Load genotypes

#This is a demo file
#Usage: java -Xms1500m -Xmx2500m -jar GWASpi.jar script scriptFile [log cli.log]
data-dir=/GWASpi/data/
[script]
0.command=load_genotypes
1.study-id=1
2.format=PLINK
3.use-dummy-samples=true
4.new-matrix-name=Matrix 42
5.description=Load genotypes of batch 42
6.file1-path=/GWASpi/input/Plink/mi_input.map
7.file2-path=/GWASpi/input/Plink/mi_input.ped
8.sample-info-path=no info file
[/script]

Line by line…

Let’s look into the example above and explain it line by line:

  • First we see two lines starting with a "#" character. These are comment lines and you can have as many as you want, as long as they start with "#".
  • Next, the "data-dir=/GWASpi/data/" line specifies where GWASpi’s datae has to be stored. If the database doesn’t allready exist, a new and empty one will be created at the specified path.
  • Following these lines starts the "[script][/script]" block itself.
  • Next comes the call to the operation command, in this case 0.command=load_genotypes

Following the operation call you will need to list a number of parameters. Each specific operation call has a given number and types of calls, which you will have to respect in name and order for the operation to run sucessfully:

  1. study-id= <- This is the Study ID of the study the new genotypes have to be loaded under. If you set this value to "1.study-id=New Study" the genotype matrix will be loaded to a fresh Study.
  2. format= <- Indicate the format/technology the data is provided in (GWASpi, PLINK…)
  3. use-dummy-samples=true <- Indicate if the samples have to be generated as dummies from the provided fomar files instead of a Sample-Info file in GWASpi format [true/false].
  4. new-matrix-name= <- The name the new matrix will show. Free text, 64 characters long.
  5. description= <- Description of the matrix. Free text, 2000 characters long.
  6. file1-path= <- Path to the 1st file, as specified in the first GUI field for the given format.
  7. file2-path= <- Path to the 2nd file, as specified in the second GUI field for the given format.
  8. sample-info-path= <- Path to the Sample-Info file, as specified in the third GUI field for the given format. This can be left empty if use-dummy-samples=true