I have multiple sets of files, so I grepped the list from a column in a seperateseparate file such as file1.txtfile1.txt. I want to change all other files by using this file1.txtfile1.txt based on a matching string.
forFor example, I am pasting three files here
File 1:
chr - seq1 NZ_JAHWGH010000010.1 0 60562 green_a4
chr - seq3 NZ_JAHWGH010000012.1 0 466573 green_a4
chr - seq5 NZ_JAHWGH010000013.1 0 125526 green_a4
chr - seq39 NZ_CAJGBF010000006.1 0 211154 green_a4
chr - seq40 NZ_CAJGBF010000007.1 0 199119 green_a4
chr - seq41 NZ_CAJGBF010000008.1 0 190934 green_a4
chr - seq42 NZ_CAJGBF010000009.1 0 178251 green_a4
I extracted the required information using grep; the command is given below:
grep "NZ_JAHWGH" file.txt |awk '{print $3}' >file1.txt
grep "NZ_CAJGBF" file.txt |awk '{print $3}' >file2.txt
Now I wanted to use this file1.txtthese file1.txt and file2.txtfile2.txt to change another filesfile. Output will be like if list in file1.txtfile1.txt matches then all matched lists should be substituted as seq1 similarly using the second file2file2.txt.txt I want to substitute all matching patterns as seq2.
For example the file is given here to be changed by using information from the previous file:
seq3 19301 20914 fill_color=green_a0
seq1 16726 18337 fill_color=green_a0
seq5 167934 169650 fill_color=green_a0
seq42 200621 202367 fill_color=red_a0
seq41 160164 161903 fill_color=green_a0
seq40 31356 33104 fill_color=green_a0
And final output after the change should be as follows:
seq1 19301 20914 fill_color=green_a0
seq1 16726 18337 fill_color=green_a0
seq1 167934 169650 fill_color=green_a0
seq2 200621 202367 fill_color=red_a0
seq2 160164 161903 fill_color=green_a0
seq2 31356 33104 fill_color=green_a0
I tried using this command:
for i in f2.txt; do
grep -wf f1.txt $i|awk '{$1="seq1";print}'; grep -wf other.txt $$i |
awk '{$1="seq1";print}'
grep -wf other.txt $i |awk|
awk '{$1="seq2";print}'; '
done
2nd attempt:
grep -wf f1.txt f2.txt|sedtxt |
sed -e 's/seq[0-9]*/seq1/g'
Is this correct? If it is correct is there any more efficient way to do it? alsoAlso it is only printing to the console. I want the output and also changes in the main file. Kindly improve my scripts.
I appreciate yout time and help.
