gscope_circo.tcl Annotations

Procedure Detail

A2M

proc A2M { {Qui {}} }

Defined in:

gscope_circo.tcl, line 1054

AddFeatures

proc AddFeatures { Nom FichierXml args }

Defined in:

gscope_circo.tcl, line 3735

AddMRna

proc AddMRna { Nom AccessCopain AccessMrna SeqNuc SeqProt }

Defined in:

gscope_circo.tcl, line 2115

AllAboutCif

proc AllAboutCif {  }

Defined in:

gscope_circo.tcl, line 1155

AllAboutMoreFrequentCodons

proc AllAboutMoreFrequentCodons {  }

Defined in:

gscope_circo.tcl, line 1146

AllAboutMoreFrequentCodonsJoy

proc AllAboutMoreFrequentCodonsJoy {  }

Defined in:

gscope_circo.tcl, line 1137

AllAboutMoreFrequentCodonsMGS

proc AllAboutMoreFrequentCodonsMGS {  }

Defined in:

gscope_circo.tcl, line 1128

AllCodons

proc AllCodons {  }

Defined in:

gscope_circo.tcl, line 2446

AllCodonsOrdered

proc AllCodonsOrdered {  }

Defined in:

gscope_circo.tcl, line 388

AllCoMa

proc AllCoMa { {Qui {}} {Quoi {}} {Frame {}} {CirCode {}} }

Defined in:

gscope_circo.tcl, line 2789

AllInMotif

proc AllInMotif { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 3693

AllInMotifFile

proc AllInMotifFile { {CC {}} }

Defined in:

gscope_circo.tcl, line 2947

BadCodon

proc BadCodon { Codon }

Defined in:

gscope_circo.tcl, line 2512

BestSilva

proc BestSilva { {Qui {}} }

Defined in:

gscope_circo.tcl, line 305

BlastColiDomains

proc BlastColiDomains {  }

Defined in:

gscope_circo.tcl, line 150

C216

proc C216 { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 2575

CalculSumOfPairsForCodonsAndCodonMatrix

proc CalculSumOfPairsForCodonsAndCodonMatrix { {Liste {}} {Save {}} }

Defined in:

gscope_circo.tcl, line 3428

ChromoCount

proc ChromoCount {  }

Defined in:

gscope_circo.tcl, line 3297

Cif

proc Cif { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 1178

CircoData

proc CircoData {  }

Defined in:

gscope_circo.tcl, line 2678

CirCode

proc CirCode { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 5064

CirCodeFor

proc CirCodeFor { CC {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 5038

CirCodeInfo

proc CirCodeInfo { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 5367

CirCodeProt

proc CirCodeProt { {GetWhat {}} }

Defined in:

gscope_circo.tcl, line 5288

CircoDir

proc CircoDir {  }

Defined in:

gscope_circo.tcl, line 3117

CodonMatrix

proc CodonMatrix { {Qui {}} {Quoi {}} {Frame {}} }

Defined in:

gscope_circo.tcl, line 4773

CodonMatrixFile

proc CodonMatrixFile { {CC {}} }

Defined in:

gscope_circo.tcl, line 2937

CodonMatrixFileHuman

proc CodonMatrixFileHuman { {CC {}} }

Defined in:

gscope_circo.tcl, line 2942

CodonMatrixNotModified

proc CodonMatrixNotModified { {Qui {}} {Quoi {}} {Frame {}} }

Defined in:

gscope_circo.tcl, line 4679

CodonMatrixRaymond

proc CodonMatrixRaymond { {Qui {}} {Quoi {}} {Frame {}} }

Defined in:

gscope_circo.tcl, line 4877

CoFreq

proc CoFreq { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 484

CoFreqPourTous

proc CoFreqPourTous {  }

Defined in:

gscope_circo.tcl, line 410

CoFreqPourTousPourRandom

proc CoFreqPourTousPourRandom {  }

Defined in:

gscope_circo.tcl, line 397

ColiDomain

proc ColiDomain { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 90

ColumnsOfCodonsInXMotifs

proc ColumnsOfCodonsInXMotifs { Nom {Frame {}} {NbCodons {}} {Cardinality {}} {RefOrg {}} }

