1. 1. GCModeller [version 1.34.0.2]
    1. 1.1. Commands
      1. 1.1.0.0.1. Help for command ‘/BBH.Select.Regulators’:
      2. 1.1.0.0.2. Help for command ‘/Build.FamilyDb’:
      3. 1.1.0.0.3. Help for command ‘/Copys’:
      4. 1.1.0.0.4. Help for command ‘/Copys.DIR’:
      5. 1.1.0.0.5. Help for command ‘/CORN’:
      6. 1.1.0.0.6. Help for command ‘/EXPORT.MotifDraws’:
      7. 1.1.0.0.7. Help for command ‘/Export.MotifSites’:
      8. 1.1.0.0.8. Help for command ‘/Export.Regprecise.Motifs’:
      9. 1.1.0.0.9. Help for command ‘/Export.Similarity.Hits’:
      10. 1.1.0.0.10. Help for command ‘/Footprints’:
    2. 1.1.0.1. Accepted Types
      1. 1.1.0.1.1. /extract
      2. 1.1.0.1.2. Help for command ‘/Hits.Context’:
      3. 1.1.0.1.3. Help for command ‘/LDM.Compares’:
      4. 1.1.0.1.4. Help for command ‘/LDM.MaxW’:
      5. 1.1.0.1.5. Help for command ‘/LDM.Selects’:
      6. 1.1.0.1.6. Help for command ‘/MAST.MotifMatches’:
      7. 1.1.0.1.7. Help for command ‘/MAST.MotifMatchs.Family’:
      8. 1.1.0.1.8. Help for command ‘/mast.Regulations’:
      9. 1.1.0.1.9. Help for command ‘/MAST_LDM.Build’:
      10. 1.1.0.1.10. Help for command ‘/MEME.Batch’:
    3. 1.1.0.2. Accepted Types
      1. 1.1.0.2.1. /in
      2. 1.1.0.2.2. /out
      3. 1.1.0.2.3. Help for command ‘/MEME.LDMs’:
      4. 1.1.0.2.4. Help for command ‘/Motif.BuildRegulons’:
      5. 1.1.0.2.5. Help for command ‘/Motif.Info’:
    4. 1.1.0.3. Accepted Types
      1. 1.1.0.3.1. /loci
      2. 1.1.0.3.2. /motifs
      3. 1.1.0.3.3. Help for command ‘/Motif.Info.Batch’:
    5. 1.1.0.4. Accepted Types
      1. 1.1.0.4.1. /motifs
      2. 1.1.0.4.2. /num_threads
      3. 1.1.0.4.3. Help for command ‘/Motif.Similarity’:
      4. 1.1.0.4.4. Help for command ‘/MotifHits.Regulation’:
      5. 1.1.0.4.5. Help for command ‘/Parser.DEGs’:
      6. 1.1.0.4.6. Help for command ‘/Parser.Locus’:
      7. 1.1.0.4.7. Help for command ‘/Parser.Log2’:
      8. 1.1.0.4.8. Help for command ‘/Parser.MAST’:
      9. 1.1.0.4.9. Help for command ‘/Parser.Modules’:
      10. 1.1.0.4.10. Help for command ‘/Parser.Operon’:
    6. 1.1.0.5. Accepted Types
      1. 1.1.0.5.1. /family
      2. 1.1.0.5.2. Help for command ‘/Parser.Pathway’:
      3. 1.1.0.5.3. Help for command ‘/Parser.RegPrecise.Operons’:
      4. 1.1.0.5.4. Help for command ‘/Parser.Regulon’:
      5. 1.1.0.5.5. Help for command ‘/Parser.Regulon.gb’:
      6. 1.1.0.5.6. Help for command ‘/Parser.Regulon.Merged’:
      7. 1.1.0.5.7. Help for command ‘/Regulator.Motifs’:
      8. 1.1.0.5.8. Help for command ‘/Regulator.Motifs.Test’:
      9. 1.1.0.5.9. Help for command ‘/regulon.export’:
      10. 1.1.0.5.10. Help for command ‘/Regulon.Reconstruct’:
      11. 1.1.0.5.11. Help for command ‘/Regulon.Reconstruct2’:
      12. 1.1.0.5.12. Help for command ‘/Regulon.Reconstructs’:
    7. 1.1.0.6. Accepted Types
      1. 1.1.0.6.1. /bbh
      2. 1.1.0.6.2. /genome
      3. 1.1.0.6.3. /door
      4. 1.1.0.6.4. Help for command ‘/Regulon.Test’:
      5. 1.1.0.6.5. Help for command ‘/RfamSites’:
      6. 1.1.0.6.6. Help for command ‘/seq.logo’:
      7. 1.1.0.6.7. Help for command ‘/Similarity.Union’:
      8. 1.1.0.6.8. Help for command ‘/Site.MAST_Scan’:
