cgout

Saves the output of CarthaGène to a file. This is different from cgsave that allows to save the current state of CarthaGène (in order to later restore it). cgout is intended merely to build log file.

Synopsis:

The cgout command is invoked either as:

• cgout Options
• cgout FilePath

Description:

The cgout command enables to save the output of the session in a file specified by the FilePath argument. If the file already exist, the output is appened to the end of the file. If a output file was already specified, the old log file is closed and the output goes to the new one.This process is terminated by using a empty string or by ending CarthaGene.

Only the inputs and outputs of the correct commands of Carthagene will be saved. You may want to launch the shell with the tee command ( under Unix) to keep a complete log (tclsh | tee logfile).

Arguments:

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
• FilePath: the path to a valid text file existing or not.

Example:

CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /homes/thomas/carthagene/test/Data/bc.cg}
CG> sem

Map -1 : log10-likelihood =  -297.78
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS3 MS4 MS5 MS6 MS7 MS8 MS9 MS10 MS11 MS12 MS13 MS14 MS15 MS...

CG> exec rm -f "carthagene.log"
...
CG> cgout "carthagene.log"

CG> heaprintd
...
CG> cgout ""

CG> exec cat "carthagene.log"

CG_log> heaprintd

Map  0 : log10-likelihood =  -297.78, log-e-likelihood =  -685.66
-------:

Data Set Number  1 :

      Markers        Distance    Cumulative  Distance   Theta       2pt
Pos  Id name         Haldane     Haldane     Kosambi    (%%age)      LOD

  1   1  MS1          19.5 cM     19.5 cM     16.8 cM    16.2 %%    15.7
  2   2  MS2           0.6 cM     20.1 cM      0.6 cM     0.6 %%    47.6
  3   3  MS3           5.8 cM     25.9 cM      5.5 cM     5.5 %%    35.1
  4   4  MS4           3.7 cM     29.6 cM      3.6 cM     3.5 %%    21.1
  5   5  MS5           3.7 cM     33.3 cM      3.6 cM     3.6 %%    15.4
  6   6  MS6           1.6 cM     34.9 cM      1.6 cM     1.6 %%    17.3
  7   7  MS7           6.7 cM     41.6 cM      6.3 cM     6.3 %%    35.1
  8   8  MS8           2.2 cM     43.8 cM      2.2 cM     2.2 %%    40.8
  9   9  MS9           3.0 cM     46.8 cM      2.9 cM     2.9 %%     7.2
 10  10 MS10           5.4 cM     52.2 cM      5.1 cM     5.1 %%     3.6
 11  11 MS11           8.6 cM     60.7 cM      7.9 cM     7.9 %%    10.9
 12  12 MS12           0.0 cM     60.7 cM      0.0 cM     0.0 %%    18.7
 13  13 MS13           0.0 cM     60.7 cM      0.0 cM     0.0 %%     6.0
 14  14 MS14           5.8 cM     66.6 cM      5.5 cM     5.5 %%     0.0
 15  15 MS15           4.6 cM     71.1 cM      4.4 cM     4.4 %%    26.6
 16  16 MS16          26.1 cM     97.2 cM     21.6 cM    20.3 %%     6.3
 17  17 MS17           0.0 cM     97.2 cM      0.0 cM     0.0 %%    16.0
 18  18 MS18           4.9 cM    102.1 cM      4.7 cM     4.6 %%    27.1
 19  19 MS19           3.0 cM    105.1 cM      2.9 cM     2.9 %%    34.8
 20  20 MS20        ----------              ----------
                     105.1 cM                 95.0 cM


       20 markers, log10-likelihood =  -297.78
                   log-e-likelihood =  -685.66

        EM calls:
           Set  1 : 2 (1,0)
        CPU Time (secs): 0.01
        Maps within -3.0: 1

CG_log> cgout
CG>