PedScript
PedScript is a tool that allows scripting of simple modifications to pedigree files.
Available Commands
ANONYMIZE
Removes all individual identifiers from a pedigree file, replacing these with arbitrary ids.
HELP
List available commands.
MENDELCHECK
Run a simple Mendelian inheritance check on the pedigrees.
NUKE
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.
QUIT
Terminate program!
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.
SAMPLE
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.
SET
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
For example:
SET TRAIT glucose TO missing WHEN TRAIT glucose > 7
TRIM
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 datafile.
WRITE PED filename
Write pedigree file.
Download
Source tarball for pedscript is available from here.
Development Status
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.