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

Relatedness

relped has one required input:

Example:

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

Note that your columns must be named ID1,ID2, and Rel. It is okay to have either duplicate entries of the same pair of IDs (but perhaps different Rel) or have entries where the IDs have been switched -- for duplicate entries, the last entry will be used.

Pedigree

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.

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 final pedigree to distinguish males, females, and unknown sex. BirthYear is converted to age for the current year under the assumption that all birthdays have passed for the year (age is used to clarify the pedigree output).

Output

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

Producing multiple plots

Due to the unavoidable randomness of how the pedigree is plotted by Graphviz, the below template can be reused to build multiple plots in a row.

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

What the above does is loop through the number 1-10 (assigning the current number to run), then calls relped with your inputs (<relatedness>, <demographics>, <parentage>) and writes multiple output files that are prepended with the run number ($run-<output>) -- and calls Graphviz to produce a rendered image for each plot of 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.