Find motif and cut adjacent bases
Dear All,
how can I find a motif in a sequence and cut X number of adjacent bases ahead and X number after the motif.
As example (motif AAATTT; 10 adjacent bases ahead and after):
> cgtcgtcgtcgtagctgtaaatttacgatcgtagctagctagtcgat
to get the fasta:
tcgtagctgtaaatttacgatcgtag
Much appreciated, thank you.
1 answer
echo "cgtcgtcgtcgtagctgtaaatttacgatcgtagctagctagtcgat" | grep -iEo '[atgc]{1,10}AAATTT[atgc]{1,10}'
tcgtagctgtaaatttacgatcgtag
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Pierre Lindenbaum
linearize https://gist.github.com/lindenb/2c0d4e11fd8a96d4c345 and loop over each NAME/SEQ
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