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MEME
Module AssemblyName: file:///G:/GCModeller/manual/bin/MEME.exe Root namespace: MEME.CLI
All of the command that available in this program has been list below:
| Function API | Info |
|---|---|
| /BBH.Select.Regulators | Select bbh result for the regulators in RegPrecise database from the regulon bbh data. |
| /Build.FamilyDb | |
| /Copys | |
| /Copys.DIR | |
| /CORN | |
| /EXPORT.MotifDraws | |
| /Export.MotifSites | Motif iteration step 1 |
| /Export.Regprecise.Motifs | |
| /Export.Similarity.Hits | Motif iteration step 2 |
| /Footprints | 3 - Generates the regulation footprints. |
| /Hits.Context | 2 |
| /LDM.Compares | |
| /LDM.MaxW | |
| /LDM.Selects | |
| /MAST.MotifMatches | |
| /MAST.MotifMatchs.Family | 1 |
| /mast.Regulations | |
| /MAST_LDM.Build | |
| /MEME.Batch | Batch meme task by using tmod toolbox. |
| /MEME.LDMs | |
| /Motif.BuildRegulons | |
| /Motif.Info | Assign the phenotype information And genomic context Info for the motif sites. [SimpleSegment] -> [MotifLog] |
| /Motif.Info.Batch | [SimpleSegment] -> [MotifLog] |
| /Motif.Similarity | Export of the calculation result from the tomtom program. |
| /MotifHits.Regulation | |
| /Parser.DEGs | |
| /Parser.Locus | |
| /Parser.Log2 | |
| /Parser.MAST | |
| /Parser.Modules | |
| /Parser.Operon | |
| /Parser.Pathway | |
| /Parser.RegPrecise.Operons | |
| /Parser.Regulon | |
| /Parser.Regulon.gb | |
| /Parser.Regulon.Merged | |
| /Regulator.Motifs | |
| /Regulator.Motifs.Test | |
| /regulon.export | |
| /Regulon.Reconstruct | |
| /Regulon.Reconstruct2 | |
| /Regulon.Reconstructs | Doing the regulon reconstruction job in batch mode. |
| /Regulon.Test | |
| /RfamSites | |
| /seq.logo | |
| /Similarity.Union | Motif iteration step 3 |
| /Site.MAST_Scan | [MAST.Xml] -> [SimpleSegment] |
| /Site.MAST_Scan.Batch | [MAST.Xml] -> [SimpleSegment] |
| /Site.RegexScan | |
| /site.scan | |
| /SiteHits.Footprints | Generates the regulation information. |
| /SWTOM.Compares | |
| /SWTOM.Compares.Batch | |
| /SWTOM.LDM | |
| /SWTOM.Query | |
| /SWTOM.Query.Batch | |
| /Tom.Query | |
| /Tom.Query.Batch | |
| /TomTOM | |
| /TomTom.LDM | |
| /TomTOM.Similarity | |
| /TOMTOM.Similarity.Batch | |
| /TomTom.Sites.Groups | |
| /Trim.MastSite | |
| --build.Regulations | Genome wide step 2 |
| --build.Regulations.From.Motifs | |
| --CExpr.WGCNA | |
| Download.Regprecise | Download Regprecise database from Web API |
| --Dump.KEGG.Family | |
| --family.statics | |
| --Get.Intergenic | |
| --GetFasta | |
| --hits.diff | |
| --Intersect.Max | |
| --logo.Batch | |
| --mapped-Back | |
| mast.compile | |
| mast.compile.bulk | Genome wide step 1 |
| --modules.regulates | Exports the Venn diagram model for the module regulations. |
| Motif.Locates | |
| MotifScan | Scan for the motif site by using fragment similarity. |
| --pathway.regulates | Associates of the pathway regulation information for the predicted virtual footprint information. |
| Regprecise.Compile | The repository parameter is a directory path which is the regprecise database root directory in the GCModeller directory, if you didn't know how to set this value, please leave it blank. |
| regulators.bbh | Compiles for the regulators in the bacterial genome mapped on the regprecise database using bbh method. |
| regulators.compile | Regprecise regulators data source compiler. |
| --site.Match | |
| --site.Matches | |
| --site.Matches.text | Using this function for processing the meme text output from the tmod toolbox. |
| --site.stat | Statics of the PCC correlation distribution of the regulation |
| --TCS.Module.Regulations | |
| --TCS.Regulations | |
| VirtualFootprint.DIP | Associate the dip information with the Sigma 70 virtual footprints. |
| wGet.Regprecise | Download Regprecise database from REST API |
Prototype: MEME.CLI::Int32 SelectRegulatorsBBH(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Select bbh result for the regulators in RegPrecise database from the regulon bbh data.