    8. 1.1.0.7. Accepted Types
      1. 1.1.0.7.1. /batch
      2. 1.1.0.7.2. Help for command ‘/Site.MAST_Scan.Batch’:
      3. 1.1.0.7.3. Help for command ‘/Site.RegexScan’:
      4. 1.1.0.7.4. Help for command ‘/site.scan’:
      5. 1.1.0.7.5. Help for command ‘/SiteHits.Footprints’:
      6. 1.1.0.7.6. Help for command ‘/SWTOM.Compares’:
      7. 1.1.0.7.7. Help for command ‘/SWTOM.Compares.Batch’:
      8. 1.1.0.7.8. Help for command ‘/SWTOM.LDM’:
      9. 1.1.0.7.9. Help for command ‘/SWTOM.Query’:
    9. 1.1.0.8. Accepted Types
      1. 1.1.0.8.1. /no-HTML
      2. 1.1.0.8.2. Help for command ‘/SWTOM.Query.Batch’:
    10. 1.1.0.9. Accepted Types
      1. 1.1.0.9.1. /no-HTML
      2. 1.1.0.9.2. Help for command ‘/Tom.Query’:
      3. 1.1.0.9.3. Help for command ‘/Tom.Query.Batch’:
      4. 1.1.0.9.4. Help for command ‘/TomTOM’:
      5. 1.1.0.9.5. Help for command ‘/TomTom.LDM’:
      6. 1.1.0.9.6. Help for command ‘/TomTOM.Similarity’:
      7. 1.1.0.9.7. Help for command ‘/TOMTOM.Similarity.Batch’:
      8. 1.1.0.9.8. Help for command ‘/TomTom.Sites.Groups’:
      9. 1.1.0.9.9. Help for command ‘/Trim.MastSite’:
      10. 1.1.0.9.10. Help for command ‘–build.Regulations’:
    11. 1.1.0.10. Accepted Types
      1. 1.1.0.10.1. /DOOR.extract
      2. 1.1.0.10.2. Help for command ‘–build.Regulations.From.Motifs’:
      3. 1.1.0.10.3. Help for command ‘–CExpr.WGCNA’:
      4. 1.1.0.10.4. Help for command ‘Download.Regprecise’:
      5. 1.1.0.10.5. Help for command ‘–Dump.KEGG.Family’:
    12. 1.1.0.11. Accepted Types
      1. 1.1.0.11.1. /in
      2. 1.1.0.11.2. Help for command ‘–family.statics’:
      3. 1.1.0.11.3. Help for command ‘–Get.Intergenic’:
      4. 1.1.0.11.4. Help for command ‘–GetFasta’:
      5. 1.1.0.11.5. Help for command ‘–hits.diff’:
      6. 1.1.0.11.6. Help for command ‘–Intersect.Max’:
      7. 1.1.0.11.7. Help for command ‘–logo.Batch’:
      8. 1.1.0.11.8. Help for command ‘–mapped-Back’:
      9. 1.1.0.11.9. Help for command ‘mast.compile’:
      10. 1.1.0.11.10. Help for command ‘mast.compile.bulk’:
    13. 1.1.0.12. Accepted Types
      1. 1.1.0.12.1. /no-meme
      2. 1.1.0.12.2. Help for command ‘–modules.regulates’:
    14. 1.1.0.13. Accepted Types
      1. 1.1.0.13.1. /in
      2. 1.1.0.13.2. Help for command ‘Motif.Locates’:
      3. 1.1.0.13.3. Help for command ‘MotifScan’:
      4. 1.1.0.13.4. Help for command ‘–pathway.regulates’:
      5. 1.1.0.13.5. Help for command ‘Regprecise.Compile’:
      6. 1.1.0.13.6. Help for command ‘regulators.bbh’:
    15. 1.1.0.14. Accepted Types
      1. 1.1.0.14.1. /regulons
      2. 1.1.0.14.2. Help for command ‘regulators.compile’:
      3. 1.1.0.14.3. Help for command ‘–site.Match’:
    16. 1.1.0.15. Accepted Types
      1. 1.1.0.15.1. /len
      2. 1.1.0.15.2. Help for command ‘–site.Matches’:
      3. 1.1.0.15.3. Help for command ‘–site.Matches.text’:
      4. 1.1.0.15.4. Help for command ‘–site.stat’:
      5. 1.1.0.15.5. Help for command ‘–TCS.Module.Regulations’:
      6. 1.1.0.15.6. Help for command ‘–TCS.Regulations’:
      7. 1.1.0.15.7. Help for command ‘VirtualFootprint.DIP’:
      8. 1.1.0.15.8. Help for command ‘wGet.Regprecise’:

