YARP

Yet Another Renumbering Package

Andres Legarra, INRA Toulouse

YARP is a series of scripts that I found useful for manipulating and recoding data. Most of them are written in awk. In most cases they are run like

./xxx.awk file1 [file2] > file_out

subped.awk

extract_subped.awk

These two programs take file1, read animals e.g. in data, and from a pedigree file2 they extract all ancestors of individuals in file1.

For some reason that I cannot remember subped.awk is more efficient (or contains no errors) than extract_subped.awk

extract_2_from_1.awk

This program takes file1, creates a list of animals, and prints out records in file2 if animals in the first column are included in file1

pongene.awk

• It takes the pedigree file and put ancestors animals in the first column if they are absent (unless they <=0),
• It also assigns year of birth (needed to create upg) for missing animals, here yob = yob(progeny)-3

extract_duplicates.awk

Remove duplicates and individuals with two identical parents

renum_order.awk

Renumbers the pedigree on file1 so that parents precede offspring. Conceived for populations with no unknown parent groups, so missing ancestors are 0. On output, it generates fileout with 6 cols, the new and the old pedigree.

renum_order_gen.awk

Same as above but considering pseudo-generation numbers, so that uncles got numbers before nieces; see Kempthorne's example in which Z may, or may not, be numbered before F.

A 0 0
B 0 0
D A B
E A D
F B E
Z A B

assign_UPGs_sire_dam.awk

It assings unknown parent groups based on year of birth and kind of missingness (both unknown or only sire unknown). In this case, for Manech Tete Rousse.

renum_order_groups.awk

Same as renum_order above but creating files wih upg's that are added after regular animals.

renum_order_mf.awk

Same as renum_order above but creating files wih metafounders that come before regular animals.

renum_order_gen_mf.awk

Same as renum_order_mf above but considering pseudo-generation numbers creating files wih metafounders that come before regular animals.

mf2upg.awk

It converts a pedigree with metafounders first to another one with upg's coded as negative numbers (so that it fits into renumf90)

renum_data.awk

This programs recodes given fields in a data set example ex_renum_data the order of print is:

• first recoded columns,
• then "untouched" fields passed to output,
• then the original complete (possibly alphanumeric) line.

In this manner the output can be read as such by blupf90 with alphanumerics included. It has not really been tested.

put_level_in_genotypes.awk

This program takes the recoded pedigree with recoded id in $1 and old id in $4, then reads a genotype file and creates a new file with recoded id instead of old id.

put_level_in_phenotypes.awk

This program takes the recoded pedigree with recoded id in $1 and old id in $4, then reads a phenotype file with id in pos posid and creates a new file with recoded id at the last column

genotype2pregs.awk

This program passes from true genotypes (nucleotide) to pregs format (0/1/2). The reference allele is the first one read on the file for each locus, a table of equivalences is generated on output. It does not check for triallelic SNPs