Usage: G:\GCModeller\manual\bin\MEME.exe /BBH.Select.Regulators /in <bbh.csv> /db <regprecise_downloads.DIR> [/out <out.csv>]
Example: MEME /BBH.Select.Regulators
Prototype: MEME.CLI::Int32 BuildFamilyDb(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Build.FamilyDb /prot <RegPrecise.prot.fasta> /pfam <pfam-string.csv> [/out <out.Xml>]
Example: MEME /Build.FamilyDb
Prototype: MEME.CLI::Int32 BatchCopy(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Copys /in <inDIR> [/out <outDIR> /file <meme.txt>]
Example: MEME /Copys
Prototype: MEME.CLI::Int32 BatchCopyDIR(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Copys.DIR /in <inDIR> /out <outDIR>
Example: MEME /Copys.DIR
Prototype: MEME.CLI::Int32 CORN(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /CORN /in <operons.csv> /mast <mastDIR> /PTT <genome.ptt> [/out <out.csv>]
Example: MEME /CORN
Prototype: MEME.CLI::Int32 ExportMotifDraw(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /EXPORT.MotifDraws /in <virtualFootprints.csv> /MEME <meme.txt.DIR> /KEGG <KEGG_Modules/Pathways.DIR> [/pathway /out <outDIR>]
Example: MEME /EXPORT.MotifDraws
Prototype: MEME.CLI::Int32 ExportTestMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Motif iteration step 1
Usage: G:\GCModeller\manual\bin\MEME.exe /Export.MotifSites /in <meme.txt> [/out <outDIR> /batch]
Example: MEME /Export.MotifSites
Prototype: MEME.CLI::Int32 ExportRegpreciseMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe
Example: MEME /Export.Regprecise.Motifs
Prototype: MEME.CLI::Int32 LoadSimilarityHits(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Motif iteration step 2
Usage: G:\GCModeller\manual\bin\MEME.exe /Export.Similarity.Hits /in <inDIR> [/out <out.Csv>]
Example: MEME /Export.Similarity.Hits
Prototype: MEME.CLI::Int32 ToFootprints(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: 3 - Generates the regulation footprints.
Usage: G:\GCModeller\manual\bin\MEME.exe /Footprints /footprints <footprints.xml> /coor <name/DIR> /DOOR <genome.opr> /maps <bbhMappings.Csv> [/out <out.csv> /cuts <0.65> /extract]
Example: MEME /Footprints
Parameters information:
[/extract]
Description: Extract the DOOR operon when the regulated gene is the first gene of the operon.