Defined in:

gscope_circo.tcl, line 3967

ColumnsOfCodonsInXMotifsPourTous

proc ColumnsOfCodonsInXMotifsPourTous { {Frame {}} {NbCodons {}} {Cardinality {}} {RefOrg {}} }

Defined in:

gscope_circo.tcl, line 3946

CompareMDScore

proc CompareMDScore {  }

Defined in:

gscope_circo.tcl, line 1986

CompareX

proc CompareX {  }

Defined in:

gscope_circo.tcl, line 3269

CompleteMAMAsProject

proc CompleteMAMAsProject {  }

Defined in:

gscope_circo.tcl, line 3045

CompleteMAMAsStatistics

proc CompleteMAMAsStatistics { {Random {}} {Ask {}} }

Defined in:

gscope_circo.tcl, line 3080

CompleteMAMAsStatisticsForAll

proc CompleteMAMAsStatisticsForAll { {Start {}} {Stop {}} {Reverse {}} }

Defined in:

gscope_circo.tcl, line 3065

CountXMotifs

proc CountXMotifs { {CC {}} }

Defined in:

gscope_circo.tcl, line 639

CountXMotifsForAll

proc CountXMotifsForAll { {Liste {}} }

Defined in:

gscope_circo.tcl, line 611

CreateAccessMRnaPourTous

proc CreateAccessMRnaPourTous {  }

Defined in:

gscope_circo.tcl, line 2317

CreateAllImagesFor

proc CreateAllImagesFor { {PdfName {}} }

Defined in:

gscope_circo.tcl, line 2839

CreateAllImagesForAllPdfTypes

proc CreateAllImagesForAllPdfTypes {  }

Defined in:

gscope_circo.tcl, line 2820

CreateColiSeqs

proc CreateColiSeqs {  }

Defined in:

gscope_circo.tcl, line 178

CreateMacsimsWithMotifsX

proc CreateMacsimsWithMotifsX { {Liste {}} {NbCodons {}} {Cardinality {}} }

Defined in:

gscope_circo.tcl, line 3772

CreateMacsimsWithMotifsXForAll

proc CreateMacsimsWithMotifsXForAll { {LesRandom {}} }

Defined in:

gscope_circo.tcl, line 3755

CreateMAMAsProject

proc CreateMAMAsProject { {NewName {}} {FichierStart {}} {Prefixe {}} {Reference {}} }

Defined in:

gscope_circo.tcl, line 2964

CreateNucAliFromProtAli

proc CreateNucAliFromProtAli { Nom }

Defined in:

gscope_circo.tcl, line 4204

CreateNucAliFromProtAliMGS

proc CreateNucAliFromProtAliMGS { Nom }

Defined in:

gscope_circo.tcl, line 2066

CreateNucAliFromProtAliMGSPourTous

proc CreateNucAliFromProtAliMGSPourTous { {Keep {}} }

Defined in:

gscope_circo.tcl, line 2056

CreateNucAliFromProtAliPourTous

proc CreateNucAliFromProtAliPourTous {  }

Defined in:

gscope_circo.tcl, line 4195

CreateNucAliTfa

proc CreateNucAliTfa { Fichier Rep Prefixe }

Defined in:

gscope_circo.tcl, line 3136

CreateNucAndProtTfaAndMsfFromNucAliTfa

proc CreateNucAndProtTfaAndMsfFromNucAliTfa { Nom Rep {IndexReference {}} }

Defined in:

gscope_circo.tcl, line 4281

CreateNucAndProtTfaAndMsfFromNucAliTfaPourTous

proc CreateNucAndProtTfaAndMsfFromNucAliTfaPourTous { Rep Prefixe {IndexReference {}} }

