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CurrentModule = BeefBLUP
beefblup Command Line Interface (CLI) documentation
A work in progress
Notice: This document is a draft for what the command-line interface for beefblup would look like as of version 1.0, if beefblup was even a command-line application to begin with (it's not). It is modeled (loosely) after the man page format. It is not intended to be taken seriously, but instead to serve as a useful thought experiment and brainstorming ground on the future of beefblup. Please use it if it clarifies things for you. If it doesn't, ignore it.
Input file
beefblup requires a very specific format of input file. The format may be in comma-separated values (CSV) or Excel 2007+ (XLSX) format. CSV files should not be quoted (and therefore cannot have commas within cell values). Other formats may be forthcoming.
A beefblup data file must have at least six columns appearing in this order:
- ID
- Sire ID
- Dam ID
- Birthdate
- Fixed effect(s)
- Response variable(s)
The first row always contains column names. The values of column names are unimportant for the first four columns, as they will always be treated the same regardless of the name. The generated report will use the column names of fixed effects and response variables as given.
Each fixed effect should have its own column, to as many as are needed. There is no limit to the number of fixed effects as defined by beefblup, however its dependencies might have some. The same rules apply to response variables.
Unknown values should be left blank (,,). Do not substitute null placeholders
(e.g. NULL, NA, 0, nothing, undefined, etc.) for unknown values.
An example spreadsheet might have the following format
| ID | Sire ID | Dam ID | Birthdate | Sex | Weaning Weight |
|---|---|---|---|---|---|
| 1 | 1/1/1990 | Male | 354 | ||
| 2 | 1 | 1/1/1990 | Female | 251 | |
| 3 | 1 | 1/1/1991 | Male | 327 | |
| 4 | 1 | 2 | 1/1/1991 | Female | 328 |
| 5 | 2 | 1/1/1991 | Male | 301 | |
| 6 | 1/1/1991 | Female | 270 | ||
| 7 | 1/1/1992 | Male | 330 |
Synopsis
beefblup [-G SNPs_file] [-M num_response_vars] [-o report_spreadsheet]
[--no-aod] [--no-year] [--no-season] [--no-autob] [--maternal] input_file
[report_file]
Command line basic syntax
The most basic input is to simply pass the input file name to the program.
beefblup filename.csv
In this case beefblup will insert fixed-effects for age-of-dam, year, and
season, and will calculate the EBVs for the response variable in the final
column. The report will then be saved as filename_report.txt.
Suppressing automatically-calculated fixed effects
If you don't wish to include one of the automatically calculated fixed-effects from your model, you can pass arguments to suppress them.
Suppress Age-of-dam
beefblup --no-aod filename.csv
Suppress year
beefblup --no-year filename.csv
Suppress season
beefblup --no-season filename.csv
Suppress all calculated fixed effects
beefblup --no-autob filename.csv
The argument --no-autob comes from the nomenclature of assigning fixed-effects
to the matrix b in Henderson's mixed-model equations.