDANQIFYAQARGIKHDEAVRMITQAFLLEPLESIAHDSLRQWLHDDLSKRLVALP-
UniRef100_A0A191ZK58UniRef100_A0A191ZEN6
MLNINNLHAKIGDKPILRGINFTVNPGEVHAIMGPNGSGKSTLCQVLGGREGYEITEGSVEFDGKDLLELSTEERAVAGLLLGFQHPVEIPGVKNIYLLKEAINAQRAAQGLEEMDTFAFMKRIKELVKTMGMDDAFLHRGVNAGFSGGEKKRNEILQMLLLQPKLALLDETDSGLDIDALKVVSEGINLLRGADRGIVLVTHYQRLLSYVEPDFVHILYKGRIIKSGDKSLALQLEAEGYqDFLE-------------------------------QDAARQQVVQWGLPTLRDEEWRWTNLRSLGRQAFS-TpAvavaTLPDNP----LaaILPd-AL-VVTFVDGQL-QGLPT-DLPAGLKLVaLAncDEALraaaF-APeaRNPNDALLALNTASATQGVVIDVAANAVIDRPV-VIrWLEGTQA---EAYSQTRVFVRLGVSAQATVIESVSGINAQLCWRNGITVIDQAANSQLHHLNLGLDGDHHLLTTRDFVRLARDARYHALSLQLAGQLVRREIDVDITDTGAHCELLGLMMPRGKQVLDTHTRIVHGAPQTTSSEHYRTIADESGRGIFKGRILVAQDAQQIAAFQDSRNLLLSDQAEIDTKPELEIYADDVKCSHGATVGRLDSEALYYLQSRGIPFAQARNLLIVGFAQELIDAAPVPALVEWLTEQVSRRLGTE--
UniRef100_A0A1F9KR22UniRef100_A0A1F9KNR9
MLVIKNLHANVAGNEILRGISLTVGAGEVHAVMGPNGSGKSTLANVLAGREGYQVTEGAVLYQGKDLLKMPPEERAREGIFLAFQYPVEIPGVSTTYFLKAALNAVRKHRGLPELDAMDFLGLVKEKMRLVEMDQALMNRPVNEGFSGGEKKRNEILQMAMLDPKLAVLDETDSGLDIDALRIVAAGVNALRGPERAMIVITHYQRLLGYIVPDYVHVLSEGRIVKSGGKELALELEEKGYSWIEE------------------------------RSGAISRFAAAGFPGVRDEEWKYTSIAPILDVPFNPArSlgDGLVRER---LgqlDLGaPVENRLVFINGRLSSELSTApRLPAGVEAGsLAaamrRSDArvasHLARyaNYDNQGFVALNTAFMEDGGFIFVPAGVVIEEPIHLVFVALSADG--AGVCYPRNLIVLERGAEASVVETYLSLERSLHFTNGVTEAVVGENCRLEHIKIQRESEEAFHIGTLQVQMGRSSRFTSHSLALGGALTRNDIDVALEGEGGDCTLNGLYIAGGRQHIDNHTRIDHVKPHCASRELYKGVLGGRARGVFNGKIYVHKAAEKSDAKQTNKNLLLSEGAWVDTKPQLEIHNNDVKCSHGSTIGQVDQDALFYLRSRGIGRSAACALLTQGFAGDVVARLPDAAGRAAIEDRVRERLEAI--_

However, "NameError: name 'MSABlockDeletion' is not defined." still appeared.

Could anyone tell me how to deal with this problem?

Thanks a lot.

Qi