pedRefiner.py

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.

[Install]

In terminal, execute

pip3 install pedRefiner
# pip2 may be working, for python2.x

Afterwards command pedRefiner.py could be launched anywhere.

[Usage]

pedRefiner.py 

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