textsearch.ihelp

emboss的linux版本的源代码

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-pattern]           string     The search pattern is a regular expression.
                                  Use a | to indicate OR.
                                  For example:
                                  human|mouse
                                  will find text with either 'human' OR
                                  'mouse' in the text (Any string is accepted)
  [-outfile]           outfile    [*.textsearch] Output file name

   Additional (Optional) qualifiers:
   -casesensitive      boolean    [N] Do a case-sensitive search
   -html               boolean    [N] Format output as an HTML table

   Advanced (Unprompted) qualifiers:
   -only               boolean    [N] This is a way of shortening the command
                                  line if you only want a few things to be
                                  displayed. Instead of specifying:
                                  '-nohead -noname -nousa -noacc -nodesc'
                                  to get only the name output, you can specify
                                  '-only -name'
   -heading            boolean    [@(!$(only))] Display column headings
   -usa                boolean    [@(!$(only))] Display the USA of the
                                  sequence
   -accession          boolean    [@(!$(only))] Display 'accession' column
   -name               boolean    [@(!$(only))] Display 'name' column
   -description        boolean    [@(!$(only))] Display 'description' column

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages