RegPrecise - SMRUCC/GCModeller GitHub Wiki

title: RegPrecise tags: [maunal, tools] date: 7/27/2016 6:40:23 PM

GCModeller [version 1.0.0.0]

Module AssemblyName: file:///G:/GCModeller/manual/bin/RegPrecise.exe Root namespace: RegPrecise.CLI

All of the command that available in this program has been list below:

Function API Info
/Build.Operons
/Build.Regulons.Batch
/CORN Join two vertices by edge if the correspondent operons: 
           i) are orthologous; 
           ii) have cantiodate transcription factor binding sites. 
           Collect all linked components. Two operons from two different genomes are called orthologous if they share at least one orthologous gene.|

|/CORN.Batch|| |/CORN.thread|| |/DOOR.Merge|| |/Download.Motifs|| |/Download.Regprecise|Download Regprecise database from Web API| |/Effector.FillNames|| |/Export.Regulators|Exports all of the fasta sequence of the TF regulator from the download RegPrecsie FASTA database.| |/Family.Hits|| |/Fasta.Downloads|Download protein fasta sequence from KEGG database.| |/Fetches|| |/Fetches.Thread|| |/Gets.Sites.Genes|| |/heap.Supports|| |/install.motifs|| |/Maps.Effector|| |/Merge.CORN|| |/Merge.RegPrecise.Fasta|| |/Prot_Motifs.EXPORT.pfamString|| |/Prot_Motifs.PfamString|| |/ProtMotifs.Downloads|Download protein domain motifs structures from KEGG ssdb.| |/Repository.Fetch|| |/Rfam.Regulates|| |/Select.TF.BBH|| |/Select.TF.Pfam-String|| |/siRNA.Maps||

Commands

Help for command '/Build.Operons':

Prototype: RegPrecise.CLI::Int32 OperonBuilder(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Build.Operons /bbh <bbh.csv> /PTT <genome.PTT> /TF-bbh <bbh.csv> [/tfHit_hash /out <out.csv> /regprecise <regprecise.Xml>]
  Example:      RegPrecise /Build.Operons

Parameters information:

       [/bbh]
    Description:  The bbh result between the annotated genome And RegPrecise database. 
                   This result was used for generates the operons, and query should be the genes in 
                   the RegPrecise database and the hits is the genes in your annotated genome.

    Example:      /bbh ""

Accepted Types

/bbh
Help for command '/Build.Regulons.Batch':

Prototype: RegPrecise.CLI::Int32 RegulonBatchBuilder(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Build.Regulons.Batch /bbh <bbh.DIR> /PTT <PTT.DIR> /tf-bbh <tf-bbh.DIR> /regprecise <regprecise.Xml> [/num_threads <-1> /hits_hash /out <outDIR>]
  Example:      RegPrecise /Build.Regulons.Batch
Help for command '/CORN':

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

  Information:  Join two vertices by edge if the correspondent operons: 
               i) are orthologous; 
               ii) have cantiodate transcription factor binding sites. 
               Collect all linked components. Two operons from two different genomes are called orthologous if they share at least one orthologous gene.
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /CORN /in <regulons.DIR> /motif-sites <motiflogs.csv.DIR> /sites <motiflogs.csv> /ref <regulons.Csv> [/out <out.csv>]
  Example:      RegPrecise /CORN
Help for command '/CORN.Batch':

Prototype: RegPrecise.CLI::Int32 CORNBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /CORN.Batch /sites <motiflogs.gff.sites.Csv.DIR> /regulons <regprecise.regulons.csv.DIR> [/name <name> /out <outDIR> /num_threads <-1> /null-regprecise]
  Example:      RegPrecise /CORN.Batch

Parameters information:

    /sites
    Description:  
    Example:      /sites ""

/regulons
    Description:  
    Example:      /regulons ""

   [/name]
    Description:  

    Example:      /name ""

Accepted Types

/sites

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.MotifLog Example:

{
    "Complement": "System.String",
    "Ends": 0,
    "ID": "System.String",
    "SequenceData": "System.String",
    "Start": 0,
    "Strand": "System.String",
    "ATGDist": 0,
    "BiologicalProcess": "System.String",
    "Family": "System.String",
    "Location": "System.String",
    "Regulog": "System.String",
    "Taxonomy": "System.String",
    "tag": "System.String",
    "tags": [
        
    ]
}
/regulons

Decalre: SMRUCC.genomics.Data.Regprecise.RegPreciseOperon Example:

{
    "BiologicalProcess": "System.String",
    "Effector": "System.String",
    "Operon": [
        "System.String"
    ],
    "Pathway": "System.String",
    "Regulators": [
        "System.String"
    ],
    "Strand": "System.String",
    "TF_trace": "System.String",
    "bbh": [
        "System.String"
    ],
    "source": "System.String"
}
/name

Decalre: System.String Example:

"System.String"
Help for command '/CORN.thread':

Prototype: RegPrecise.CLI::Int32 CORNSingleThread(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /CORN.thread /hit <regulons.Csv> /hit-sites <motiflogs.csv> /sites <query.motiflogs.csv> /ref <query.regulons.Csv> [/null-regprecise /out <out.csv>]
  Example:      RegPrecise /CORN.thread

Parameters information:

    /hit
    Description:  
    Example:      /hit ""

/hit-sites
    Description:  
    Example:      /hit-sites ""

/sites
    Description:  
    Example:      /sites ""

/ref
    Description:  
    Example:      /ref ""

   [/null-regprecise]
    Description:  Does the motif log data have the RegPrecise database value? If this parameter is presented that which it means the site data have no RegPrecise data.

