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https://github.com/MillironX/beefblup.git
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46 lines
1.2 KiB
Bash
Executable file
46 lines
1.2 KiB
Bash
Executable file
#!/bin/bash
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#=
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exec julia --project="$(realpath "$(dirname "${BASH_SOURCE[0]}")")" "${BASH_SOURCE[0]}" "$@"
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=#
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# beefblup cli
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# Provides a convenient CLI for using beefblup
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# cSpell:includeRegExp #.*
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# cSpell:includeRegExp ("""|''')[^\1]*\1
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# Import packages
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using BeefBLUP
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using ArgParse
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# If this is run without arguments, catch that before parsing
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if isempty(ARGS)
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BeefBLUP.beefblup()
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exit()
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end
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# Setup the argument table
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argsettings = ArgParseSettings()
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@add_arg_table argsettings begin
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"datafile"
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help = "datasheet containing the pedigree, fixed effects, and response trait formatted in CSV"
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required = true
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arg_type = String
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"resultsfile"
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help = "filename for storing the results of the analysis"
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required = false
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arg_type = String
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"--heritability", "-t"
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help = "heritability of the response trait being analyzed"
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required = true
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arg_type = Float64
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end
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arguments = parse_args(argsettings)
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h2 = arguments["heritability"]
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if isnothing(arguments["resultsfile"])
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BeefBLUP.beefblup(arguments["datafile"], h2)
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exit()
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end
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BeefBLUP.beefblup(arguments["datafile"], arguments["resultsfile"], h2)
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