Example: /extract ""
Prototype: MEME.CLI::Int32 HitContext(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: 2
Usage: G:\GCModeller\manual\bin\MEME.exe /Hits.Context /footprints <footprints.Xml> /PTT <genome.PTT> [/out <out.Xml> /RegPrecise <RegPrecise.Regulations.Xml>]
Example: MEME /Hits.Context
Prototype: MEME.CLI::Int32 CompareMotif(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /LDM.Compares /query <query.LDM.Xml> /sub <subject.LDM.Xml> [/out <outDIR>]
Example: MEME /LDM.Compares
Prototype: MEME.CLI::Int32 LDMMaxLen(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /LDM.MaxW [/in <sourceDIR>]
Example: MEME /LDM.MaxW
Prototype: MEME.CLI::Int32 Selectes(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /LDM.Selects /trace <footprints.xml> /meme <memeDIR> [/out <outDIR> /named]
Example: MEME /LDM.Selects
Prototype: MEME.CLI::Int32 MotifMatch2(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /MAST.MotifMatches /meme <meme.txt.DIR> /mast <MAST_OUT.DIR> [/out <out.csv>]
Example: MEME /MAST.MotifMatches
Prototype: MEME.CLI::Int32 MotifMatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: 1
Usage: G:\GCModeller\manual\bin\MEME.exe /MAST.MotifMatchs.Family /meme <meme.txt.DIR> /mast <MAST_OUT.DIR> [/out <out.Xml>]
Example: MEME /MAST.MotifMatchs.Family
Prototype: MEME.CLI::Int32 MastRegulations(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /mast.Regulations /in <mastSites.Csv> /correlation <sp_name/DIR> /DOOR <DOOR.opr> [/out <footprint.csv> /cut <0.65>]
Example: MEME /mast.Regulations
Prototype: MEME.CLI::Int32 BuildPWMDb(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /MAST_LDM.Build /source <sourceDIR> [/out <exportDIR:=./> /evalue <1e-3>]
Example: MEME /MAST_LDM.Build
Prototype: MEME.CLI::Int32 MEMEBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Batch meme task by using tmod toolbox.
Usage: G:\GCModeller\manual\bin\MEME.exe /MEME.Batch /in <inDIR> [/out <outDIR> /evalue <1> /nmotifs <30> /mod <zoops> /maxw <100>]
Example: MEME /MEME.Batch
Parameters information:
/in
Description: A directory path which contains the fasta sequence for the meme motifs analysis.
Example: /in ""
[/out]
Description: A directory path which outputs the meme.txt data to that directory.
Example: /out ""
Prototype: MEME.CLI::Int32 MEME2LDM(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /MEME.LDMs /in <meme.txt> [/out <outDIR>]
Example: MEME /MEME.LDMs
Prototype: MEME.CLI::Int32 BuildRegulons(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Motif.BuildRegulons /meme <meme.txt.DIR> /model <FootprintTrace.xml> /DOOR <DOOR.opr> /maps <bbhmappings.csv> /corrs <name/DIR> [/cut <0.65> /out <outDIR>]
Example: MEME /Motif.BuildRegulons
Prototype: MEME.CLI::Int32 MotifInfo(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Assign the phenotype information And genomic context Info for the motif sites. [SimpleSegment] -> [MotifLog]
Usage: G:\GCModeller\manual\bin\MEME.exe /Motif.Info /loci <loci.csv> [/motifs <motifs.DIR> /gff <genome.gff> /atg-dist 250 /out <out.csv>]
Example: MEME /Motif.Info
Parameters information:
/loci
Description: The motif site info data set, type Is simple segment.
Example: /loci ""
/motifs
Description: A directory which contains the motifsitelog data in the xml file format. Regulogs.Xml source directory
Example: /motifs ""
Prototype: MEME.CLI::Int32 MotifInfoBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: [SimpleSegment] -> [MotifLog]
Usage: G:\GCModeller\manual\bin\MEME.exe /Motif.Info.Batch /in <sites.csv.inDIR> /gffs <gff.DIR> [/motifs <regulogs.motiflogs.MEME.DIR> /num_threads -1 /atg-dist 350 /out <out.DIR>]
Example: MEME /Motif.Info.Batch
Parameters information:
/motifs
Description: Regulogs.Xml source directory
Example: /motifs ""
[/num_threads]
Description: Default Is -1, means auto config of the threads number.
Example: /num_threads ""
Prototype: MEME.CLI::Int32 MEMETOM_MotifSimilarity(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Export of the calculation result from the tomtom program.
