Xfam - SMRUCC/GCModeller GitHub Wiki

title: Xfam tags: [maunal, tools] date: 7/27/2016 6:40:32 PM

GCModeller [version 1.0.0.0]

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

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

Function API Info
/Export.Blastn
/Export.Blastn.Batch
/Export.hmmscan
/Export.hmmsearch
/Export.Pfam.UltraLarge
/Load.cmscan
/Load.cmsearch
/Rfam
/Rfam.Align
/Rfam.GenomicsContext
/Rfam.Regulatory
/Rfam.Regulons
/Rfam.SeedsDb.Dump
/Rfam.Sites.seq
--Install.Rfam

Commands

Help for command '/Export.Blastn':

Prototype: Xfam.CLI::Int32 ExportBlastn(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Export.Blastn /in <blastout.txt> [/out <blastn.Csv>]
  Example:      Xfam /Export.Blastn
Help for command '/Export.Blastn.Batch':

Prototype: Xfam.CLI::Int32 ExportBlastns(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Export.Blastn.Batch /in <blastout.DIR> [/out outDIR /large /num_threads <-1> /no_parallel]
  Example:      Xfam /Export.Blastn.Batch
Help for command '/Export.hmmscan':

Prototype: Xfam.CLI::Int32 ExportHMMScan(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Export.hmmscan /in <input_hmmscan.txt> [/evalue 1e-5 /out <pfam.csv>]
  Example:      Xfam /Export.hmmscan
Help for command '/Export.hmmsearch':

Prototype: Xfam.CLI::Int32 ExportHMMSearch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Export.hmmsearch /in <input_hmmsearch.txt> [/prot <query.fasta> /out <pfam.csv>]
  Example:      Xfam /Export.hmmsearch
Help for command '/Export.Pfam.UltraLarge':

Prototype: Xfam.CLI::Int32 ExportUltraLarge(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Export.Pfam.UltraLarge /in <blastOUT.txt> [/out <out.csv> /evalue <0.00001> /coverage <0.85> /offset <0.1>]
  Example:      Xfam /Export.Pfam.UltraLarge
Help for command '/Load.cmscan':

Prototype: Xfam.CLI::Int32 LoadDoc(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Load.cmscan /in <stdout.txt> [/out <out.Xml>]
  Example:      Xfam /Load.cmscan
Help for command '/Load.cmsearch':

Prototype: Xfam.CLI::Int32 LoadCMSearch(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Load.cmsearch /in <stdio.txt> /out <out.Xml>
  Example:      Xfam /Load.cmsearch
Help for command '/Rfam':

Prototype: Xfam.CLI::Int32 RfamAnalysis(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Rfam /in <blastMappings.Csv.DIR> /PTT <pttDIR> [/prefix <sp_prefix> /out <out.Rfam.csv> /offset 10 /non-directed]
  Example:      Xfam /Rfam

Parameters information:

       [/prefix]
    Description:  Optional for the custom RNA id, is this parameter value is nothing, then the id prefix will be parsed from the PTT file automaticslly.

    Example:      /prefix ""

Accepted Types

/prefix
Help for command '/Rfam.Align':

Prototype: Xfam.CLI::Int32 RfamAlignment(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Rfam.Align /query <sequence.fasta> [/rfam <DIR> /out <outDIR> /num_threads -1 /ticks 1000]
  Example:      Xfam /Rfam.Align

Parameters information:

       [/formatdb]
    Description:  If the /rfam directory parameter is specific and the database is not formatted, then this value should be TRUE for local blast. 
                   If /rfam parameter is not specific, then the program will using the system database if it is exists, and the database is already be formatted as the installation of the database is includes this formation process.

    Example:      /formatdb ""

Accepted Types

/formatdb
Help for command '/Rfam.GenomicsContext':

Prototype: Xfam.CLI::Int32 RfamGenomicsContext(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Rfam.GenomicsContext /in <scan_sites.Csv> /PTT <genome.PTT> [/dist 500 /out <out.csv>]
  Example:      Xfam /Rfam.GenomicsContext
Help for command '/Rfam.Regulatory':

Prototype: Xfam.CLI::Int32 RfamRegulatory(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Rfam.Regulatory /query <RfamilyMappings.csv> /mast <mastsites.csv> [/out <out.csv>]
  Example:      Xfam /Rfam.Regulatory
Help for command '/Rfam.Regulons':

Prototype: Xfam.CLI::Int32 RFamRegulons(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Rfam.Regulons /in <cmsearch.hits.csv> /regulons <regprecise.regulons.hits.csv> [/out <out.csv>]
  Example:      Xfam /Rfam.Regulons
Help for command '/Rfam.SeedsDb.Dump':

Prototype: Xfam.CLI::Int32 DumpSeedsDb(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Rfam.SeedsDb.Dump /in <rfam.seed> [/out <rfam.csv>]
  Example:      Xfam /Rfam.SeedsDb.Dump
Help for command '/Rfam.Sites.seq':

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

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe /Rfam.Sites.Seq /nt <nt.fasta> /sites <sites.csv> [/out out.fasta]
  Example:      Xfam /Rfam.Sites.seq
Help for command '--Install.Rfam':

Prototype: Xfam.CLI::Int32 InstallRfam(Microsoft.VisualBasic.CommandLine.CommandLine)

  Information:  
  Usage:        G:\GCModeller\manual\bin\Xfam.exe --Install.Rfam /seed <rfam.seed>
  Example:      Xfam --Install.Rfam

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