KEGG_tools - SMRUCC/GCModeller GitHub Wiki

title: KEGG_tools tags: [maunal, tools] date: 7/27/2016 6:40:18 PM

GCModeller [version 3.0.854.0]

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

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

Function API Info
/16S_rRNA
/blastn Blastn analysis of your DNA sequence on KEGG server for the functional analysis.
/Compile.Model KEGG pathway model compiler
/Download.Ortholog Downloads the KEGG gene ortholog annotation data from the web server.
/Download.Pathway.Maps
/Dump.sp
/Fasta.By.Sp
/Get.prot_motif
/Gets.prot_motif
/Imports.SSDB
/Pathways.Downloads.All
/Pull.Seq Downloads the missing sequence in the local KEGG database from the KEGG database server.
/Query.KO
/Views.mod_stat
-Build.KO Download data from KEGG database to local server.
Download.Sequence
--Dump.Db
--Export.KO
-function.association.analysis
--Get.KO
--part.from source and ref should be in KEGG annotation format.
-query Query the KEGG database for nucleotide sequence and protein sequence by using a keywork.
-query.orthology
-query.ref.map
-ref.map.download
-Table.Create

Commands

Help for command '/16S_rRNA':

Prototype: KEGG_tools.CLI::Int32 Download16SRNA(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /16s_rna [/out <outDIR>]
  Example:      KEGG_tools /16S_rRNA
Help for command '/blastn':

Prototype: KEGG_tools.CLI::Int32 Blastn(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Blastn analysis of your DNA sequence on KEGG server for the functional analysis.
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /blastn /query <query.fasta> [/out <outDIR>]
  Example:      KEGG_tools /blastn
Help for command '/Compile.Model':

Prototype: KEGG_tools.CLI::Int32 Compile(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  KEGG pathway model compiler
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Compile.Model /pathway <pathwayDIR> /mods <modulesDIR> /sp <sp_code> [/out <out.Xml>]
  Example:      KEGG_tools /Compile.Model
Help for command '/Download.Ortholog':

Prototype: KEGG_tools.CLI::Int32 DownloadOrthologs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Downloads the KEGG gene ortholog annotation data from the web server.
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Download.Ortholog -i <gene_list_file.txt/gbk> -export <exportedDIR> [/gbk /sp <KEGG.sp>]
  Example:      KEGG_tools /Download.Ortholog
Help for command '/Download.Pathway.Maps':

Prototype: KEGG_tools.CLI::Int32 DownloadPathwayMaps(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Download.Pathway.Maps /sp <kegg.sp_code> [/out <EXPORT_DIR>]
  Example:      KEGG_tools /Download.Pathway.Maps
Help for command '/Dump.sp':

Prototype: KEGG_tools.CLI::Int32 DumpOrganisms(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Dump.sp [/res sp.html /out <out.csv>]
  Example:      KEGG_tools /Dump.sp
Help for command '/Fasta.By.Sp':

Prototype: KEGG_tools.CLI::Int32 GetFastaBySp(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Fasta.By.Sp /in <KEGG.fasta> /sp <sp.list> [/out <out.fasta>]
  Example:      KEGG_tools /Fasta.By.Sp
Help for command '/Get.prot_motif':

Prototype: KEGG_tools.CLI::Int32 ProteinMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Get.prot_motif /query <sp:locus> [/out out.json]
  Example:      KEGG_tools /Get.prot_motif
Help for command '/Gets.prot_motif':

Prototype: KEGG_tools.CLI::Int32 GetsProteinMotifs(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Gets.prot_motif /query <query.txt/genome.PTT> [/PTT /sp <kegg-sp> /out <out.json> /update]
  Example:      KEGG_tools /Gets.prot_motif
Help for command '/Imports.SSDB':

Prototype: KEGG_tools.CLI::Int32 ImportsDb(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Imports.SSDB /in <source.DIR> [/out <ssdb.csv>]
  Example:      KEGG_tools /Imports.SSDB
Help for command '/Pathways.Downloads.All':