Usage: G:\GCModeller\manual\bin\MEME.exe /Motif.Similarity /in <tomtom.DIR> /motifs <MEME_OUT.DIR> [/out <out.csv> /bp.var]
Example: MEME /Motif.Similarity
Prototype: MEME.CLI::Int32 HitsRegulation(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /MotifHits.Regulation /hits <motifHits.Csv> /source <meme.txt.DIR> /PTT <genome.PTT> /correlates <sp/DIR> /bbh <bbhh.csv> [/out <out.footprints.Csv>]
Example: MEME /MotifHits.Regulation
Prototype: MEME.CLI::Int32 ParserDEGs(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.DEGs /degs <deseq2.csv> /PTT <genomePTT.DIR> /door <genome.opr> /out <out.DIR> [/log-fold 2]
Example: MEME /Parser.DEGs
Prototype: MEME.CLI::Int32 ParserLocus(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.Locus /locus <locus.txt> /PTT <genomePTT.DIR> /DOOR <genome.opr> [/out <out.DIR>]
Example: MEME /Parser.Locus
Prototype: MEME.CLI::Int32 ParserLog2(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.Log2 /in <log2.csv> /PTT <genomePTT.DIR> /DOOR <genome.opr> [/factor 1 /out <outDIR>]
Example: MEME /Parser.Log2
Prototype: MEME.CLI::Int32 ParserMAST(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.MAST /sites <mastsites.csv> /ptt <genome-context.pttDIR> /door <genome.opr> [/out <outDIR>]
Example: MEME /Parser.MAST
Prototype: MEME.CLI::Int32 ModuleParser(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.Modules /KEGG.Modules <KEGG.modules.DIR> /PTT <genomePTT.DIR> /DOOR <genome.opr> [/locus <union/initx/locus, default:=union> /out <fasta.outDIR>]
Example: MEME /Parser.Modules
Prototype: MEME.CLI::Int32 ParserNextIterator(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.Operon /in <footprint.csv> /PTT <PTTDIR> [/out <outDIR> /family /offset <50> /all]
Example: MEME /Parser.Operon
Parameters information:
[/family]
Description: Group the source by family? Or output the source in one fasta set
Example: /family ""
Prototype: MEME.CLI::Int32 PathwayParser(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.Pathway /KEGG.Pathways <KEGG.pathways.DIR> /PTT <genomePTT.DIR> /DOOR <genome.opr> [/locus <union/initx/locus, default:=union> /out <fasta.outDIR>]
Example: MEME /Parser.Pathway
Prototype: MEME.CLI::Int32 ParserRegPreciseOperon(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.RegPrecise.Operons /operon <operons.Csv> /PTT <PTT_DIR> [/corn /DOOR <genome.opr> /id <null> /locus <union/initx/locus, default:=union> /out <outDIR>]
Example: MEME /Parser.RegPrecise.Operons
Prototype: MEME.CLI::Int32 RegulonParser(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.Regulon /inDIR <regulons.inDIR> /out <fasta.outDIR> /PTT <genomePTT.DIR> [/door <genome.opr>]
Example: MEME /Parser.Regulon
Prototype: MEME.CLI::Int32 RegulonParser2(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.Regulon.gb /inDIR <regulons.inDIR> /out <fasta.outDIR> /gb <genbank.gbk> [/door <genome.opr>]
Example: MEME /Parser.Regulon.gb
Prototype: MEME.CLI::Int32 RegulonParser3(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Parser.Regulon.Merged /in <merged.Csv> /out <fasta.outDIR> /PTT <genomePTT.DIR> [/DOOR <genome.opr>]
Example: MEME /Parser.Regulon.Merged
Prototype: MEME.CLI::Int32 RegulatorMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Regulator.Motifs /bbh <bbh.csv> /regprecise <genome.DIR> [/out <outDIR>]
Example: MEME /Regulator.Motifs
Prototype: MEME.CLI::Int32 TestRegulatorMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Regulator.Motifs.Test /hits <familyHits.Csv> /motifs <motifHits.Csv> [/out <out.csv>]
Example: MEME /Regulator.Motifs.Test
Prototype: MEME.CLI::Int32 ExportRegulon(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /regulon.export /in <sw-tom_out.DIR> /ref <regulon.bbh.xml.DIR> [/out <out.csv>]
Example: MEME /regulon.export
Prototype: MEME.CLI::Int32 RegulonReconstruct(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Regulon.Reconstruct /bbh <bbh.csv> /genome <RegPrecise.genome.xml> /door <operon.door> [/out <outfile.csv>]
Example: MEME /Regulon.Reconstruct
Prototype: MEME.CLI::Int32 RegulonReconstructs2(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Regulon.Reconstruct2 /bbh <bbh.csv> /genome <RegPrecise.genome.DIR> /door <operons.opr> [/out <outDIR>]
Example: MEME /Regulon.Reconstruct2
Prototype: MEME.CLI::Int32 RegulonReconstructs(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Doing the regulon reconstruction job in batch mode.