GCModeller [version 1.34.0.2]

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

Commands


Help for command ‘/BBH.Select.Regulators’:

Prototype: MEME.CLI::Int32 SelectRegulatorsBBH(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Build.FamilyDb’:

Prototype: MEME.CLI::Int32 BuildFamilyDb(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Copys’:

Prototype: MEME.CLI::Int32 BatchCopy(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /Copys /in <inDIR> [/out <outDIR> /file <meme.txt>]
Example: MEME /Copys
Help for command ‘/Copys.DIR’:

Prototype: MEME.CLI::Int32 BatchCopyDIR(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /Copys.DIR /in <inDIR> /out <outDIR>
Example: MEME /Copys.DIR
Help for command ‘/CORN’:

Prototype: MEME.CLI::Int32 CORN(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /CORN /in <operons.csv> /mast <mastDIR> /PTT <genome.ptt> [/out <out.csv>]
Example: MEME /CORN
Help for command ‘/EXPORT.MotifDraws’:

Prototype: MEME.CLI::Int32 ExportMotifDraw(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Export.MotifSites’:

Prototype: MEME.CLI::Int32 ExportTestMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Motif iteration step 1
Usage: G:\GCModeller\manual\bin\MEME.exe /Export.MotifSites /in <meme.txt> [/out <outDIR> /batch]
Example: MEME /Export.MotifSites
Help for command ‘/Export.Regprecise.Motifs’:

Prototype: MEME.CLI::Int32 ExportRegpreciseMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe
Example: MEME /Export.Regprecise.Motifs
Help for command ‘/Export.Similarity.Hits’:

Prototype: MEME.CLI::Int32 LoadSimilarityHits(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Footprints’:

Prototype: MEME.CLI::Int32 ToFootprints(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/extract]
Description: Extract the DOOR operon when the regulated gene is the first gene of the operon.

Example: /extract ""

Accepted Types

/extract
Help for command ‘/Hits.Context’:

Prototype: MEME.CLI::Int32 HitContext(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/LDM.Compares’:

Prototype: MEME.CLI::Int32 CompareMotif(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /LDM.Compares /query <query.LDM.Xml> /sub <subject.LDM.Xml> [/out <outDIR>]
Example: MEME /LDM.Compares
Help for command ‘/LDM.MaxW’:

Prototype: MEME.CLI::Int32 LDMMaxLen(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /LDM.MaxW [/in <sourceDIR>]
Example: MEME /LDM.MaxW
Help for command ‘/LDM.Selects’:

Prototype: MEME.CLI::Int32 Selectes(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /LDM.Selects /trace <footprints.xml> /meme <memeDIR> [/out <outDIR> /named]
Example: MEME /LDM.Selects
Help for command ‘/MAST.MotifMatches’:

Prototype: MEME.CLI::Int32 MotifMatch2(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/MAST.MotifMatchs.Family’:

Prototype: MEME.CLI::Int32 MotifMatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/mast.Regulations’:

Prototype: MEME.CLI::Int32 MastRegulations(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/MAST_LDM.Build’:

Prototype: MEME.CLI::Int32 BuildPWMDb(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /MAST_LDM.Build /source <sourceDIR> [/out <exportDIR:=./> /evalue <1e-3>]
Example: MEME /MAST_LDM.Build
Help for command ‘/MEME.Batch’:

Prototype: MEME.CLI::Int32 MEMEBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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 /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 ""

Accepted Types

/in
/out
Help for command ‘/MEME.LDMs’:

Prototype: MEME.CLI::Int32 MEME2LDM(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /MEME.LDMs /in <meme.txt> [/out <outDIR>]
Example: MEME /MEME.LDMs
Help for command ‘/Motif.BuildRegulons’:

Prototype: MEME.CLI::Int32 BuildRegulons(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Motif.Info’:

Prototype: MEME.CLI::Int32 MotifInfo(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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    /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 ""

Accepted Types

/loci
/motifs
Help for command ‘/Motif.Info.Batch’:

Prototype: MEME.CLI::Int32 MotifInfoBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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 /motifs
Description: Regulogs.Xml source directory

Example: /motifs ""

[/num_threads]
Description: Default Is -1, means auto config of the threads number.

Example: /num_threads ""

Accepted Types

/motifs
/num_threads
Help for command ‘/Motif.Similarity’:

Prototype: MEME.CLI::Int32 MEMETOM_MotifSimilarity(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/MotifHits.Regulation’:

Prototype: MEME.CLI::Int32 HitsRegulation(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.DEGs’:

Prototype: MEME.CLI::Int32 ParserDEGs(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.Locus’:

Prototype: MEME.CLI::Int32 ParserLocus(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.Log2’:

Prototype: MEME.CLI::Int32 ParserLog2(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.MAST’:

Prototype: MEME.CLI::Int32 ParserMAST(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.Modules’:

Prototype: MEME.CLI::Int32 ModuleParser(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.Operon’:

Prototype: MEME.CLI::Int32 ParserNextIterator(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/family]
Description: Group the source by family? Or output the source in one fasta set

Example: /family ""

Accepted Types

/family
Help for command ‘/Parser.Pathway’:

Prototype: MEME.CLI::Int32 PathwayParser(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.RegPrecise.Operons’:

Prototype: MEME.CLI::Int32 ParserRegPreciseOperon(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.Regulon’:

Prototype: MEME.CLI::Int32 RegulonParser(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.Regulon.gb’:

Prototype: MEME.CLI::Int32 RegulonParser2(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Parser.Regulon.Merged’:

Prototype: MEME.CLI::Int32 RegulonParser3(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Regulator.Motifs’:

Prototype: MEME.CLI::Int32 RegulatorMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /Regulator.Motifs /bbh <bbh.csv> /regprecise <genome.DIR> [/out <outDIR>]
Example: MEME /Regulator.Motifs
Help for command ‘/Regulator.Motifs.Test’:

Prototype: MEME.CLI::Int32 TestRegulatorMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/regulon.export’:

Prototype: MEME.CLI::Int32 ExportRegulon(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Regulon.Reconstruct’:

Prototype: MEME.CLI::Int32 RegulonReconstruct(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Regulon.Reconstruct2’:

Prototype: MEME.CLI::Int32 RegulonReconstructs2(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Regulon.Reconstructs’:

Prototype: MEME.CLI::Int32 RegulonReconstructs(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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    /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 ""

Accepted Types

/bbh
/genome
/door
Help for command ‘/Regulon.Test’:

Prototype: MEME.CLI::Int32 RegulonTest(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/RfamSites’:

Prototype: MEME.CLI::Int32 RfamSites(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /RfamSites /source <sourceDIR> [/out <out.fastaDIR>]
Example: MEME /RfamSites
Help for command ‘/seq.logo’:

Prototype: MEME.CLI::Int32 SequenceLogoTask(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /seq.logo /in <meme.txt> [/out <outDIR>]
Example: MEME /seq.logo
Help for command ‘/Similarity.Union’:

Prototype: MEME.CLI::Int32 UnionSimilarity(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Site.MAST_Scan’:

Prototype: MEME.CLI::Int32 SiteMASTScan(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/batch]
Description: If this parameter presented in the CLI, then the parameter /mast will be used as a DIR.

