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How To Add A Unique Identifier For Fasta File To A Long List Of Sequences

I have a long list of sequences and I want to convert this list to a fasta file. How do I add > and a unique identifier to each line?

thanks!

sequence fasta
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updated by Martin A Hansen Martin A Hansen • written by Stevebob • Stevebob

2 answers

Awk is a possibility. Assuming one sequence per line in a file called sequencefile.txt:

awk '{print ">" NR; print $0}' sequencefile.txt

NR is the line number, so it will be unique relative to the sequences in sequencefile.txt.

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written by Sean Davis Sean Davis

You can accept this as the answer by clicking on the checkmark just under the votes.

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written by Sean Davis Sean Davis

"assuming" is the grandma' of Satan :o)

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written by Martin A Hansen Martin A Hansen

With Biopieces www.biopieces.org) you do:

read_tab -i in.tab -k SEQ | add_ident -k SEQ_NAME | write_fasta -o out.fasta -x

More info here: add_ident

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written by Martin A Hansen Martin A Hansen

That is nice, but a little overkilling.

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written by lh3 lh3

If you are using biopieces for further steps downstream then what you call slight overkill does make sense. Granted it doesn't look like stevebob was already using biopieces but maybe this gave him a push towards discovering it..

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written by Daniel Daniel

biopieces is a very convenient toolbox. It works very well, thanks Maasha!

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written by Manu Prestat Manu Prestat

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