3.5.1 Pedigree Format Codes

Pedigree format codes consisting of a string of characters are used to describe the contents of a pedigree file. The simplest pedigree file that can be read by PyPedal is shown above; the pedigree format for this file is asd. A pedigree format is required for reading a pedigree; there is no default code used, and PyPedal wil halt with an error if you do not specify one. You specify the format using an option statement at the start of your program:
options['pedformat'] = 'asd'
Please note that the format codes are case-sensitive, which means that "a" is considered to be a different code than "A". The codes currently recognized by PyPedal are listed in Table 3.2.

As noted, all pedigrees must contain columns corresponding to animals, sires, and dams, either in the 'asd' or 'ASD' formats (it is not recommended that you mix them such as in 'AsD'). Pedigree codes should be entered in the same order in which the columns occur in the pedigee file. The character that separates alleles when the 'L' format code is used cannot be the same character used to separate columns in the pedigree file. If you do use the same character, PyPedal will write an error message to the log file and screen and halt. The herd column type simply refers to a management group identifier, and can correspond to a herd, flock, litter, etc.

If you used an earlier version of PyPedal you may have added a pedigree format string, e.g. "% asd", to your pedigree file(s). You no longer need to include that string in your pedigrees, and if PyPedal sees one while reading a pedigree file it will ignore it.

Note that if your pedigree file uses strings for animal, sire, and dam IDs (the ASD pedigree format codes) you may need to override the missing_parent option, which is "0" by default. For example, the pedigree file shown in Figure uses animal0 to denote unknown parents. If "options['missing_parent'] = 'animal0'" is not set before the pedigree file is loaded missing parents will be treated as animals with unknown parents, rather than as unknown parents.

Pedigree format codes. Code & Description

\begin{xtabular}{l\vert p{4in}}
a & animal ('a' or 'A' REQUIRED)\\
s & sire (...
...es a column that should be skipped (one allowed per pedigree)\\
\end{xtabular}
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