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Question: cut a fasta file into two columns of pos and single base
0
gravatar for mittjohns
21 months ago by
mittjohns • 30
United States
mittjohns • 30 wrote:

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!
position sequence base fasta • 462 views
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modified 21 months ago by Pierre Lindenbaum ♦ 133k • written 21 months ago by mittjohns • 30
2
gravatar for Pierre Lindenbaum
21 months ago by
Pierre Lindenbaum ♦ 133k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 133k wrote:
grep -v '^>' in.fasta | tr -d '\n' | grep -o .  | cat -n
ADD COMMENT • link written 21 months ago by Pierre Lindenbaum ♦ 133k

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

ADD REPLY • link written 21 months ago by GenoMax ♦ 94k

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

ADD REPLY • link written 21 months ago by mittjohns • 30
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