relped

README

relped

relped builds a pedigree from relatedness.

Installation

Before using relped there are a few programs you need to install:

• Git: allows you to download relped
• Go: allows you to compile relped
• Graphviz: allows you to render relped's output

After installing the programs above, getting relped installed should be as easy as:

go get -u github.com/rhagenson/relped

Input

relped has one required input, Relatedness, and two optional inputs, Parentage and Demographics.

Relatedness

Example:

ID1,ID2,Rel
123,456,0.50
...

Note that your columns must be named ID1,ID2, and Rel. If your file has duplicate entries of the same ID pair in either order, only the last entry will be used. Rel entries may be either a decimal value or one of: PO, FS, HS, U, indicating known parent-offspring, full-sibling, half-sibling, or unrelated pair, respectively.

Parentage

Example:

ID,Sire,Dam
123,456,789
...

Note that your columns must be named ID,Sire, and Dam. If your file contains duplicate ID entries, only the last entry will be used.

Sire and Dam are used the same as if you had added a PO called record into the relatedness input between ID and either Sire or Dam with the additional information of known direction such that Sire and Dam are plotted above ID in the pedigree. Unknown Sire and/or Dam may be denoted via a 0 or ? entry.

Demographics

Example:

ID,Sex,BirthYear
123,Male,1990
...

Note that your columns must be named ID,Sex, and BirthYear. If your file contains duplicate ID entries, only the last entry will be used. Sex entries of either full word or first letter are recognized (e.g. M or Male) -- matching is case insensitive.

Sex is used to change the formatting attributes in the pedigree to distinguish males, females, and individuals of unknown sex. BirthYear is converted to age in the current year under the assumption that all birthdays have passed this year and helps to direct the pedigree so older individuals are plotted above younger individuals.

Output

relped produces a Graphviz-formatted file (directed or undirected, depending on input) with attributes deemed visually appropriate for building pedigrees. Unlike in a typically pedigree, all nodes at the same level in the plot may not be the same age, however all connections will be the same between runs of relped.

Producing multiple plots

Due to the unavoidable randomness of how a pedigree is laid out by Graphviz, the below command template can be used to build multiple plots consecutively so that you may pick the most visually appropriate pedigree.

for run in {1..10}
do
  relped build \
    --relatedness <relatedness> \
    --demographics <demographics> \
    --parentage <parentage> \
    --output $run-<output> \
  && dot -Tsvg -O $run-<output>
done

What the above does is loop through the numbers 1-10 (assigning the current number to run), then calls relped with your inputs (<relatedness>, <demographics>, and <parentage>) and writes multiple output files that are prepended with the run number ($run-<output>) -- then it calls Graphviz to produce rendered images in the format stated (note there is no space in -Tsvg).

Contributing

If you find a bug, have a feature request, or otherwise would like to contact the author concerning use of relped, please open an issue.

License

This work is licensed under the the MIT License, see full terms of use in LICENSE file.