Usage: G:\GCModeller\manual\bin\MEME.exe /Regulon.Reconstructs /bbh <bbh_EXPORT_csv.DIR> /genome <RegPrecise.genome.DIR> [/door <operon.door> /out <outDIR>]
Example: MEME /Regulon.Reconstructs
Parameters information:
/bbh
Description: A directory which contains the bbh export csv data from the localblast tool.
Example: /bbh ""
/genome
Description: The directory which contains the RegPrecise bacterial genome downloads data from the RegPrecise web server.
Example: /genome ""
/door
Description: Door file which is the prediction data of the bacterial operon.
Example: /door ""
Prototype: MEME.CLI::Int32 RegulonTest(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Regulon.Test /in <meme.txt> /reg <genome.bbh.regulon.xml> /bbh <maps.bbh.Csv>
Example: MEME /Regulon.Test
Prototype: MEME.CLI::Int32 RfamSites(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /RfamSites /source <sourceDIR> [/out <out.fastaDIR>]
Example: MEME /RfamSites
Prototype: MEME.CLI::Int32 SequenceLogoTask(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /seq.logo /in <meme.txt> [/out <outDIR>]
Example: MEME /seq.logo
Prototype: MEME.CLI::Int32 UnionSimilarity(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Motif iteration step 3
Usage: G:\GCModeller\manual\bin\MEME.exe /Similarity.Union /in <preSource.fasta.DIR> /meme <meme.txt.DIR> /hits <similarity_hist.Csv> [/out <out.DIR>]
Example: MEME /Similarity.Union
Prototype: MEME.CLI::Int32 SiteMASTScan(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: [MAST.Xml] -> [SimpleSegment]
Usage: G:\GCModeller\manual\bin\MEME.exe /Site.MAST_Scan /mast <mast.xml/DIR> [/batch /out <out.csv>]
Example: MEME /Site.MAST_Scan
Parameters information:
[/batch]
Description: If this parameter presented in the CLI, then the parameter /mast will be used as a DIR.
Example: /batch ""
Prototype: MEME.CLI::Int32 SiteMASTScanBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: [MAST.Xml] -> [SimpleSegment]
Usage: G:\GCModeller\manual\bin\MEME.exe /Site.MAST_Scan /mast <mast.xml.DIR> [/out <out.csv.DIR> /num_threads <-1>]
Example: MEME /Site.MAST_Scan.Batch
Prototype: MEME.CLI::Int32 SiteRegexScan(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Site.RegexScan /meme <meme.txt> /nt <nt.fasta> [/batch /out <out.csv>]
Example: MEME /Site.RegexScan
Prototype: MEME.CLI::Int32 SiteScan(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /site.scan /query <LDM.xml> /subject <subject.fasta> [/out <outDIR>]
Example: MEME /site.scan
Prototype: MEME.CLI::Int32 SiteHitsToFootprints(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Generates the regulation information.
Usage: G:\GCModeller\manual\bin\MEME.exe /SiteHits.Footprints /sites <MotifSiteHits.Csv> /bbh <bbh.Csv> /meme <meme.txt_DIR> /PTT <genome.PTT> /DOOR <DOOR.opr> [/queryHash /out <out.csv>]
Example: MEME /SiteHits.Footprints
Prototype: MEME.CLI::Int32 SWTomCompares(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /SWTOM.Compares /query <query.meme.txt> /subject <subject.meme.txt> [/out <outDIR> /no-HTML]
Example: MEME /SWTOM.Compares
Prototype: MEME.CLI::Int32 SWTomComparesBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /SWTOM.Compares.Batch /query <query.meme.DIR> /subject <subject.meme.DIR> [/out <outDIR> /no-HTML]
Example: MEME /SWTOM.Compares.Batch
Prototype: MEME.CLI::Int32 SWTomLDM(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /SWTOM.LDM /query <ldm.xml> /subject <ldm.xml> [/out <outDIR> /method <pcc/ed/sw; default:=pcc>]
Example: MEME /SWTOM.LDM
Prototype: MEME.CLI::Int32 SWTomQuery(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /SWTOM.Query /query <meme.txt> [/out <outDIR> /method <pcc> /bits.level 1.6 /minW 6 /no-HTML]
Example: MEME /SWTOM.Query
Parameters information:
[/no-HTML]
Description: If this parameter is true, then only the XML result will be export.