Example: /batch ""

Accepted Types

/batch
Help for command ‘/Site.MAST_Scan.Batch’:

Prototype: MEME.CLI::Int32 SiteMASTScanBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Site.RegexScan’:

Prototype: MEME.CLI::Int32 SiteRegexScan(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /Site.RegexScan /meme <meme.txt> /nt <nt.fasta> [/batch /out <out.csv>]
Example: MEME /Site.RegexScan
Help for command ‘/site.scan’:

Prototype: MEME.CLI::Int32 SiteScan(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /site.scan /query <LDM.xml> /subject <subject.fasta> [/out <outDIR>]
Example: MEME /site.scan
Help for command ‘/SiteHits.Footprints’:

Prototype: MEME.CLI::Int32 SiteHitsToFootprints(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/SWTOM.Compares’:

Prototype: MEME.CLI::Int32 SWTomCompares(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/SWTOM.Compares.Batch’:

Prototype: MEME.CLI::Int32 SWTomComparesBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/SWTOM.LDM’:

Prototype: MEME.CLI::Int32 SWTomLDM(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/SWTOM.Query’:

Prototype: MEME.CLI::Int32 SWTomQuery(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/no-HTML]
Description: If this parameter is true, then only the XML result will be export.

Example: /no-HTML ""

Accepted Types

/no-HTML
Help for command ‘/SWTOM.Query.Batch’:

Prototype: MEME.CLI::Int32 SWTomQueryBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/no-HTML]
Description: If this parameter is true, then only the XML result will be export.

Example: /no-HTML ""

Accepted Types

/no-HTML
Help for command ‘/Tom.Query’:

Prototype: MEME.CLI::Int32 TomQuery(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Tom.Query.Batch’:

Prototype: MEME.CLI::Int32 TomQueryBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/TomTOM’:

Prototype: MEME.CLI::Int32 TomTOMMethod(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/TomTom.LDM’:

Prototype: MEME.CLI::Int32 LDMTomTom(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/TomTOM.Similarity’:

Prototype: MEME.CLI::Int32 MEMEPlantSimilarity(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /TomTOM.Similarity /in <TOM_OUT.DIR> [/out <out.Csv>]
Example: MEME /TomTOM.Similarity
Help for command ‘/TOMTOM.Similarity.Batch’:

Prototype: MEME.CLI::Int32 MEMEPlantSimilarityBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe /TOMTOM.Similarity.Batch /in <inDIR> [/out <out.csv>]
Example: MEME /TOMTOM.Similarity.Batch
Help for command ‘/TomTom.Sites.Groups’:

Prototype: MEME.CLI::Int32 ExportTOMSites(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘/Trim.MastSite’:

Prototype: MEME.CLI::Int32 Trim(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘–build.Regulations’:

Prototype: MEME.CLI::Int32 Build(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/DOOR.extract]
Description: Extract the operon structure genes after assign the operon information.

Example: /DOOR.extract ""

Accepted Types

/DOOR.extract
Help for command ‘–build.Regulations.From.Motifs’:

Prototype: MEME.CLI::Int32 BuildFromMotifSites(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘–CExpr.WGCNA’:

Prototype: MEME.CLI::Int32 WGCNAModsCExpr(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘Download.Regprecise’:

Prototype: MEME.CLI::Int32 DownloadRegprecise2(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Download Regprecise database from Web API
Usage: G:\GCModeller\manual\bin\MEME.exe Download.Regprecise [/work ./ /save <saveXml>]
Example: MEME Download.Regprecise
Help for command ‘–Dump.KEGG.Family’:

Prototype: MEME.CLI::Int32 KEGGFamilyDump(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe --Dump.KEGG.Family /in <in.fasta> [/out <out.csv>]
Example: MEME --Dump.KEGG.Family

Parameters information:

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/in
Description: The RegPrecise formated title fasta file.

