Create param file

Automatic generation of parameter file

The library has a module bpf90tools.tools.tempconfig, which offers templates (examples) on how to correctly build an object with parameters to be passed to Params. You can take it from the lib and modify it.

The contents of tempconfig:

BASE_TEMPLET_SINGLE_BLUP = {
    'DATAFILE': [''],
    'TRAITS': [''],
    'FIELDS_PASSED TO OUTPUT': ['1'],
    'RESIDUAL_VARIANCE': ['0.5492E-01'],
    'EFFECT': ['8 cross alpha', '10 cov', '1 cross alpha'],
    'RANDOM': ['animal'],
    'FILE': [''],
    'FILE_POS': ['1 2 3 0 0'],
    '(CO)VARIANCES': ['0'],
    'OPTION sol': ['se'],
    'OPTION alpha_size': ['40'],
    'OPTION fact_once': ['memory'],
    'OPTION': ['use_yams'],
}

BASE_TEMPLET_SINGLE_GBLUP = {
    'DATAFILE': [''],
    'TRAITS': ['12'],
    'FIELDS_PASSED TO OUTPUT': ['1'],
    'RESIDUAL_VARIANCE': ['0.5492E-01'],
    'EFFECT': ['8 cross alpha', '10 cov', '1 cross alpha'],
    'RANDOM': ['animal'],
    'FILE': [''],
    'FILE_POS': ['1 2 3 0 0'],
    'SNP_FILE': [""],
    '(CO)VARIANCES': ['0'],
    'OPTION sol': ['se'],
    'OPTION alpha_size': ['40'],
    'OPTION fact_once': ['memory'],
    'OPTION': ['use_yams'],
}

Note

The object is a slavar, where key is the exact name of the parameter, value is the value or type of its property.

Note

The OPTION parameter can be grouped. It looks like this:

‘OPTION’: [‘sol se’, ‘alpha_size 40’, ‘fact_once memory’, ‘use_yams’].

Create param

Import lib:

from bpf90tools import Params

from bpf90tools.tools.tempconfig import (
    BASE_TEMPLET_SINGLE_BLUP,
    BASE_TEMPLET_SINGLE_GBLUP
)

1. Recording a template object

• for blup:

  create_param_blup = Params(
      file_config="./foldtest/test1/exm_create_param/param_exm_blup.txt"
  )
  create_param_blup.create(BASE_TEMPLET_SINGLE_BLUP)
  

Result:

#PARAMETER FILE
DATAFILE

TRAITS

FIELDS_PASSED TO OUTPUT
1
RESIDUAL_VARIANCE
    0.5492E-01
EFFECT
8 cross alpha
EFFECT
10 cov
EFFECT
1 cross alpha
RANDOM
animal
FILE

FILE_POS
1 2 3 0 0
(CO)VARIANCES
    0
OPTION sol se
OPTION alpha_size 40
OPTION fact_once memory
OPTION use_yams

• for gblup:

  create_param_gblup = Params(
      file_config="./foldtest/test1/exm_create_param/param_exm_gblup.txt"
  )
  create_param_gblup.create(BASE_TEMPLET_SINGLE_GBLUP)
  

Result:

#PARAMETER FILE
DATAFILE

TRAITS
12
FIELDS_PASSED TO OUTPUT
1
RESIDUAL_VARIANCE
    0.5492E-01
EFFECT
8 cross alpha
EFFECT
10 cov
EFFECT
1 cross alpha
RANDOM
animal
FILE

FILE_POS
1 2 3 0 0
SNP_FILE

(CO)VARIANCES
    0
OPTION sol se
OPTION alpha_size 40
OPTION fact_once memory
OPTION use_yams

2. Template modification - adding values in place of omissions

• for blup:

  object_param_blup = BASE_TEMPLET_SINGLE_BLUP.copy()
  object_param_blup.update({
      'DATAFILE': ['data.txt'],
      'TRAITS': ['2'],
      'RESIDUAL_VARIANCE': ['0.5492E-01'],
      'EFFECT': ['8 cross alpha', '6 cross alpha', '10 cov', '1 cross alpha'],
      'RANDOM': ['diagonal'],
      'FILE': ['pedigree.txt'],
  })
  
  create_param_blup = Params(
      file_config="./foldtest/test1/exm_create_param/param_exm_blup_mod.txt"
  )
  create_param_blup.create(object_param_blup)
  