Example: /no-HTML ""
Prototype: MEME.CLI::Int32 SWTomQueryBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /SWTOM.Query.Batch /query <meme.txt.DIR> [/out <outDIR> /SW-offset 0.6 /method <pcc> /bits.level 1.5 /minW 4 /SW-threshold 0.75 /tom-threshold 0.75 /no-HTML]
Example: MEME /SWTOM.Query.Batch
Parameters information:
[/no-HTML]
Description: If this parameter is true, then only the XML result will be export.
Example: /no-HTML ""
Prototype: MEME.CLI::Int32 TomQuery(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Tom.Query /query <ldm.xml/meme.txt> [/out <outDIR> /method <pcc/ed; default:=pcc> /cost <0.7> /threshold <0.65> /meme]
Example: MEME /Tom.Query
Prototype: MEME.CLI::Int32 TomQueryBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Tom.Query.Batch /query <inDIR> [/out <outDIR> /method <pcc/ed; default:=pcc> /cost 0.7 /threshold <0.65>]
Example: MEME /Tom.Query.Batch
Prototype: MEME.CLI::Int32 TomTOMMethod(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /TomTOM /query <meme.txt> /subject <LDM.xml> [/out <outDIR> /method <pcc/ed; default:=pcc> /cost <0.7> /threshold <0.3>]
Example: MEME /TomTOM
Prototype: MEME.CLI::Int32 LDMTomTom(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /TomTom.LDM /query <ldm.xml> /subject <ldm.xml> [/out <outDIR> /method <pcc/ed/sw; default:=sw> /cost <0.7> /threshold <0.65>]
Example: MEME /TomTom.LDM
Prototype: MEME.CLI::Int32 MEMEPlantSimilarity(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /TomTOM.Similarity /in <TOM_OUT.DIR> [/out <out.Csv>]
Example: MEME /TomTOM.Similarity
Prototype: MEME.CLI::Int32 MEMEPlantSimilarityBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /TOMTOM.Similarity.Batch /in <inDIR> [/out <out.csv>]
Example: MEME /TOMTOM.Similarity.Batch
Prototype: MEME.CLI::Int32 ExportTOMSites(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /TomTom.Sites.Groups /in <similarity.csv> /meme <meme.DIR> [/grep <regex> /out <out.DIR>]
Example: MEME /TomTom.Sites.Groups
Prototype: MEME.CLI::Int32 Trim(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe /Trim.MastSite /in <mastSite.Csv> /locus <locus_tag> /correlations <DIR/name> [/out <out.csv> /cut <0.65>]
Example: MEME /Trim.MastSite
Prototype: MEME.CLI::Int32 Build(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Genome wide step 2
Usage: G:\GCModeller\manual\bin\MEME.exe --build.Regulations /bbh <regprecise.bbhMapped.csv> /mast <mastSites.csv> [/cutoff <0.6> /out <out.csv> /sp <spName> /DOOR <genome.opr> /DOOR.extract]
Example: MEME --build.Regulations
Parameters information:
[/DOOR.extract]
Description: Extract the operon structure genes after assign the operon information.
