NCBI_tools - SMRUCC/GCModeller GitHub Wiki

title: NCBI_tools tags: [maunal, tools] date: 7/27/2016 6:40:21 PM

GCModeller [version 1.0.0.0]

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

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

Function API Info
/Assign.Taxonomy
/Assign.Taxonomy.SSU
/Associate.Taxonomy
/Build_gi2taxi
/Export.GI
/gi.Match
/Nt.Taxonomy

Commands

Help for command '/Assign.Taxonomy':

Prototype: NCBI_tools.CLI::Int32 AssignTaxonomy(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\NCBI_tools.exe /Assign.Taxonomy /in <in.DIR> /gi <regexp> /index <fieldName> /tax <NCBI nodes/names.dmp> /gi2taxi <gi2taxi.txt/bin> [/out <out.DIR>]
  Example:      NCBI_tools /Assign.Taxonomy
Help for command '/Assign.Taxonomy.SSU':

Prototype: NCBI_tools.CLI::Int32 AssignTaxonomy2(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\NCBI_tools.exe /Assign.Taxonomy.SSU /in <in.DIR> /index <fieldName> /ref <SSU-ref.fasta> [/out <out.DIR>]
  Example:      NCBI_tools /Assign.Taxonomy.SSU
Help for command '/Associate.Taxonomy':

Prototype: NCBI_tools.CLI::Int32 AssociateTaxonomy(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\NCBI_tools.exe /Associate.Taxonomy /in <in.DIR> /tax <ncbi_taxonomy:names,nodes> /gi2taxi <gi2taxi.bin> [/gi <nt.gi.csv> /out <out.DIR>]
  Example:      NCBI_tools /Associate.Taxonomy
Help for command '/Build_gi2taxi':

Prototype: NCBI_tools.CLI::Int32 Build_gi2taxi(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\NCBI_tools.exe /Build_gi2taxi /in <gi2taxi.dmp> [/out <out.dat>]
  Example:      NCBI_tools /Build_gi2taxi
Help for command '/Export.GI':

Prototype: NCBI_tools.CLI::Int32 ExportGI(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\NCBI_tools.exe /Export.GI /in <ncbi:nt.fasta> [/out <out.csv>]
  Example:      NCBI_tools /Export.GI
Help for command '/gi.Match':

Prototype: NCBI_tools.CLI::Int32 giMatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\NCBI_tools.exe /gi.Match /in <nt.parts.fasta> /gi2taxid <gi2taxid.dmp> [/out <gi_match.txt>]
  Example:      NCBI_tools /gi.Match
Help for command '/Nt.Taxonomy':

Prototype: NCBI_tools.CLI::Int32 NtTaxonomy(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\NCBI_tools.exe /Nt.Taxonomy /in <nt.fasta> /gi2taxi <gi2taxi.bin> /tax <ncbi_taxonomy:names,nodes> [/out <out.fasta>]
  Example:      NCBI_tools /Nt.Taxonomy

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