    Example:      /null-regprecise ""

   [/out]
    Description:  
    Example:      /out ""

Accepted Types

/hit

Decalre: SMRUCC.genomics.Data.Regprecise.RegPreciseOperon Example:

{
    "BiologicalProcess": "System.String",
    "Effector": "System.String",
    "Operon": [
        "System.String"
    ],
    "Pathway": "System.String",
    "Regulators": [
        "System.String"
    ],
    "Strand": "System.String",
    "TF_trace": "System.String",
    "bbh": [
        "System.String"
    ],
    "source": "System.String"
}
/hit-sites

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.MotifLog Example:

{
    "Complement": "System.String",
    "Ends": 0,
    "ID": "System.String",
    "SequenceData": "System.String",
    "Start": 0,
    "Strand": "System.String",
    "ATGDist": 0,
    "BiologicalProcess": "System.String",
    "Family": "System.String",
    "Location": "System.String",
    "Regulog": "System.String",
    "Taxonomy": "System.String",
    "tag": "System.String",
    "tags": [
        
    ]
}
/sites

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.MotifLog Example:

{
    "Complement": "System.String",
    "Ends": 0,
    "ID": "System.String",
    "SequenceData": "System.String",
    "Start": 0,
    "Strand": "System.String",
    "ATGDist": 0,
    "BiologicalProcess": "System.String",
    "Family": "System.String",
    "Location": "System.String",
    "Regulog": "System.String",
    "Taxonomy": "System.String",
    "tag": "System.String",
    "tags": [
        
    ]
}
/ref

Decalre: SMRUCC.genomics.Data.Regprecise.RegPreciseOperon Example:

{
    "BiologicalProcess": "System.String",
    "Effector": "System.String",
    "Operon": [
        "System.String"
    ],
    "Pathway": "System.String",
    "Regulators": [
        "System.String"
    ],
    "Strand": "System.String",
    "TF_trace": "System.String",
    "bbh": [
        "System.String"
    ],
    "source": "System.String"
}
/null-regprecise

Decalre: System.Boolean Example:

true
/out

Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.MotifLog Example:

{
    "Complement": "System.String",
    "Ends": 0,
    "ID": "System.String",
    "SequenceData": "System.String",
    "Start": 0,
    "Strand": "System.String",
    "ATGDist": 0,
    "BiologicalProcess": "System.String",
    "Family": "System.String",
    "Location": "System.String",
    "Regulog": "System.String",
    "Taxonomy": "System.String",
    "tag": "System.String",
    "tags": [
        
    ]
}
Help for command '/DOOR.Merge':

Prototype: RegPrecise.CLI::Int32 MergeDOOR(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /DOOR.Merge /in <operon.csv> /DOOR <genome.opr> [/out <out.opr>]
  Example:      RegPrecise /DOOR.Merge
Help for command '/Download.Motifs':

Prototype: RegPrecise.CLI::Int32 DownloadMotifSites(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Download.Motifs /imports <RegPrecise.DIR> [/export <EXPORT_DIR>]
  Example:      RegPrecise /Download.Motifs
Help for command '/Download.Regprecise':

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

  Information:  Download Regprecise database from Web API
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe Download.Regprecise [/work ./ /save <saveXml>]
  Example:      RegPrecise /Download.Regprecise
Help for command '/Effector.FillNames':

Prototype: RegPrecise.CLI::Int32 EffectorFillNames(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Effector.FillNames /in <effectors.csv> /compounds <metacyc.compounds> [/out <out.csv>]
  Example:      RegPrecise /Effector.FillNames
Help for command '/Export.Regulators':

Prototype: RegPrecise.CLI::Int32 ExportRegulators(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Exports all of the fasta sequence of the TF regulator from the download RegPrecsie FASTA database.
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Export.Regulators /imports <regprecise.downloads.DIR> /Fasta <regprecise.fasta> [/locus-out /out <out.fasta>]
  Example:      RegPrecise /Export.Regulators

Parameters information:

       [/locus-out]
    Description:  Does the program saves a copy of the TF locus_tag list at the mean time of the TF fasta sequence export.

