cut a fasta file into two columns of pos and single base
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!
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Pierre Lindenbaum
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written
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mittjohns •
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mittjohns •
1 answer
grep -v '^>' in.fasta | tr -d '\n' | grep -o . | cat -n
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Pierre Lindenbaum
thanks Pierre, a brilliant use of grep -o and cat -n.
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mittjohns •
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