pedRefiner 0.1.0

Trivial tool that takes a list of animal IDs, extracts a pedigree file for the given IDs and all their ancestors’ IDs, builds a new pedigree file with them sorted, and dumps the output to a new file.

Suggested usage of PedRefiner: the pipeline() method.

param 1 lst_fn: file containing animal list to be grepped from the pedigree, one line each

param 2 ped_fn: input pedigree file, 3 col

param 3 opt_fn: output pedigree file, 3 col

param 4 gen_max: (0) maximum recursive generation to grep for EVERYONE in lst_fn

param 5 missing_in: (‘.’) missing value for input file, default = ‘.’

param 6 missing_out: (‘.’) missing value for output file, default = ‘.’

param 7 sep_in: (‘,’) separator for input file, default = ‘,’ i.e. csv

param 8 sep_out: (‘,’) separator for output file, default = ‘,’, i.e. csv

param 9 xref_fn: (None) cross-reference file to modify output pedigree

param 10 flag_r: (False) bool, output descendant IDs if True

Example:

• Python

  from pedRefiner import PedRefiner

  pr = PedRefiner()

  # pr.help()

  pr.pipeline(‘animal_list’, ‘ped.input.csv’, ‘ped.output.csv’, gen_max=3)

• Bash

  # 1 2 3 4gen_max 5missin 6missout 7sepin 8sepout 9 10

  pedRefiner.py ANM_LST PED_INPUT.csv PED_OUTPUT.csv [3 0 0 , , xref True]

Description:

• extracts the pedigree of all the ancestors of the animals in the anmList file;

• if ‘-r’ option is given, prints out all the descendants’ IDs from the anmList file instead of print out the refined pedigree;

• xref the pedigree info if specified a whitespace-delimited 3-col xref file with 1st col as command:

  # line starting with sharp will be ignored

  # cmd = A : [A]ll ID1 (col1, 2 and 3) will be changed to ID2

  A ID1 ID2

  # cmd = S : All ID1 in the [S]ire (2nd) column will be changed to ID2

  S ID1 ID2

  # cmd = D : All ID1 in the [D]am (3rd) column will be changed to ID2

  D ID1 ID2

• force accepting the latest version if multiple entries for the same animal were detected;

Updates:

• version 2017-02-23 prevent unexpected order for complex pedigree while specifying rec_gen_max

• version 2017-02-22 - modified to be a non-recursive version to prevent segmentation fault for a very very very long pedigree - only maintaining python version

• version 2016-03-31 added -r option: will print out all the descendants’ IDs from anmList, recursively to the end

• version 2015-07-13 added output: pedOut.ID2Gender according to the ped, and ‘M’ for unknown

• version 2015-07-02 added xref to correct animal IDs: replace 1st col with 2nd col

• version 2015-06-29 prevent segmentation fault 11 due to pedigree loop

• version 2015-06-12 added updating pre-loaded empty entries

• version 2015-04-15 added a 3rd parameter to determine the recursive generations

• version 2014-11-10 modified check() so that all the errors would be checked in one run added sort()

• version 2014-04-15 initial version