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Microarray template format

Every microarray template file is made by three different sections:

  1. A line that starts in ## containing metadata info for the file itself
  2. (Optional) Several lines containing comments starting in #
  3. (Optional) Lines that will be skipped
  4. Several lines containing the actual entries of the file

1. Metadata

The metadata line is essentialy a JSON with the following field:

  1. input_format: specify the format of the lines in the 3rd sections (e.g., {id}\t{chromosome}\t{position}\n)
  2. output_format: specify how a microarray file will be generated starting by the template (e.g., {id}\t{chromosome}\t{position}\t{result}\n)
  3. file_extention: specify the extension of the output file (e.g., .txt)
  4. undetermined: specify what's the placeholder to indicate that a result is not available (e.g., 00)
  5. skip: how many lines to skip after the header

2. Comments

The comments are lines starting with a #. In the future it will be possible to use Jinjia variables here but at the moment this feature is not implemented.

3. Result entries

Each line here must match the format specified in input_format.

Example

Putting all together, this is an example of a valid template file: 

## {"input_format":"{id}\t{chromosome}\t{position}\n", "output_format":"{id}\t{chromosome}\t{position}\t{result}\n", "file_extension":".txt", "undetermined":"--", "skip":1}
# This is a comment
rsid    chromosome  position    genotype
rs00001 chr1    1

Using a VCF file to populate a microarray file with this template will produce a file that can be like this as it matches the output_format specified above: 

# This is a comment
rsid    chromosome  position    genotype
rs00001 chr1    1   AA