Match patterns between two files and extract certain range of strings
Hi,
I need help to match patterns from between two different files and extract region of strings.
inputfile1.fa
inputfile2.txt
The output file as below. It should contain the strings extracted from inputfile1.fa according to start and stop numbers (in blue) indicated in inputfile2.txt as shown above.
I have tried to match these two files using bioinformatics tools like seqtk and bedtools but they did not give me what I want and some of their data requirements just don't fit mine. I am still learning awk and I want to do this in awk. Below are one of the codes that I did to match the two files but failed and I do not know how to extract certain regions of characters.
Would appreciate your kind help. thanks
Last edited by bunny_merah19; 12-09-2019 at 10:57 AM..
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