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grouper's Issues

SeqModi error

SeqModi function is not handling certain modifications correctly.

Example:
query = qVEqGPSTGAK
modis = Q1(Deamidated); Q4(Deamidated)
output = Q(dam)(dam)VEQ(dam)(dam)GPSTGAK
what output should be : Q(dam)VEQ(dam)GPSTGAK

Example :
query = VSSCCGSVCSDQGcSQDLcQETCcRPSCCQTTCCR
modis = C14(DeStreak); C19(DeStreak); C24(Carbamidomethyl)
output = VSSCCGSVCS((car)DeStreak)QG((car)((car)DeStreak)eStreak)SQ((car)DeStreak)L((car)((car)DeStreak)eStreak)QETC((car)((car)DeStreak)eStreak)RPSCCQTTCCR

Example :
query : mVNSccGSVcSDQGCGQDLcQETcccPScCQTTccR
modis : N-Term(Acetyl); M1(Oxidation); C5(Carbamidomethyl); C6(Carbamidomethyl); C10(Carbamidomethyl); C20(DeStreak); C24(DeStreak); C25(DeStreak); C26(DeStreak); C29(DeStreak); C34(Carbamidomethyl); C35(Carbamidomethyl)

output : M(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))C(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))oxI((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))))VNSC(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))C(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))GSVC(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))SDQGCGQDLC(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))QETC(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))C(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))C(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))PSC(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))CQTTC(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))C(((DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))(D(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))St(DE(car)StrE(car)aK(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car))(DE(car)St(DE(car)StrE(car)aK(car))E(car)aK(car))K(car)))R

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