Prototype: KEGG_tools.CLI::Int32 DownloadsAllPathways(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Pathways.Downloads.All [/out <outDIR>]
  Example:      KEGG_tools /Pathways.Downloads.All
Help for command '/Pull.Seq':

Prototype: KEGG_tools.CLI::Int32 PullSequence(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Downloads the missing sequence in the local KEGG database from the KEGG database server.
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe 
  Example:      KEGG_tools /Pull.Seq
Help for command '/Query.KO':

Prototype: KEGG_tools.CLI::Int32 QueryKOAnno(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Query.KO /in <blastnhits.csv> [/out <out.csv> /evalue 1e-5 /batch]
  Example:      KEGG_tools /Query.KO
Help for command '/Views.mod_stat':

Prototype: KEGG_tools.CLI::Int32 Stats(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe /Views.mod_stat /in <KEGG_Modules/Pathways_DIR> /locus <in.csv> [/locus_map Gene /pathway /out <out.csv>]
  Example:      KEGG_tools /Views.mod_stat
Help for command '-Build.KO':

Prototype: KEGG_tools.CLI::Int32 BuildKEGGOrthology(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Download data from KEGG database to local server.
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe -Build.KO [/fill-missing]
  Example:      KEGG_tools -Build.KO
Help for command 'Download.Sequence':

Prototype: KEGG_tools.CLI::Int32 DownloadSequence(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe Download.Sequence /query <querySource.txt> [/out <outDIR> /source <existsDIR>]
  Example:      KEGG_tools Download.Sequence
Help for command '--Dump.Db':

Prototype: KEGG_tools.CLI::Int32 DumpDb(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe --Dump.Db /KEGG.Pathways <DIR> /KEGG.Modules <DIR> /KEGG.Reactions <DIR> /sp <sp.Code> /out <out.Xml>
  Example:      KEGG_tools --Dump.Db
Help for command '--Export.KO':

Prototype: KEGG_tools.CLI::Int32 ExportKO(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe 
  Example:      KEGG_tools --Export.KO
Help for command '-function.association.analysis':

Prototype: KEGG_tools.CLI::Int32 FunctionAnalysis(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe -function.association.analysis -i <matrix_csv>
  Example:      KEGG_tools -function.association.analysis
Help for command '--Get.KO':

Prototype: KEGG_tools.CLI::Int32 GetKOAnnotation(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe --Get.KO /in <KASS-query.txt>
  Example:      KEGG_tools --Get.KO
Help for command '--part.from':

Prototype: KEGG_tools.CLI::Int32 GetSource(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  source and ref should be in KEGG annotation format.
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe --part.from /source <source.fasta> /ref <referenceFrom.fasta> [/out <out.fasta> /brief]
  Example:      KEGG_tools --part.from
Help for command '-query':

Prototype: KEGG_tools.CLI::Int32 QueryGenes(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  Query the KEGG database for nucleotide sequence and protein sequence by using a keywork.
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe -query -keyword <keyword> -o <out_dir>
  Example:      KEGG_tools -query
Help for command '-query.orthology':

Prototype: KEGG_tools.CLI::Int32 QueryOrthology(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe -query.orthology -keyword <gene_name> -o <output_csv>
  Example:      KEGG_tools -query.orthology
Help for command '-query.ref.map':

Prototype: KEGG_tools.CLI::Int32 DownloadReferenceMap(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe -query.ref.map -id <id> -o <out_dir>
  Example:      KEGG_tools -query.ref.map
Help for command '-ref.map.download':

Prototype: KEGG_tools.CLI::Int32 DownloadReferenceMapDatabase(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe -ref.map.download -o <out_dir>
  Example:      KEGG_tools -ref.map.download
Help for command '-Table.Create':

Prototype: KEGG_tools.CLI::Int32 CreateTABLE(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\KEGG_tools.exe -table.create -i <input_dir> -o <out_csv>
  Example:      KEGG_tools -Table.Create

Parameters information:

    -i
    Description:  This parameter specific the source directory input of the download data.

    Example:      -i ""

Accepted Types

-i

New

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