Defined in:

gscope_circo.tcl, line 4136

CreateProtAliTfaFromNucAliTfaForJoy

proc CreateProtAliTfaFromNucAliTfaForJoy { Nom }

Defined in:

gscope_circo.tcl, line 4172

CreateProtAliTfaFromNucAliTfaForJoyPourTous

proc CreateProtAliTfaFromNucAliTfaForJoyPourTous {  }

Defined in:

gscope_circo.tcl, line 4163

CreeBanqueBlastFromSilva

proc CreeBanqueBlastFromSilva {  }

Defined in:

gscope_circo.tcl, line 139

CreeCirCode

proc CreeCirCode {  }

Defined in:

gscope_circo.tcl, line 5048

DecortiqueBlastRnaDomain

proc DecortiqueBlastRnaDomain { {FichierBlast {}} {FichierHits {}} }

Defined in:

gscope_circo.tcl, line 26

DiBase

proc DiBase { {X {}} {I {}} }

Defined in:

gscope_circo.tcl, line 2598

ExtractFromExonNuc

proc ExtractFromExonNuc { Access {Fichier {}} }

Defined in:

gscope_circo.tcl, line 4344

FastaFromBestSilva

proc FastaFromBestSilva { {Qui {}} }

Defined in:

gscope_circo.tcl, line 251

FichesGraphDir

proc FichesGraphDir {  }

Defined in:

gscope_circo.tcl, line 2932

FreCo

proc FreCo { {iX {}} {GetWhat {}} }

Defined in:

gscope_circo.tcl, line 2519

FromCif

proc FromCif { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 1447

FromRnaAli

proc FromRnaAli { {Qui {}} {Quoi {}} {Quid {}} }

Defined in:

gscope_circo.tcl, line 1827

HideRandomData

proc HideRandomData {  }

Defined in:

gscope_circo.tcl, line 5

HtmlForAllCodonMatrix

proc HtmlForAllCodonMatrix { {Frame {}} {Norm {}} }

Defined in:

gscope_circo.tcl, line 2745

InformeChromoLocPourTous

proc InformeChromoLocPourTous { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 3280

InformeColumnsOfCodonsInXMotifs

proc InformeColumnsOfCodonsInXMotifs {  }

Defined in:

gscope_circo.tcl, line 4015

InformeEHomsaReferencePourTous

proc InformeEHomsaReferencePourTous {  }

Defined in:

gscope_circo.tcl, line 4046

InformeNbXMotifsPourTous

proc InformeNbXMotifsPourTous {  }

Defined in:

gscope_circo.tcl, line 4026

IsX0

proc IsX0 { Codon }

Defined in:

gscope_circo.tcl, line 4502

JoinedRnaMotifsFor

proc JoinedRnaMotifsFor { Z Y {Brut {}} }

Defined in:

gscope_circo.tcl, line 1786

Karim

proc Karim { NomOuSeq {Frame {}} {NbCodons {}} {Cardinality {}} }

Defined in:

gscope_circo.tcl, line 4409

li

proc li {  }

Defined in:

gscope_circo.tcl, line 2698

LongueurTotale

proc LongueurTotale { Org }

Defined in:

gscope_circo.tcl, line 3246

MacsimRsfDir

proc MacsimRsfDir { {CC {}} }

Defined in:

gscope_circo.tcl, line 2907

MacsimXmlDir

proc MacsimXmlDir { {CC {}} }

Defined in:

gscope_circo.tcl, line 2912

MAMAsOrg

proc MAMAsOrg { {Qui {}} }

Defined in:

gscope_circo.tcl, line 3940

MAMAsSeq

proc MAMAsSeq { {Nom {}} {Org {}} {NucOrProt {}} {Gap {}} }

Defined in:

gscope_circo.tcl, line 3862

MGSAccessMrna

proc MGSAccessMrna { {RepOrthologs {}} {Racine {}} }

Defined in:

gscope_circo.tcl, line 2336

MGSConvertToRsfAndMacsimPourTous

proc MGSConvertToRsfAndMacsimPourTous { {Cc {}} }

Defined in:

gscope_circo.tcl, line 2015

MGSConvertToRsfAndMacsimPourTousAllRandoms

proc MGSConvertToRsfAndMacsimPourTousAllRandoms {  }

Defined in:

gscope_circo.tcl, line 2001

MGSCreateAllNuctfa

proc MGSCreateAllNuctfa {  }

Defined in:

gscope_circo.tcl, line 1948

MGSCreateAllNuctfaForEachOrganism

proc MGSCreateAllNuctfaForEachOrganism {  }

Defined in:

