Fasta length count format

Question

[baurumon]

Hi, i have used awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' seq.fasta to count sequence length. How can i get the output in below format.

Thanks in advance

head length

NC_035897.1:11929374-11930116 742

NC_035897.1:11929384-11930116 732

[GenoMax]

Use tr command to change the new line characters to a tab. It is unclear if you want to go in the other direction but if that is the case then switch tab and new lines.

[baurumon]

hi genomax, I want head and length column. tr command is printing one after another. sorry for mistake.

[Sej Modha]

See RamRS's solution on: Sequence length from Fasta

[baurumon]

i asked my colleague to install seqkit but it going to take time. is there any way to do it with sed or awk?

[Sej Modha]

It is advisable to search for this sort of problems on Google first before it is posted on this platform, please take a look at Brief Reminder On How To Ask A Good Question.

A simple Google search provided this and it could be the solution you're after - https://www.danielecook.com/generate-fasta-sequence-lengths/

Answer 1

[kloetzl]

This should do it:

awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' seq.fasta | paste - -