pitr - SMRUCC/GCModeller GitHub Wiki

title: pitr tags: [maunal, tools] date: 7/27/2016 6:40:22 PM

ProteinInteraction [version 1.0.0.0]

Module AssemblyName: file:///G:/GCModeller/manual/bin/pitr.exe Root namespace: ProteinTools.Interactions.CLI

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

Function API Info
--align.LDM
--Contacts
--CrossTalks.Probability
--Db.From.Exists
--domain.Interactions
--interact.TCS
--Merge.Pfam
--predicts.TCS
--Profiles.Create
--ProtFasta.Downloads
--ProtFasta.Downloads.Batch
--signature
--SwissTCS.Downloads

Commands

Help for command '--align.LDM':

Prototype: ProteinTools.Interactions.CLI::Int32 GenerateModel(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --align.LDM /in <source.fasta>
  Example:      pitr --align.LDM
Help for command '--Contacts':

Prototype: ProteinTools.Interactions.CLI::Int32 Contacts(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --Contacts /in <in.DIR>
  Example:      pitr --Contacts
Help for command '--CrossTalks.Probability':

Prototype: ProteinTools.Interactions.CLI::Int32 CrossTalksCal(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --CrossTalks.Probability /query <pfam-string.csv> /swiss <swissTCS_pfam-string.csv> [/out <out.CrossTalks.csv> /test <queryName>]
  Example:      pitr --CrossTalks.Probability
Help for command '--Db.From.Exists':

Prototype: ProteinTools.Interactions.CLI::Int32 DbMergeFromExists(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --Db.From.Exists /aln <clustal-aln.DIR> /pfam <pfam-string.csv>
  Example:      pitr --Db.From.Exists
Help for command '--domain.Interactions':

Prototype: ProteinTools.Interactions.CLI::Int32 DomainInteractions(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --domain.Interactions /pfam <pfam-string.csv> /swissTCS <swissTCS.DIR>
  Example:      pitr --domain.Interactions
Help for command '--interact.TCS':

Prototype: ProteinTools.Interactions.CLI::Int32 TCSParser(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --interact.TCS /door <door.opr> /MiST2 <mist2.xml> /swiss <tcs.csv.DIR> /out <out.DIR>
  Example:      pitr --interact.TCS
Help for command '--Merge.Pfam':

Prototype: ProteinTools.Interactions.CLI::Int32 MergePfam(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --Merge.Pfam /in <in.DIR>
  Example:      pitr --Merge.Pfam
Help for command '--predicts.TCS':

Prototype: ProteinTools.Interactions.CLI::Int32 Predicts(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --predicts.TCS /pfam <pfam-string.csv> /prot <prot.fasta> /Db <interaction.xml>
  Example:      pitr --predicts.TCS
Help for command '--Profiles.Create':

Prototype: ProteinTools.Interactions.CLI::Int32 CreateProfiles(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --Profiles.Create /MiST2 <MiST2.xml> /pfam <pfam-string.csv> [/out <out.csv>]
  Example:      pitr --Profiles.Create
Help for command '--ProtFasta.Downloads':

Prototype: ProteinTools.Interactions.CLI::Int32 ProtFastaDownloads(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --ProtFasta.Downloads /in <sp.DIR>
  Example:      pitr --ProtFasta.Downloads
Help for command '--ProtFasta.Downloads.Batch':

Prototype: ProteinTools.Interactions.CLI::Int32 ProtFastaDownloadsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --ProtFasta.Downloads.Batch /in <sp.DIR.Source>
  Example:      pitr --ProtFasta.Downloads.Batch
Help for command '--signature':

Prototype: ProteinTools.Interactions.CLI::Int32 SignatureGenerates(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --signature /in <aln.fasta> [/p-cut <0.95>]
  Example:      pitr --signature
Help for command '--SwissTCS.Downloads':

Prototype: ProteinTools.Interactions.CLI::Int32 DownloadEntireDb(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\pitr.exe --SwissTCS.Downloads /out <out.DIR>
  Example:      pitr --SwissTCS.Downloads

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