gscope_circo.tcl, line 1921

MGSCreateDatabase

proc MGSCreateDatabase { {Liste {}} }

Defined in:

gscope_circo.tcl, line 2270

MGSLaTotale

proc MGSLaTotale {  }

Defined in:

gscope_circo.tcl, line 1960

MGSMrna

proc MGSMrna { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 2218

MoreFrequentCodons

proc MoreFrequentCodons { {RepNucTfa {}} {FichierData {}} {Organism {}} }

Defined in:

gscope_circo.tcl, line 788

MoreFrequentCodonsPourJoy

proc MoreFrequentCodonsPourJoy {  }

Defined in:

gscope_circo.tcl, line 763

MoreFrequentCodonsPourMGS

proc MoreFrequentCodonsPourMGS {  }

Defined in:

gscope_circo.tcl, line 732

MoreFrequentCodonsPourTous

proc MoreFrequentCodonsPourTous {  }

Defined in:

gscope_circo.tcl, line 749

MRna

proc MRna { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 2130

MsfOnOneLine

proc MsfOnOneLine { Nom InDir OutDir {AliTfaDir {}} {ShowCodons {}} {DoNotUnSet {}} }

Defined in:

gscope_circo.tcl, line 4065

MutateNucAliTfa

proc MutateNucAliTfa { {NewDir {}} }

Defined in:

gscope_circo.tcl, line 2705

OLD_SPCandCMforReference

proc OLD_SPCandCMforReference { Pilier Frame Caller }

Defined in:

gscope_circo.tcl, line 3396

OnChro

proc OnChro { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 3303

OverlapRna

proc OverlapRna { {Z {}} {LocDSource {}} {LocFSource {}} {Destin {}} {Source {}} {GetWhat {}} }

Defined in:

gscope_circo.tcl, line 1801

Pml

proc Pml { {QuiZ {}} {Qui {}} Quoi }

Defined in:

gscope_circo.tcl, line 1422

PmlFromColiTo

proc PmlFromColiTo { Z {Action {}} {FicDestin {}} {FicSource {}} }

Defined in:

gscope_circo.tcl, line 1380

PossibleFichesGraphPdfTypes

proc PossibleFichesGraphPdfTypes {  }

Defined in:

gscope_circo.tcl, line 2829

PossiblesOrganismsInStartFile

proc PossiblesOrganismsInStartFile { FichierStart }

Defined in:

gscope_circo.tcl, line 2952

PrintBothCodonMatrix

proc PrintBothCodonMatrix { Frame {Norm {}} {Random {}} }

Defined in:

gscope_circo.tcl, line 4627

PrintCodonMatrix

proc PrintCodonMatrix { Frame {Norm {}} {Random {}} }

Defined in:

gscope_circo.tcl, line 4559

RandomCodonMatrix

proc RandomCodonMatrix { R {Qui {}} {Quoi {}} {Frame {}} }

Defined in:

gscope_circo.tcl, line 4547

ReferenceOrg

proc ReferenceOrg {  }

Defined in:

gscope_circo.tcl, line 2738

RemoveEmptyPiliers

proc RemoveEmptyPiliers { Qui }

Defined in:

gscope_circo.tcl, line 194

RenameMAMA

proc RenameMAMA {  }

Defined in:

gscope_circo.tcl, line 5325

RepSil

proc RepSil {  }

Defined in:

gscope_circo.tcl, line 130

RepSilva

proc RepSilva {  }

Defined in:

gscope_circo.tcl, line 134

ReRunConvertWithClustalw

proc ReRunConvertWithClustalw { Nom }

Defined in:

gscope_circo.tcl, line 4255

ReRunConvertWithClustalwPourTous

proc ReRunConvertWithClustalwPourTous {  }

Defined in:

gscope_circo.tcl, line 4248

RiboNomme

proc RiboNomme { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 1569

RiboRec

proc RiboRec { Root {Ident {}} }

Defined in:

gscope_circo.tcl, line 1555

Rna16SC216

proc Rna16SC216 { {With {}} {Start {}} {Stop {}} }

Defined in:

