Re: [Gusdev-gusdev] plugin inventory

[Steve F. <st...@pc...>]

keith-

i have attached below the set of plugins that exist in our old cvs. 
these, in addition to the ones in the current cvs under */*/plugin are 
the totality.   besides fasta and blat, i am not sure they cover any on 
your list.  plugins that haven't been moved to the new cvs are 
definitely not gus 3.0 compliant.

if you guys are going to gear up to write this number of plugins, i 
think it might make sense to ask how much do they have in common, and 
consider developing a small api to help out (or extend the plugin api). 
 i would be willing to assist in this.

steve

ps, sorry for the delay in answering.

AddPredictedSequences.pm                    LoadBlastSim4.pm
AnnotatorsInterfaceSubmitter.pm*            LoadBlastSimilaritiesPK.pm
AssemblyProteinInstance.pm                  LoadBLATAlignments.pm
AssignAASequenceCellRoles.pm                LoadCenTelo.pm
AssignEGADCellRoles.pm                      LoadCorePromoter.pm
AssignLibraryDistributionToAssemblies.pm    LoadEndSequencePairs.pm
AssignRNANameAndDescription.pm              LoadEPCR.pm*
AssignSequenceDescription.pm                LoadEpitopeFeatures.pm
BaseComposition.pm                          LoadFromTigrXml.pm
CalculateAASeqVariations.pm                 LoadGadflyRelease.pm
CalculateGeneFeatureESTOverlaps.pm          LoadGeneFeaturesFromEMBL.pm
CalculateGeneFeatureSAGETagLinks.pm         LoadGeneFeaturesFromGenBank.pm
CalculateGeneFeatureSeqOverlaps.pm          LoadGeneFeaturesFromXML.pm
CalculateGeneTrapLinks.pm                   LoadGoldenPathVirSeq.pm
ChangeGenBankGeneFeatures.pm                LoadGoOntology.pm
CheckAndFixCodingStart.pm                   LoadLowComplexityAAFeatures.pm
ConvertSequenceGapsToGappedSequence.pm      LoadLowComplexityNAFeatures.pm
CopyAASeqGoFuncToProtGoFunc.pm              LoadMGIInfo.pm
CopyCRAndGOFToAASequence.pm                 LoadNRDB.pm
CorrPositions.pm                            LoadORNLDraftGenePredictions.pm
CreateAllGenesStatistics.pm                 LoadOrnlPredictions.pm
CreateCloneSet.pm                           LoadPromRec.pm
CreateUCSCVirtualChromosomes.pm             LoadrRNAs.pm
CreateVirtualSequence.pm                    LoadTaxon.pm
CrossMatch.pm                               LoadTrnas.pm
CVS/                                        LoadWms.pm
DeleteAssembliesWithNoAssemblySequences.pm  LoadWorkflowFromXML.pm
DeleteBadAssemblies.pm                      MakeAAFeaturesForAssemblies.pm
DeleteDuplicatedAssemblySequences.pm        MakeAssemblySequences.pm
DeleteGenePredictions.pm                    MakeGoPredictionRules.pm
DeleteGoPredictions.pm                      MakeGoPredictions.pm
DeleteSimilarities.pm                       MakeIndexWordLink.pm
DisplayTable.pm                             MakeIndexWordSimLink.pm
DocumentTables.pm                           MakeProjectLink.pm
ExtractAndBlockAssemblySequences.pm         MakeRNAAnddProtein.pm
ExtractEsts.pm                              MakeRNAAndProtein.pm
ExtractPromoters.pm                         MakeRNAClustersForAssemblies.pm
FixCodingStart.pm                           ManageGoRules.pm
FixLibdbEST.pm                              MarkAssemblySequencesBad.pm
FixMissingNASequenceIds.pm                  MergeGenes.pm
FixSequenceLength.pm                        MouseGeneMap.pm*
FixStemCellIds.pm                           MoveSimilaritiesToAssembly.pm
FixStroCDBExtDbId.pm                        OpticalMapMatch.pm
FrameFinder.pm                              PointSimilaritiesToNewTable.pm
GBParser.pm                                 ReassembleDOTSRNA.pm
GenePlotReport.pm                           RemoveDeletedAssemblies.pm
GenerateSageTags.pm                         RepeatMaskSequence.pm
GoComparison.pm                             ReplaceChars.pm
IdentifyAndLoadSnpsFromAssemblies.pm        RestrictionDigest.pm
ImportCloneSeqDbest.pm                      RestrictionDigestSeqs.pm
ImportFpcFlatfile.pm                        RNAProteinIntegration.pm
ImportLibDbest.pm                           SetAssSeqQualStartStop.pm
ImportNASequences.pm                        Sim4.pm
ImportPfam.pm                               StartWorkflow.pm*
ImportPlasmoDBPrediction.pm                 Template.pm
ImportSangerPredictionsFromGFF.pm           TessLoadGoldenPathRepeats.pm
InsertDbRefAndDbRefNASequence.pm            TestUpdateEfficiency.pm
InsertNewExternalNASequences.pm             triv_trans.pm
InsertNewExternalNRDBSequences.pm           UpdateDotsAssembliesWithCap4.pm
InsertNewExternalSequences.pm               UpdateGeneAndRNAConf.pm
InsertSubSeq.pm                             UpdateGusFromXML.pm*
InsertWorkflowInit.pm                       VersionAndDeleteSimilarities.pm
LinkGenesToRNAs.pm                          WipeGeneFeaturePredictions.pm
LoadArachneAssembly.pm                      WipeORNLPredictions.pm
LoadBdgpRelease.pm



Keith James wrote:

>Hi,
>
>I'm looking into the inventory of Perl module plugins which we could
>possibly need to perform our standard analyses on data housed in
>GUS. I've jotted down a list below. For the purposes of planning at
>our end, I'd be interested in knowing if any of these either exist or
>are planned.
>
>blast (I know this exists)
>blat
>fasta
>repeatmasker
>seg
>reputer
>glimmer(m)
>phat
>geneid
>hmmgene
>genewise/estwise etc.
>tRNAscan-SE
>infernal
>emboss programs (any)
>hmmer/hmmpfam
>FingerPRINTScan
>pfscan
>tmhmm
>signalp
>clustal
>DNA block aligner
>TCoffee
>
>thanks,
>
>Keith
>
>  
>