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I have a positions file with markers in col1 and position defined by chromosome and location in col2 and col3

m1 ch1 1
m2 ch1 5
m3 ch1 50
m4 ch2 567
m5 ch2 4567
m6 ch2 7766
m7 ch2 554433...

thank you, would you also point out what is wrong with my code? It will help a lot in my learning.

Hi RudiC, thank you, will this help deal with the 345 million records in the score table problem? Is there a way we can avoid the 3 for loops? Thanks a lot for your help.

Hi experts,

I have a score matrix like below, where the 3rd column ( 1 max, 0 min) says how close the 2nd column variable is to the 1st column variable

a b 0.3
a c ...

I want to sum and average all other columns by first column

GR1 1 4 7
GR1 2 5 8
GR1 3 6 9
GR2 11 14 17
GR2 13 16 19...

Hi all,

I want to extract rows with the pattern ALPHANUMERIC/ALPHANUMNERIC in the 2nd column.
I dont wan rows with more than 1 slash or without any slash in 2nd column.


a a/b
b a/b/c
c...

Its going into an infinite loop , printing the header only repeatedly, using FNR also does the same thing.

col1 col2 col3
col1 col2 col3
col1 col2 col3
......

I have a list

a
b
c
d

I want to search this list to have partial matches in column 2 in data file

col1 col2 col3
1 a/e aa
2 b/e aa
3 z/y aa
4 t/u bb
5 d/f aa
6 a/t aa


and...

Perfect, thanks. :)

This is very easy , but I`m struggling .. please help modify my script,

I want to count the number of h and n , from the second column group by the first. The second column is binary, can only...

thanks, working great ! I will try to learn from this

Yes, the numerator is the minor base count, or the second highest base count.,,

M1 it is T (2)
M2 and M3 , the highest and the second highest are the same , so its 4

Thanks for your suggestions, would you please look at the script now? Also please help with the calculation of m, I feel I have the structure of the code right, but not providing with the desired...

Hello,

Please help create the following report.

I have a matrix

- S1 S2 S3 S4
M1 AA AA TT -
M2 AG AG AA GG
M3 GG TT - -

a first lookup table

M3 chr7 4.456
M1 chr7 28.9...

Hi all, please consider the following scenario. I have 979 csv files in a folder each with 3 lines, first line col2 has fixed value "a", second line col2 has "b" and third line col2 has "a/b".
The...

thank you, but the issue is you have fixed the reads, as I had mentioned it is quite variable (sometimes ranging upto 70), , can we modify this script to accommodate those types of conditions?

I...

Please assist with the following.


I have readings R1, R2,..Rn from plants from different fields , sometimes replicated. I need to first consolidate the replicates by their mean value per plant...

Hello Praveen, thank you for the solution. However there might be some problem. The number of rows returned is much less than what is in the input




$ cat prav
Group77 T1 AA ...

Don, they are sorted -k1,1 -k4,4.

T1 and T2 values can be among the set of 6 : aa,gg,tt,cc,dd,ii

Important to note that the groups with T1 and T2 values equal and groups with either/both T1...

Given the example input with missing data, I would like to have an output with imputed data.

Hello all,

this is quite complex, so please allow me some space to make the problem clear.

I have several groups which has 3 types T1,T2 and T1*T2.

The T1 (and T2) values are always in...

Thank you, my only concern is with reading these data files twice. They can be upto 25Gbs in the future, right now, they are in manageable range.

Please consider the following file, I have many groups which can be of 3 types, T1 (Serial_Number 1) T2 (Serial_Number 2) and T1*T2 (all other Serial_Number).

I want to only consider groups that...

hi, can you please help me convert my data

i have paired comparisons (col 3) in long format for 750 variables (col 1 and 2), i need to convert into wide format. the diagonal must be 0s, and the...