PedScript

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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.