I have a folder containing 500 files from different individuals:
$ ls HI.3577.005.Index_25.QPG4_KS2W-35_all_PA HI.3577.005.Index_27.QPH4_SD1W-13_all_PA HI.3577.005.Index_9.QPA2_KS2W-8_all_PA HI.3577.007.Index_1.Q004B_SD1A-1_all_PA HI.3577.007.Index_21.Q076C_SD2W-23_all_PA HI.3577.007.Index_23.Q079_KS1A-15_all_PA
Each of these individuals belongs to a population (in the example above individuals belong to KS2W, SD1W, KS2W, SD1A, SD2W, and KS1A respectively). Each of my files looks as follows (this sample belongs to from "MK4" population):
$ head HI.3579.001.Index_9.Q089_MK4-4R_all_PA Ha8_00040788 1 Ha4_00024045 1 Ha4_00025366 1 Ha16_00022130 0 Ha16_00023451 0 Ha8_00040789 1 Ha4_00025367 1 Ha4_00024046 0 Ha16_00022131 1 Ha16_00023452 1
or another sample from MK4 population
$ head HI.221.009.Index_9.P089_MK4-4R_all_PA Ha8_00040788 1 Ha4_00024045 1 Ha4_00025366 1 Ha16_00022130 1 Ha16_00023451 1 Ha8_00040789 1 Ha4_00025367 1 Ha4_00024046 0 Ha16_00022131 1 Ha16_00023452 1
the first column is genes and the second columns refers to the presence of that gene (coded as 1) or absence of gene (coded as 0).
For all individuals belonging to each of the populations, I would like to count the total number individuals that have the gene and individuals that do not have the gene.
For example, for the 2 examples above, as they both belong to MK4 population my desired output is going to looke like this:
$ head MK4 Ha8_00040788 2 0 Ha4_00024045 2 0 Ha4_00025366 2 0 Ha16_00022130 1 1 Ha16_00023451 1 1 Ha8_00040789 2 0 Ha4_00025367 2 0 Ha4_00024046 0 2
The first column is the gene, the second column is the number of individuals in the MK4 population that have the gene and the third column is the number of individuals that do not have that gene.
I have made a file containing population IDs
$ head pop.txt KS2W SD1W SD1A KS1A
Can anyone suggest me how I could do this? thanks