Result:

#PARAMETER FILE
DATAFILE
data.txt
TRAITS
2
FIELDS_PASSED TO OUTPUT
1
RESIDUAL_VARIANCE
    0.5492E-01
EFFECT
8 cross alpha
EFFECT
6 cross alpha
EFFECT
10 cov
EFFECT
1 cross alpha
RANDOM
diagonal
FILE
pedigree.txt
FILE_POS
1 2 3 0 0
(CO)VARIANCES
    0
OPTION sol se
OPTION alpha_size 40
OPTION fact_once memory
OPTION use_yams

• for gblup:

  object_param_gblup = BASE_TEMPLET_SINGLE_GBLUP.copy()
  object_param_gblup.update({
      'DATAFILE': ['dataphen.txt'],
      'TRAITS': ['12'],
      'FIELDS_PASSED TO OUTPUT': ['1'],
      'RESIDUAL_VARIANCE': ['0.5492E-01'],
      'EFFECT': ['8 cross alpha', '10 cov', '1 cross alpha'],
      'RANDOM': ['animal'],
      'FILE': ['ped.txt'],
      'FILE_POS': ['1 2 3 0 0'],
      'SNP_FILE': ["snp.txt"],
      '(CO)VARIANCES': ['0.123'],
  })
  
  create_param_gblup = Params(
      file_config="./foldtest/test1/exm_create_param/param_exm_gblup_mod.txt"
  )
  create_param_gblup.create(object_param_gblup)
  

Result:

#PARAMETER FILE
DATAFILE
dataphen.txt
TRAITS
12
FIELDS_PASSED TO OUTPUT
1
RESIDUAL_VARIANCE
    0.5492E-01
EFFECT
8 cross alpha
EFFECT
10 cov
EFFECT
1 cross alpha
RANDOM
animal
FILE
ped.txt
FILE_POS
1 2 3 0 0
SNP_FILE
snp.txt
(CO)VARIANCES
    0.123
OPTION sol se
OPTION alpha_size 40
OPTION fact_once memory
OPTION use_yams

3. Composition of the object according to the proposed file

For example, we have this config:

DATAFILE
 datarep
TRAITS
 4
FIELDS_PASSED TO OUTPUT

WEIGHT(S)

RESIDUAL_VARIANCE
  1.0
EFFECT
 2 cross alpha
EFFECT
 3 cross alpha
EFFECT
 8 cov
EFFECT
 1 cross alpha
RANDOM
 animal
OPTIONAL
 pe
FILE
 ped1
FILE_POS
 1 2 3 0 0
PED_DEPTH
 3
(CO)VARIANCES
  0.65
(CO)VARIANCES_PE
  0.21

In the form of a dictionary:

object_param = {
    'DATAFILE': ['datarep'],
    'TRAITS': ['4'],
    'FIELDS_PASSED TO OUTPUT': [''],
    'WEIGHT(S)': [''],
    'RESIDUAL_VARIANCE': ['1.0'],
    'EFFECT': ['2 cross alpha', '3 cross alpha', '8 cov', '1 cross alpha'],
    'RANDOM': ['animal'],
    'FILE': ['ped1'],
    'FILE_POS': ['1 2 3 0 0'],
    'PED_DEPTH': ['3'],
    '(CO)VARIANCES': ['0.65'],
    '(CO)VARIANCES_PE': ['0.21'],
}

Generate param:

create_param = Params(
    file_config="./foldtest/test1/exm_create_param/param_exm_rand.txt"
)
create_param.create(object_param)

Result:

#PARAMETER FILE
DATAFILE
datarep
TRAITS
4
FIELDS_PASSED TO OUTPUT

WEIGHT(S)

RESIDUAL_VARIANCE
    1.0
EFFECT
2 cross alpha
EFFECT
3 cross alpha
EFFECT
8 cov
EFFECT
1 cross alpha
RANDOM
animal
FILE
ped1
FILE_POS
1 2 3 0 0
PED_DEPTH
3
(CO)VARIANCES
    0.65
(CO)VARIANCES_PE
0.21