handling dates in python

I have this data set with elementary test-day records from Manech Tete Noire also known as burubeltza

64422506;01;45000130047;052;03;2014;1;26FEB2014;0;02APR2014

64422506;01;45000130047;052;03;2014;1;26FEB2014;0;05MAY2014

64422506;01;45000130047;052;03;2014;1;26FEB2014;0;05JUN2014

64422506;01;45000130047;052;03;2015;2;07DEC2014;0;30DEC2014

and I need to compute difference between date of lambing and date of milk recording. I thought it would be easy using python(3).

import copy
import datetime

First, read and parse the data

fname=sys.argv[1]
fhand=open(fname)
for i,line in enumerate(fhand):
    Dacont = line.split(sep=";")[9]
    Datago = line.split(sep=";")[7]

Then, I need to convert these strings 26FEB2014 into something meaningful using module datetime, and compute the difference:

    daysfrommisebas= datetime.datetime.strptime(Dacont.lower(),'%d%b%Y') - datetime.datetime.strptime(Datago.lower(), '%d%b%Y')
and finally, print it, not forgetting to paste the strings using "+" and removing the EOL in "line":


    print(line.rstrip('\n')+";"+str(daysfrommisebas.days))

renumf90 anf preGSf90 with pedigree and genotypes only

Right, so you have genotypes and pedigree and you would like to use preGSf90 to build G and A22, or for quality control, or for whatever reason. Then you are told to use renumf90 first, but how can you use it with no phenotypes?

Well you can just create your own, fake ones. So, if your genotyped animals are in file marker.geno.clean with this aspect

  64000670990546 12012020210211

     45214790003 12111120211101

     45214790004 22111020110102

you can simply create a random number for each animal, and a file with "animal" and overall mean, using awk:

awk '{print 1,$1,rand()}' marker.geno.clean > phenotypes.txt

and then use the basic renumf90 parameter file in https://artadia.blogspot.com/2019/03/basic-renumf90-parameter-file.html.

After that, you edit the renf90.par file to put the required OPTIONS. For instance, these are the options to get lots of information, check heritability of gene content 

OPTION msg 100

OPTION h2_gene_content