complex.txt

emboss的linux版本的源代码

                                  complex 



Function

   Find the linguistic complexity in nucleotide sequences

Description

Usage

   Here is a sample session with complex


% complex -omnia 
Find the linguistic complexity in nucleotide sequences
Input nucleotide sequence(s): tembl:*
Window length [100]: 
Step size [5]: 
Minimum word length [4]: 
Maximum word length [6]: 
Output file [hs989235.complex]: 
output sequence(s) [hs989235.fasta]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   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 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

Input file format

  Input files for usage example

   'tembl:*' is a sequence entry in the example nucleic acid database
   'tembl'

Output file format

   Sequence TEMBL:HHTETRA contains repeats and is included in the test
   database for repeat analysis.

  Output files for usage example

  File: complex.ujtable

  File: hs989235.complex

Length of window : 100
jmin : 4
jmax : 6
step : 5
Execution without simulation
----------------------------------------------------------------------------
|                  |                  |                  |                  |
|     number of    |      name of     |     length of    |      value of    |
|     sequence     |     sequence     |     sequence     |     complexity   |
|                  |                  |                  |                  |
----------------------------------------------------------------------------
         1                    HS989235            495             0.7210
         2                    AB009602            561             0.6688
         3                      HSCAD5           3170             0.6921
         4                         HSD            781             0.6991
         5                      HSEGL1           3919             0.6618
         6                       HSFAU            518             0.6739
         7                      HSFAU1           2016             0.7105
         8                       HSFOS           6210             0.6681
         9                       HSEF2           3075             0.6925
        10                        HSHT           1658             0.7314
        11                       HSTS1          18596             0.6668
        12                      HSNFG9          33760             0.6661
        13                    AB000095           2399             0.6569
        14                    AB009062            532             0.6465
        15                     HSFERG1            512             0.5609
        16                     HSFERG2           1132             0.7217
        17                    AC004629         116019             0.6478
        18                    AP000504         100000             0.6611
        19                    AF129756         184666             0.6562
        20                    AB000360           2582             0.6710
        21                       HSHBB          73308             0.6544
        22                     CEZK637          40699             0.6307
        23                      PDRHOD           1675             0.6201
        24                    AAHSP70B           4712             0.7110
        25                      GMGL01           3400             0.3981
        26                    GMLLBPS1            852             0.5986
        27                    GMLLBPS2           1698             0.5225
        28                       ECLAC           7477             0.7137
        29                      ECLACA           1832             0.6916
        30                      ECLACI           1113             0.7480
        31                      ECLACY           1500             0.6801
        32                      ECLACZ           3078             0.7278
        33                      PAAMIB           1212             0.6596