Find motif and cut adjacent bases

Question

[PolDE]

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.

Answer 1

[Pierre Lindenbaum]

 echo "cgtcgtcgtcgtagctgtaaatttacgatcgtagctagctagtcgat" | grep -iEo '[atgc]{1,10}AAATTT[atgc]{1,10}' 
tcgtagctgtaaatttacgatcgtag

[PolDE]

thanks! and if I have a fasta file with multiple sequences as input?

[Pierre Lindenbaum]

linearize https://gist.github.com/lindenb/2c0d4e11fd8a96d4c345 and loop over each NAME/SEQ

[PolDE]

loop over? how can I run the command on a file input with 10000 fasta sequences?