Question

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

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12.5 years ago

Stevebob ▴ 20

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 • 7.3k views

ADD COMMENT • link updated 12.5 years ago by Martin A Hansen 3.0k • written 12.5 years ago by Stevebob ▴ 20

score 6 · Answer 1 · 2011-10-27

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12.5 years ago

Sean Davis 26k

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.

ADD COMMENT • link 12.5 years ago by Sean Davis 26k

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

ADD REPLY • link 12.5 years ago by Sean Davis 26k

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

ADD REPLY • link 12.5 years ago by Martin A Hansen 3.0k

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worked great, thanks!

ADD REPLY • link 12.5 years ago by Stevebob ▴ 20

score 1 · Answer 2 · 2011-10-27

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12.5 years ago

Martin A Hansen 3.0k

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

ADD COMMENT • link 12.5 years ago by Martin A Hansen 3.0k

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That is nice, but a little overkilling.

ADD REPLY • link 12.5 years ago by lh3 33k

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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..