tcode.ihelp

emboss的linux版本的源代码

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -window             integer    [200] This is the number of nucleotide bases
                                  over which the TESTCODE statistic will be
                                  performed each time. The window will then
                                  slide along the sequence, covering the same
                                  number of bases each time. (Integer 200 or
                                  more)
*  -outfile            report     [*.tcode] Output report file name
*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -datafile           datafile   [Etcode.dat] The default data file is
                                  Etcode.dat and contains coding probabilities
                                  for each base. The probabilities are for
                                  both positional and compositional
                                  information.
   -step               integer    [3] The selected window will, by default,
                                  slide along the nucleotide sequence by three
                                  bases at a time, retaining the frame
                                  (although the algorithm is not frame
                                  sensitive). This may be altered to increase
                                  or decrease the increment of the slide.
                                  (Integer 1 or more)
   -plot               toggle     [N] On selection a graph of the sequence (X
                                  axis) plotted against the coding score (Y
                                  axis) will be displayed. Sequence above the
                                  green line is coding, that below the red
                                  line is non-coding.

   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
   -rformat            string     Report format
   -rname              string     Base file name
   -rextension         string     File name extension
   -rdirectory         string     Output directory
   -raccshow           boolean    Show accession number in the report
   -rdesshow           boolean    Show description in the report
   -rscoreshow         boolean    Show the score in the report
   -rusashow           boolean    Show the full USA in the report
   -rmaxall            integer    Maximum total hits to report
   -rmaxseq            integer    Maximum hits to report for one sequence

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         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