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GREP from multiFasta file and keep headers

Hi there,

I am new to coding, consider yourself warned :D

I have a multifasta file with 3' UTR sequences of variable length. I would like to extract a 6-mer sequence; AGTCTC with 20 nts upstream and 20 nts downstream (but not the rest of the sequence from that 3'UTR or that particular line, just these 20+6+20 nucleotides). I know I can do that with Grep;

grep -   "....................AGTCTC...................." 3UTR.fa  > 3UTR2.fa

However, this doesn't give me a new Fasta file with headers.. I know I can use the -B option but this give me all the lines from header to my sequence of interest.

Any suggestions are much appreciated!

Cheers, Marie

grep header multifasta
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updated by cpad0112 cpad0112 • written by marie.lorans • marie.lorans

your command line above with grep implies that each record in your fasta file takes only two lines (?). One line for the header, and one line for the sequence. So you just have to use the option -B 1 of grep (one line before)

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre. My sequence is not in a single line, so -B 1 won't do. Perhaps what I'm trying is not possible with grep

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written by marie.lorans • marie.lorans

try using tools like seqkit which supports grep and multiline fasta.

$ seqkit -w 0 grep -srip .{20}AGTCTC.{20} input.fa -o output.fa
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written by cpad0112 cpad0112

1 answer

linerarize, grep, convert back to fasta

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written by Pierre Lindenbaum Pierre Lindenbaum

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