Example: /DOOR.extract ""
Prototype: MEME.CLI::Int32 BuildFromMotifSites(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --build.Regulations.From.Motifs /bbh <regprecise.bbhMapped.csv> /motifs <motifSites.csv> [/cutoff <0.6> /sp <spName> /out <out.csv>]
Example: MEME --build.Regulations.From.Motifs
Prototype: MEME.CLI::Int32 WGCNAModsCExpr(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --CExpr.WGCNA /mods <CytoscapeNodes.txt> /genome <genome.DIR|*.PTT;*.fna> /out <DIR.out>
Example: MEME --CExpr.WGCNA
Prototype: MEME.CLI::Int32 DownloadRegprecise2(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Download Regprecise database from Web API
Usage: G:\GCModeller\manual\bin\MEME.exe Download.Regprecise [/work ./ /save <saveXml>]
Example: MEME Download.Regprecise
Prototype: MEME.CLI::Int32 KEGGFamilyDump(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --Dump.KEGG.Family /in <in.fasta> [/out <out.csv>]
Example: MEME --Dump.KEGG.Family
Parameters information:
/in
Description: The RegPrecise formated title fasta file.
Example: /in ""
Prototype: MEME.CLI::Int32 FamilyStatics(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --family.statics /sites <motifSites.csv> /mods <directory.kegg_modules>
Example: MEME --family.statics
Prototype: MEME.CLI::Int32 GetIntergenic(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --Get.Intergenic /PTT <genome.ptt> /nt <genome.fasta> [/o <out.fasta> /len 100 /strict]
Example: MEME --Get.Intergenic
Prototype: MEME.CLI::Int32 GetFasta(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --GetFasta /bbh <bbhh.csv> /id <subject_id> /regprecise <regprecise.fasta>
Example: MEME --GetFasta
Prototype: MEME.CLI::Int32 DiffHits(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --hits.diff /query <bbhh.csv> /subject <bbhh.csv> [/reverse]
Example: MEME --hits.diff
Prototype: MEME.CLI::Int32 MaxIntersection(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --Intersect.Max /query <bbhh.csv> /subject <bbhh.csv>
Example: MEME --Intersect.Max
Prototype: MEME.CLI::Int32 LogoBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --logo.Batch -in <inDIR> [/out <outDIR>]
Example: MEME --logo.Batch
Prototype: MEME.CLI::Int32 SiteMappedBack(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --mapped-Back /meme <meme.text> /mast <mast.xml> /ptt <genome.ptt> [/out <out.csv> /offset <10> /atg-dist <250>]
Example: MEME --mapped-Back
Prototype: MEME.CLI::Int32 CompileMast(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe mast.compile /mast <mast.xml> /ptt <genome.ptt> [/no-meme /no-regInfo /p-value 1e-3 /mast-ldm <DIR default:=GCModeller/Regprecise/MEME/MAST_LDM> /atg-dist 250]
Example: MEME mast.compile
Prototype: MEME.CLI::Int32 CompileMastBuck(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Genome wide step 1
Usage: G:\GCModeller\manual\bin\MEME.exe mast.compile.bulk /source <source_dir> [/ptt <genome.ptt> /atg-dist <500> /no-meme /no-regInfo /p-value 1e-3 /mast-ldm <DIR default:=GCModeller/Regprecise/MEME/MAST_LDM> /related.all]
Example: MEME mast.compile.bulk
Parameters information:
[/no-meme]
Description: Specific that the mast site construction will without and meme pwm MAST_LDM model.
Example: /no-meme ""
Prototype: MEME.CLI::Int32 ModuleRegulates(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Exports the Venn diagram model for the module regulations.
Usage: G:\GCModeller\manual\bin\MEME.exe --modules.regulates /in <virtualfootprints.csv> [/out <out.DIR> /mods <KEGG_modules.DIR>]
Example: MEME --modules.regulates
Parameters information:
/in
Description: The footprints data required of fill out the pathway Class, category and type information before you call this function.
If the fields is blank, then your should specify the /mods parameter.
Example: /in ""
Prototype: MEME.CLI::Int32 MotifLocites(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe Motif.Locates -ptt <bacterial_genome.ptt> -meme <meme.txt> [/out <out.csv>]
Example: MEME Motif.Locates
Prototype: MEME.CLI::Int32 MotifScan(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Scan for the motif site by using fragment similarity.
Usage: G:\GCModeller\manual\bin\MEME.exe MotifScan -nt <nt.fasta> /motif <motifLDM.xml/LDM_Name/FamilyName> [/delta <default:80> /delta2 <default:70> /offSet <default:5> /out <saved.csv>]
Example: MEME MotifScan
Prototype: MEME.CLI::Int32 PathwayRegulations(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Associates of the pathway regulation information for the predicted virtual footprint information.