    Example:      /locus-out ""

Accepted Types

/locus-out
Help for command '/Family.Hits':

Prototype: RegPrecise.CLI::Int32 FamilyHits(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Family.Hits /bbh <bbh.csv> [/regprecise <RegPrecise.Xml> /pfamKey <query.pfam-string> /out <out.DIR>]
  Example:      RegPrecise /Family.Hits
Help for command '/Fasta.Downloads':

Prototype: RegPrecise.CLI::Int32 DownloadFasta(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Download protein fasta sequence from KEGG database.
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe Fasta.Downloads /source <sourceDIR> [/out <outDIR> /keggTools <kegg.exe>]
  Example:      RegPrecise /Fasta.Downloads
Help for command '/Fetches':

Prototype: RegPrecise.CLI::Int32 Fetch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Fetches /ncbi <all_gbk.DIR> /imports <inDIR> /out <outDIR>
  Example:      RegPrecise /Fetches
Help for command '/Fetches.Thread':

Prototype: RegPrecise.CLI::Int32 FetchThread(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Fetches.Thread /gbk <gbkDIR> /query <query.txt> /out <outDIR>
  Example:      RegPrecise /Fetches.Thread
Help for command '/Gets.Sites.Genes':

Prototype: RegPrecise.CLI::Int32 GetSites(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Gets.Sites.Genes /in <tf.bbh.csv> /sites <motiflogs.csv> [/out <out.csv>]
  Example:      RegPrecise /Gets.Sites.Genes
Help for command '/heap.Supports':

Prototype: RegPrecise.CLI::Int32 Supports(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /heap.supports /in <inDIR> [/out <out.Csv> /T /l]
  Example:      RegPrecise /heap.Supports
Help for command '/install.motifs':

Prototype: RegPrecise.CLI::Int32 InstallRegPreciseMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /install.motifs /imports <motifs.DIR>
  Example:      RegPrecise /install.motifs
Help for command '/Maps.Effector':

Prototype: RegPrecise.CLI::Int32 Effectors(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Maps.Effector /imports <RegPrecise.DIR> [/out <out.csv>]
  Example:      RegPrecise /Maps.Effector
Help for command '/Merge.CORN':

Prototype: RegPrecise.CLI::Int32 MergeCORN(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Merge.CORN /in <inDIR> [/out <outDIR>]
  Example:      RegPrecise /Merge.CORN
Help for command '/Merge.RegPrecise.Fasta':

Prototype: RegPrecise.CLI::Int32 MergeDownload(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Merge.RegPrecise.Fasta [/in <inDIR> /out outDIR /offline]
  Example:      RegPrecise /Merge.RegPrecise.Fasta
Help for command '/Prot_Motifs.EXPORT.pfamString':

Prototype: RegPrecise.CLI::Int32 ProteinMotifsEXPORT(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Prot_Motifs.EXPORT.pfamString /in <motifs.json> /PTT <genome.ptt> [/out <pfam-string.csv>]
  Example:      RegPrecise /Prot_Motifs.EXPORT.pfamString
Help for command '/Prot_Motifs.PfamString':

Prototype: RegPrecise.CLI::Int32 ProtMotifToPfamString(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Prot_Motifs.PfamString /in <RegPrecise.Download_DIR> [/fasta <RegPrecise.fasta> /out <pfam-string.csv>]
  Example:      RegPrecise /Prot_Motifs.PfamString
Help for command '/ProtMotifs.Downloads':

Prototype: RegPrecise.CLI::Int32 DownloadProteinMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Download protein domain motifs structures from KEGG ssdb.
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /ProtMotifs.Downloads /source <source.DIR> [/kegg.Tools <./kegg.exe>]
  Example:      RegPrecise /ProtMotifs.Downloads
Help for command '/Repository.Fetch':

Prototype: RegPrecise.CLI::Int32 FetchRepostiory(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Repository.Fetch /imports <RegPrecise.Xml> /genbank <NCBI_Genbank_DIR> [/full /out <outDIR>]
  Example:      RegPrecise /Repository.Fetch
Help for command '/Rfam.Regulates':

Prototype: RegPrecise.CLI::Int32 RfamRegulates(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Rfam.Regulates /in <RegPrecise.regulons.csv> /rfam <rfam_search.csv> [/out <out.csv>]
  Example:      RegPrecise /Rfam.Regulates
Help for command '/Select.TF.BBH':

Prototype: RegPrecise.CLI::Int32 SelectTFBBH(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Select.TF.BBH /bbh <bbh.csv> /imports <RegPrecise.downloads.DIR> [/out <out.bbh.csv>]
  Example:      RegPrecise /Select.TF.BBH
Help for command '/Select.TF.Pfam-String':

Prototype: RegPrecise.CLI::Int32 SelectTFPfams(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /Select.TF.Pfam-String /pfam-string <RegPrecise.pfam-string.csv> /imports <regprecise.downloads.DIR> [/out <TF.pfam-string.csv>]
  Example:      RegPrecise /Select.TF.Pfam-String
Help for command '/siRNA.Maps':

Prototype: RegPrecise.CLI::Int32 siRNAMaps(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\RegPrecise.exe /siRNA.Maps /in <siRNA.csv> /hits <blastn.csv> [/out <out.csv>]
  Example:      RegPrecise /siRNA.Maps

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