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[[Category: Software]]
[[Category: Software]]
'''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.
== Download ==
== Download ==
Source tarball for pedscript is available from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-pedscript-2010-06-04.tar.gz here].
Source tarball for pedscript is available from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-pedscript-2010-06-04.tar.gz 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 [mailto:goncalo@umich.edu Goncalo Abecasis].