Example: /in ""

Accepted Types

/in
Help for command ‘–family.statics’:

Prototype: MEME.CLI::Int32 FamilyStatics(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe --family.statics /sites <motifSites.csv> /mods <directory.kegg_modules>
Example: MEME --family.statics
Help for command ‘–Get.Intergenic’:

Prototype: MEME.CLI::Int32 GetIntergenic(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘–GetFasta’:

Prototype: MEME.CLI::Int32 GetFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe --GetFasta /bbh <bbhh.csv> /id <subject_id> /regprecise <regprecise.fasta>
Example: MEME --GetFasta
Help for command ‘–hits.diff’:

Prototype: MEME.CLI::Int32 DiffHits(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe --hits.diff /query <bbhh.csv> /subject <bbhh.csv> [/reverse]
Example: MEME --hits.diff
Help for command ‘–Intersect.Max’:

Prototype: MEME.CLI::Int32 MaxIntersection(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe --Intersect.Max /query <bbhh.csv> /subject <bbhh.csv>
Example: MEME --Intersect.Max
Help for command ‘–logo.Batch’:

Prototype: MEME.CLI::Int32 LogoBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe --logo.Batch -in <inDIR> [/out <outDIR>]
Example: MEME --logo.Batch
Help for command ‘–mapped-Back’:

Prototype: MEME.CLI::Int32 SiteMappedBack(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘mast.compile’:

Prototype: MEME.CLI::Int32 CompileMast(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘mast.compile.bulk’:

Prototype: MEME.CLI::Int32 CompileMastBuck(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/no-meme]
Description: Specific that the mast site construction will without and meme pwm MAST_LDM model.

Example: /no-meme ""

Accepted Types

/no-meme
Help for command ‘–modules.regulates’:

Prototype: MEME.CLI::Int32 ModuleRegulates(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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/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 ""

Accepted Types

/in
Help for command ‘Motif.Locates’:

Prototype: MEME.CLI::Int32 MotifLocites(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\MEME.exe Motif.Locates -ptt <bacterial_genome.ptt> -meme <meme.txt> [/out <out.csv>]
Example: MEME Motif.Locates
Help for command ‘MotifScan’:

Prototype: MEME.CLI::Int32 MotifScan(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘–pathway.regulates’:

Prototype: MEME.CLI::Int32 PathwayRegulations(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘Regprecise.Compile’:

Prototype: MEME.CLI::Int32 CompileRegprecise(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘regulators.bbh’:

Prototype: MEME.CLI::Int32 RegulatorsBBh(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/regulons]
Description: The data source of the /bbh parameter is comes from the regulons bbh data.

Example: /regulons ""

Accepted Types

/regulons
Help for command ‘regulators.compile’:

Prototype: MEME.CLI::Int32 RegulatorsCompile()

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Information:  Regprecise regulators data source compiler.
Usage: G:\GCModeller\manual\bin\MEME.exe
Example: MEME regulators.compile
Help for command ‘–site.Match’:

Prototype: MEME.CLI::Int32 SiteMatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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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:

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   [/len]
Description: If not specific this parameter, then the function will trying to parsing the length value from the meme text automatically.

Example: /len ""

Accepted Types

/len
Help for command ‘–site.Matches’:

Prototype: MEME.CLI::Int32 SiteMatches(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘–site.Matches.text’:

Prototype: MEME.CLI::Int32 SiteMatchesText(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘–site.stat’:

Prototype: MEME.CLI::Int32 SiteStat(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘–TCS.Module.Regulations’:

Prototype: MEME.CLI::Int32 TCSRegulateModule(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘–TCS.Regulations’:

Prototype: MEME.CLI::Int32 TCSRegulations(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘VirtualFootprint.DIP’:

Prototype: MEME.CLI::Int32 VirtualFootprintDIP(Microsoft.VisualBasic.CommandLine.CommandLine)

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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
Help for command ‘wGet.Regprecise’:

Prototype: MEME.CLI::Int32 DownloadRegprecise(Microsoft.VisualBasic.CommandLine.CommandLine)

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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