Usage: G:\GCModeller\manual\bin\MEME.exe --pathway.regulates -footprints <virtualfootprint.csv> /pathway <DIR.KEGG.Pathways> [/out <./PathwayRegulations/>]
Example: MEME --pathway.regulates
Prototype: MEME.CLI::Int32 CompileRegprecise(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: The repository parameter is a directory path which is the regprecise database root directory in the GCModeller directory, if you didn't know how to set this value, please leave it blank.
Usage: G:\GCModeller\manual\bin\MEME.exe Regprecise.Compile [<repository>]
Example: MEME Regprecise.Compile
Prototype: MEME.CLI::Int32 RegulatorsBBh(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Compiles for the regulators in the bacterial genome mapped on the regprecise database using bbh method.
Usage: G:\GCModeller\manual\bin\MEME.exe regulators.bbh /bbh <bbhDIR/bbh.index.Csv> [/save <save.csv> /direct /regulons /maps <genome.gb>]
Example: MEME regulators.bbh
Parameters information:
[/regulons]
Description: The data source of the /bbh parameter is comes from the regulons bbh data.
Example: /regulons ""
Prototype: MEME.CLI::Int32 RegulatorsCompile()
Information: Regprecise regulators data source compiler.
Usage: G:\GCModeller\manual\bin\MEME.exe
Example: MEME regulators.compile
Prototype: MEME.CLI::Int32 SiteMatch(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --site.Match /meme <meme.text> /mast <mast.xml> /out <out.csv> [/ptt <genome.ptt> /len <150,200,250,300,350,400,450,500>]
Example: MEME --site.Match
Parameters information:
[/len]
Description: If not specific this parameter, then the function will trying to parsing the length value from the meme text automatically.
Example: /len ""
Prototype: MEME.CLI::Int32 SiteMatches(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --site.Matches /meme <DIR.meme.text> /mast <DIR.mast.xml> /out <out.csv> [/ptt <genome.ptt>]
Example: MEME --site.Matches
Prototype: MEME.CLI::Int32 SiteMatchesText(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Using this function for processing the meme text output from the tmod toolbox.
Usage: G:\GCModeller\manual\bin\MEME.exe --site.Matches.text /meme <DIR.meme.text> /mast <DIR.mast.xml> /out <out.csv> [/ptt <genome.ptt> /fasta <original.fasta.DIR>]
Example: MEME --site.Matches.text
Prototype: MEME.CLI::Int32 SiteStat(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Statics of the PCC correlation distribution of the regulation
Usage: G:\GCModeller\manual\bin\MEME.exe --site.stat /in <footprints.csv> [/out <out.csv>]
Example: MEME --site.stat
Prototype: MEME.CLI::Int32 TCSRegulateModule(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --TCS.Module.Regulations /MiST2 <MiST2.xml> /footprint <footprints.csv> /Pathways <KEGG_Pathways.DIR>
Example: MEME --TCS.Module.Regulations
Prototype: MEME.CLI::Int32 TCSRegulations(Microsoft.VisualBasic.CommandLine.CommandLine)
Information:
Usage: G:\GCModeller\manual\bin\MEME.exe --TCS.Regulations /TCS <DIR.TCS.csv> /modules <DIR.mod.xml> /regulations <virtualfootprint.csv>
Example: MEME --TCS.Regulations
Prototype: MEME.CLI::Int32 VirtualFootprintDIP(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Associate the dip information with the Sigma 70 virtual footprints.
Usage: G:\GCModeller\manual\bin\MEME.exe VirtualFootprint.DIP vf.csv <csv> dip.csv <csv>
Example: MEME VirtualFootprint.DIP
Prototype: MEME.CLI::Int32 DownloadRegprecise(Microsoft.VisualBasic.CommandLine.CommandLine)
Information: Download Regprecise database from REST API
Usage: G:\GCModeller\manual\bin\MEME.exe wGet.Regprecise [/repository-export <dir.export, default: ./> /updates]
Example: MEME wGet.Regprecise
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