complex.ihelp

来自「emboss的linux版本的源代码」· IHELP 代码 · 共 83 行

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -lwin               integer    [100] Window length (Any integer value)
   -step               integer    [5] Displacement of the window over the
                                  sequence (Any integer value)
   -jmin               integer    [4] Minimum word length (Integer from 2 to
                                  20)
   -jmax               integer    [6] Maximum word length (Integer from 2 to
                                  50)
  [-outfile]           outfile    [*.complex] Output file name
*  -outseq             seqoutall  [<sequence>.<format>] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -omnia              toggle     [N] Calculate over a set of sequences
   -sim                integer    [0] Calculate the linguistic complexity by
                                  comparison with a number of simulations
                                  having a uniform distribution of bases (Any
                                  integer value)
   -freq               boolean    [N] Execute the simulation of a sequence
                                  based on the base frequency of the original
                                  sequence
   -print              boolean    [N] Generate a file named UjTable containing
                                  the values of Uj for each word j in the
                                  real sequence(s) and in any simulated
                                  sequences
   -ujtablefile        outfile    [complex.ujtable] Program complex temporary
                                  output file

   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
   -odirectory2        string     Output directory

   "-ujtablefile" associated qualifiers
   -odirectory         string     Output directory

   "-outseq" associated qualifiers
   -osformat           string     Output seq format
   -osextension        string     File name extension
   -osname             string     Base file name
   -osdirectory        string     Output directory
   -osdbname           string     Database name to add
   -ossingle           boolean    Separate file for each entry
   -oufo               string     UFO features
   -offormat           string     Features format
   -ofname             string     Features file name
   -ofdirectory        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