gscope_circo.tcl, line 2399

RnaMotif

proc RnaMotif { {Qui {}} {Quoi {}} }

Defined in:

gscope_circo.tcl, line 1688

SeeRnaMotifs

proc SeeRnaMotifs { Z }

Defined in:

gscope_circo.tcl, line 1773

SeeSeqs

proc SeeSeqs {  }

Defined in:

gscope_circo.tcl, line 1767

ShowXMotifs

proc ShowXMotifs { Nom {Frame {}} {N {}} {C {}} }

Defined in:

gscope_circo.tcl, line 4370

SPCandCMforReference

proc SPCandCMforReference { Pilier Frame Caller }

Defined in:

gscope_circo.tcl, line 3369

StatisticsForCodons

proc StatisticsForCodons {  }

Defined in:

gscope_circo.tcl, line 3113

Sum

proc Sum { F }

Defined in:

gscope_circo.tcl, line 4977

SumOfPairsDir

proc SumOfPairsDir { {CC {}} }

Defined in:

gscope_circo.tcl, line 2917

SumOfPairsForCodonsAndCodonMatrix

proc SumOfPairsForCodonsAndCodonMatrix { Pilier Frame }

Defined in:

gscope_circo.tcl, line 3340

SumOfPairsForCodonsDir

proc SumOfPairsForCodonsDir {  }

Defined in:

gscope_circo.tcl, line 2922

SumOfPairsForCodonsHumanDir

proc SumOfPairsForCodonsHumanDir {  }

Defined in:

gscope_circo.tcl, line 2927

SupprimeDoublonsDansTFAs

proc SupprimeDoublonsDansTFAs { {Rep {}} {RepSortie {}} }

Defined in:

gscope_circo.tcl, line 1879

TestAllFreCo

proc TestAllFreCo {  }

Defined in:

gscope_circo.tcl, line 2458

TestC216

proc TestC216 {  }

Defined in:

gscope_circo.tcl, line 2567

TestCC1

proc TestCC1 {  }

Defined in:

gscope_circo.tcl, line 2870

TestCC2

proc TestCC2 {  }

Defined in:

gscope_circo.tcl, line 2878

TestCC3

proc TestCC3 {  }

Defined in:

gscope_circo.tcl, line 2885

TestCirCode

proc TestCirCode {  }

Defined in:

gscope_circo.tcl, line 5026

TestCM

proc TestCM {  }

Defined in:

gscope_circo.tcl, line 4997

TestCodonMatrix

proc TestCodonMatrix {  }

Defined in:

gscope_circo.tcl, line 5010

TestColi

proc TestColi {  }

Defined in:

gscope_circo.tcl, line 167

TestFreCo

proc TestFreCo {  }

Defined in:

gscope_circo.tcl, line 2497

TestRandomCodonMatrix

proc TestRandomCodonMatrix {  }

Defined in:

gscope_circo.tcl, line 4539

TunnelThermus

proc TunnelThermus {  }

Defined in:

gscope_circo.tcl, line 1043

WantedOrganism

proc WantedOrganism { {Org {}} }

Defined in:

gscope_circo.tcl, line 3122

WantedOrganisms

proc WantedOrganisms {  }

Defined in:

gscope_circo.tcl, line 3126

X0

proc X0 { {GetWhat {}} }

Defined in:

gscope_circo.tcl, line 4526

X0MotifsFeaturesDir

proc X0MotifsFeaturesDir { {CC {}} }

Defined in:

gscope_circo.tcl, line 2892

X1MotifsFeaturesDir

proc X1MotifsFeaturesDir { {CC {}} }

Defined in:

gscope_circo.tcl, line 2897

X2MotifsFeaturesDir

proc X2MotifsFeaturesDir { {CC {}} }

Defined in:

gscope_circo.tcl, line 2902

XCodons

proc XCodons { Frame }

Defined in:

gscope_circo.tcl, line 777

XMotifs

proc XMotifs { NomOuSeq {Frame {}} {NbCodons {}} {Cardinality {}} }

Defined in:

gscope_circo.tcl, line 4455

YCodeFor

proc YCodeFor { {Org {}} {GetWhat {}} }

Defined in:

gscope_circo.tcl, line 667