Hi,
I have fasta file containing loci of like 500 introns. I don't know how to have just the first 100 bases using awk command lines. I have the following command that I used to pick the last 100 nt of the sequences. I thought it might help: sed -Ee 's/^.*(.{100})$/\1/' file.fasta
Thanks, Farid
2 answers
I found this post that should be of use to you:
https://ro-che.info/articles/2016-08-23-fasta-first-n-sequences
I thought it might help:
sed -Ee 's/^.*(.{100})$/\1/' file.fasta
Anyone who understands the command above can figure this out for themselves.
So start there. Find a sed tutorial and learn how that command works. Then you can make your own. It's likely faster than waiting for generous strangers to spoonfeed you what you want to know.
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did you try
sed -E '/>/! s/^(.{100}).*/\1/'? or you can use seqkit (seqkit subseq -r 1:100). With awk:awk -v OFS="\n" '{getline seq} {print $0, substr(seq,1,100)}'