Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe --align /query <query.csv> /subject <subject.csv> [/out <out.DIR> /inst]
  Example:      SMART --align 

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe --align.family /In <In.bbh.csv> /query <query-pfam.csv> /subject <subject-pfam.csv> [/out <out.DIR> /mp <mp-align:0.65> /lev <lev-align:0.65>]
  Example:      SMART --align.family 

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe -build_cache -i <fsa_file> [-o <export_file> -db <cdd_db_name> -cdd <cdd_db_path> -grep_script <script>]
  Example:      SMART -build_cache 

       [-cdd]
    Description:  The cdd database directory, if this switch value is null then system will using the default position in the profile file.

    Example:      -cdd ""

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe 
  Example:      SMART -buildsmart 

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe convert -i <input_file> [-o <xml_file>]
  Example:      SMART convert 

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe export -keyword <keyword_list> [-m <any/all>] -o <export_file> [-d <db_name> -casesense <T/F>]
  Example:      SMART export 

    -d
    Description:  This switch value can be both a domain database name or a fasta file path.

    Example:      -d ""

-keyword
    Description:  The keyword list will be use for the sequence record search, each keyword should seperated by comma character.

    Example:      -keyword "HTH,GGDEF,Clp,REC"

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe --Export.Domains /in <pfam-string.csv>
  Example:      SMART --Export.Domains 

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe --Export.Pfam-String /in <blast_out.txt>
  Example:      SMART --Export.Pfam-String 

  Information:  Family Annotation by MPAlignment
  Usage:        G:\GCModeller\manual\bin\SMART.exe --Family.Align /query <pfam-string.csv> [/threshold 0.65 /mp 0.65 /Name <null>]
  Example:      SMART --Family.Align 

       [/Name]
    Description:  The database name of the aligned subject, if this value is empty or not exists in the source, then the entired Family database will be used.

    Example:      /Name ""

  Information:  Build the Family database for the protein family annotation by MPAlignment.
  Usage:        G:\GCModeller\manual\bin\SMART.exe --Family.Domains /regprecise <regulators.fasta> /pfam <pfam-string.csv>
  Example:      SMART --Family.Domains 

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe --Family.Stat /in <anno_out.csv>
  Example:      SMART --Family.Stat 

  Information:  The gene id in the blast output log file are not well format for reading and program processing, so before you generate the venn diagram you should call this command to parse the gene id from the log file. You can also done this id parsing job using other tools.
  Usage:        G:\GCModeller\manual\bin\SMART.exe grep -i <xml_log_file> -q <script_statements> -h <script_statements>
  Example:      SMART grep grep -i C:\Users\WORKGROUP\Desktop\blast_xml_logs\1__8004_ecoli_prot.log.xml -q "tokens | 4" -h "'tokens | 2';'tokens ' ' 0'"

    -q
    Description:  The parsing script for parsing the gene_id from the blast log file, this switch value is consist of sevral operation tokens, and each token is separate by the ';' character and the token unit in each script token should seperate by the ' character.
              There are two basic operation in this parsing script:
               tokens - Split the query or hit name string into sevral piece of string by the specific delimiter character and           get the specifc location unit in the return string array.
                 Usage:   tokens <delimiter> <position>
                 Example: tokens | 3 match - match a gene id using a specific pattern regular expression.
                 usage:   match <regular_expression>
                 Example: match .+[-]\d{5}

    Example:      -q "'tokens | 5';'match .+[-].+'"

-h
    Description:  The parsing script for parsing the gene_id from the blast log file, this switch value is consist of sevral operation tokens, and each token is separate by the ';' character and the token unit in each script token should seperate by the ' character.
              There are two basic operation in this parsing script:
               tokens - Split the query or hit name string into sevral piece of string by the specific delimiter character and           get the specifc location unit in the return string array.
                 Usage:   tokens <delimiter> <position>
                 Example: tokens | 3 match - match a gene id using a specific pattern regular expression.
                 usage:   match <regular_expression>
                 Example: match .+[-]\d{5}

    Example:      -h "'tokens | 5';'match .+[-].+'"

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe --manual-Build /pfam-string <pfam-string.csv> /name <familyName>
  Example:      SMART --manual-Build 

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe --MPAlignment /sbh <sbh.csv> /query <pfam-string.csv> /subject <pfam-string.csv> [/mp <0.65> /out <out.csv>]
  Example:      SMART --MPAlignment 

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe pure_domain -i <input_smart_log> -o <output_file>
  Example:      SMART pure_domain 

  Information:  
  Usage:        G:\GCModeller\manual\bin\SMART.exe --SelfAlign /query <pfam-string.csv> /subject <subject.csv> /aln <mpalignment.csv> [/lstID <lstID.txt> /mp <0.65> /id <id>]
  Example:      SMART --SelfAlign 

       [/lstID]
    Description:  If this parameter is not empty, then the /aln parameter will be disable

    Example:      /lstID ""

   [/id]
    Description:  If this parameter is not null, then the record of this query or hits will be used to subset the alignment set.

    Example:      /id ""