Use tools f90

This module discusses examples of using shell objects to run BLUPF90 programs

Import libs:

from bpf90tools import (
    Renumf90,
    AIremlf90,
    Remlf90,
    Blupf90
)

Renumf90

Data processing and preparation using:

renum = Renumf90(
    app="renumf90",                 # for win renumf90.exe
    work_dir="./foldtest/test1",
    fn_par="param.txt"
)
renum.run()

The result of the renumf90 program execution is a set of files (more details in doc.): renadd04.ped, renf90.fields, renf90.dat, renf90.inb, renf90.par, renf90.tables.

Note

renumf90_console_output.log is a file generated by the shell. It stores information about program execution, which is output to the console.

AIremlf90

Using AIremlf90 to calculate variances:

aireml = AIremlf90(
    app="airemlf90",                # for win airemlf90.exe
    work_dir="./foldtest/test1",
    fn_par="renf90.par"
)
aireml.run()

The result of the program operation is saved to the file airemlf90.log:

AIREMLF90 ver. 1.149
 In round         36 convergence =  0.712257048487E-03
 delta convergence =  0.994040299577E-06
-2logL =       0.24653657     : AIC =        4.2465366
Genetic variance(s) for effect  4
  0.71609E-04
Residual variance(s)
  0.41366
inverse of AI matrix (Sampling Variance)
  0.13285E-05 -0.48971E-06
 -0.48971E-06  0.11398
Correlations from inverse of AI matrix
   1.0000     -0.12585E-02
 -0.12585E-02   1.0000
SE for G
  0.11526E-02
SE for R
  0.33761

Note

airemlf90_console_output.log is a file generated by the shell. It stores information about program execution, which is output to the console.

Remlf90

Using of Remlf90 to calculate variants:

reml = Remlf90(
    app="remlf90",                      # for win airemlf90.exe
    work_dir="./foldtest/test1",
    fn_par="renf90.par"
)
reml.run()

The result of the program operation is saved to the file remlf90.log:

REMLF90 ver. 1.86
 Final Estimates
Genetic variance(s) for effect  4
  0.9417E-04
Residual variance(s)
  0.9420
 In round       4148 convergence =  0.996781495046E-10
-2logL =        1.4856567       AIC =        5.4856567

Note

remlf90_console_output.log is a file generated by the shell. It stores information about program execution, which is output to the console.

Blupf90

Using Blupf90 to calculate breeding value estimates:

blup = Blupf90(
    app="blupf90",                  # for win blupf90.exe
    work_dir="./foldtest/test1",
    fn_par="renf90.par"
)
blup.run()

The result of the execution is stored in the solutions file:

trait/effect level  solution          s.e.
   1   1         1         -0.21337720          0.47468396
   1   1         2          0.00000000          0.00000000
   1   2         1        -12.45754690         22.12147091
   1   2         2        -11.60488568         21.96909516
   1   2         3        -12.63970827         22.99779542
   1   2         4        -12.25754758         22.12147643
   1   3         1         22.05395473         21.91343740
   1   4         1          0.00005158          0.00897511
   1   4         2          0.00005618          0.00846196
   1   4         3         -0.00002650          0.00846193
   1   4         4          0.00004680          0.00846186
   1   4         5         -0.00002956          0.00846189
   1   4         6          0.00000149          0.00846216
   1   4         7          0.00003811          0.00897534
   1   4         8          0.00001997          0.00897535
   1   4         9          0.00000303          0.00872283
   1   4        10          0.00003390          0.00846213
   1   4        11          0.00001065          0.00846213
   1   4        12         -0.00002415          0.00846214
   1   4        13         -0.00000962          0.00846214
   1   4        14         -0.00002326          0.00846211
   1   4        15          0.00001248          0.00846213