cut a fasta file into two columns of pos and single base

Question

[mittjohns]

What’s the most efficient (fast and simple code) way to convert/cut a fasta file (either part or the whole sequence) of a chromosome into two column tab-delimited format of pos and base? For example:

fasta file

>chr2
ATGCATTC...

converted pos-base file

1 A
2 T
3 G
4 C
…

I know we can write a script to do so. But this seems to be a task for a one-liner or some existing tools. Thanks!

Answer 1

[Pierre Lindenbaum]

grep -v '^>' in.fasta | tr -d '\n' | grep -o .  | cat -n

[GenoMax]

A multi-fasta file will be numbered consecutively, correct? OP should keep that in mind.

[mittjohns]

thanks Pierre, a brilliant use of grep -o and cat -n.