PedScript is a tool that allows scripting of simple modifications to pedigree files.
Removes all individual identifiers from a pedigree file, replacing these with arbitrary ids.
List available commands.
Run a simple Mendelian inheritance check on the pedigrees.
Break all family links, marking everyone as unrelated. Can be useful when combined with the SAMPLE command, to ensure that the sampled pedigree is still valid.
READ DATA filename
Loads a data file with name filename.
READ PED filename
Loads a pedigree file with name filename. Should be preceded by a call to READ DATA.
This command samples a number of individuals or families to a file. The syntax is:
SAMPLE number [FOUNDERS|FAMILIES|PERSONS] TO file
For example, to sample 100 individuals to a file, you might issue the following series of commands:
NUKE TRIM WRITE DATA 100persons.dat SAMPLE 100 PERSONS TO 100persons.ped
This sequence of commands would do the following:
- The NUKE command would mark all individuals as unrelated, to ensure the resulting pedigree file is valid even if only a subset of individuals are sampled from some families.
- The TRIM command removes individuals with no data, so that all sampled individuals include some interesting information.
- The WRITE DATA command generates an appropriate data file.
- The SAMPLE command actually does the sampling.
The set command allows you to edit traits and covariates in the pedigree. It works as follows:
SET [TRAIT|COVAR] label TO value WHEN [TRAIT|COVAR|MARKER] label [COMPARISON] value
SET TRAIT glucose TO missing WHEN TRAIT glucose > 7
Remove uninformative individuals (those who don't have phenotype data are not essential to describe relationships between other pedigre members) from the pedigree.
WRITE DAT filename
WRITE PED filename
Write pedigree file.
Source tarball for pedscript is available from here.
PedScript was written in 2004 and is, currently, not actively maintained. If you find a bug, we'll try to fix it - e-mail Goncalo Abecasis.