I do not understand what output you are trying to produce.
For each input gene line do you want:
one output line with the gene number and 10 averages from all 13 samples,
thirteen output lines with the gene number and the 10 averages from one sample on each line, or
one output line with the gene number and 130 averages where each set of 10 averages comes from one sample?
Can you show us the exact output you're hoping to produce from the data provided in your sample input for genes 1 and 2?
Was the data for gene 3 in your sample truncated, or will some inputs have missing fields that should be treated as zero values when computing the averages?
Hi Don,
Thank you for your response. Good questions and I am glad at least you replied. Thank you so much.
Here are the answers for your questions.
I want "one output line with the gene number and 130 averages where each set of 10 averages comes from one sample"
Since the data is very big, I will use the below small example assuming I have only one sample.
Here the 2.6 is coming from averaging 1 in second column through 1 in 11th column. 5.9 is coming from averaging from 22.5(12th column) till 7 (21st column). Please remember that if the 11th column was to be any value greater than 10.0% like 10.1% or 10.8% or anything, then we will be averaging only until the 10th column.
The main input file from the link that I gave in my earlier post, has 13 samples' 1% to 100% values and only two rows. In the output file, we will have Gene column plus 130 average values. Makes sense?
There will be no gene3 in an input file. It will always be 2 rows (first line is header and second line is the values for averaging) with 13 sample being chopped into different varying percentages. There will be no missing fields. For every column header, there is a value associated with it in the input file.
Also I have a batch of files like 4000. I give a folder with the extension, and the script should be reading each file and following the averaging conditions of differentiating exact 10.0% (to consider for average) and any other values greater than 10.0% like 10.1% or 10.2% or 10.3% etc (to not consider this column and the column before it).
Please ask as many questions as possible and I will be glad to answer.
Coming to what I have tried so far, I have been trying to read the headers and print each set into a different file and then do the computation and put it back and then move to the other sample. This seems to be very time taking.
All your time and understanding is highly appreciated.
Hi All,
I need the modification for the below mentioned code (found in one more post https://www.unix.com/shell-programming-scripting/27161-script-generate-average-values.html) to find the average values for all the columns(but for a specific rows) and print the averages side by side.
I have... (4 Replies)
Hi,
I have a file which looks like this:
FID IID MISS_PHENO N_MISS N_GENO F_MISS
12AB43131 12AB43131 N 17774 906341 0.01961
65HJ87451 65HJ87451 N 10149 906341 0.0112
43JJ21345 43JJ21345 N 2826 906341 0.003118I would... (11 Replies)
Hi to all,
I have two files. File1 has no header, two columns:
sample1 A
sample2 B
sample3 B
sample4 C
sample5 A
sample6 D
sample7 D
File2 has a header, except for the first 3 columns (chr,start,end). "sample1" is the header for the 4th ,5th ,6th columns, "sample2" is the header... (4 Replies)
Hello,
I have some tab delimited text files with a three header rows. The headers look like, (sorry the tabs look so messy).
index group Name input input input input input input input input input input input... (9 Replies)
Hi experts,
I want to group by average, for multiple columns starting column $7 until NF,
group by ($1-$5), please help
For just 7th column, I can do
awk '
NR>1{
arr += $7
count += 1
}
END{
for (a in arr) {
print a, arr/count
... (10 Replies)
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Hello,
I have to fish out some specific columns from a file based on the header value. I have the list of columns I need in a different file. I thought I could read in the list of headers I need,
# file with header names of required columns in required order
headers_file=$2
# read contents... (11 Replies)
hello, I have three files in the following order
==> File1 <==
1 20977000 20977000 A C 1.00 0,15 15 45
1 115829313 115829313 G A 0.500 6,7 13 99
==> File2 <==
1 20977000 20977000 A C 1.00 0,13 13 39
1 115829313 ... (5 Replies)
I have files that have the following columns
chr pos ref alt sample 1 sample 2 sample 3
chr2 179644035 G A 1,107 0,1 58,67
chr7 151945167 G T 142,101 100,200 500,700
chr13 31789169 CTT CT,C 6,37,8 0,0,0 15,46,89
chr22 ... (3 Replies)