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Add sequence lengths to headers in a fasta file

Hi all. I have a fasta file and would like to add the sequence lengths to the headers by keeping the sequences. Thank you!

My file:

>Seq_1
MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGI
KILAGKQKPNLGKYDDPPDWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAA
KGTVGSILDRKDETKTQAIVCQQLDLTHLKERNVEDLSGGELQRFACAVVCIQK

>Seq_2
MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTSQSKIAWISETLCIGCGI
CIKKCPFGALSIVNLPSNLEKETTHRYCANAFKLHRLPIPRPGEVLGLVGTNGIGKSTAL
KGTVGSILDRKDETKTQTVVCQQLDLTHLKERNVEDLSGGELQRFACAVVCIQKADIFMF
DEPSSYLDVKQRLKAAITIRSLINPDRYIIV

Desired output (the length info can follow after any delimiter):

>Seq_1[174]
MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGI
KILAGKQKPNLGKYDDPPDWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAA
KGTVGSILDRKDETKTQAIVCQQLDLTHLKERNVEDLSGGELQRFACAVVCIQK

>Seq_2[211]
MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTSQSKIAWISETLCIGCGI
CIKKCPFGALSIVNLPSNLEKETTHRYCANAFKLHRLPIPRPGEVLGLVGTNGIGKSTAL
KGTVGSILDRKDETKTQTVVCQQLDLTHLKERNVEDLSGGELQRFACAVVCIQKADIFMF
DEPSSYLDVKQRLKAAITIRSLINPDRYIIV
sequence
• 4,262 views • link
updated by WouterDeCoster WouterDeCoster • written by jan • jan

Perhaps provide where you want to use it for and what you tried.... Are you seeking unix, perl or other programming approaches? Is scaling an issue (over millions of sequences or of extreme length)? Is the fasta header always that format or is something else to be expected as well?

• 0 views • link
written by ALchEmiXt ALchEmiXt

1 answer

seqkit + awk on Linux/OS X

cat seqs.fa | seqkit fx2tab --length | awk -F "\t" '{print $1"["$4"]\t"$2}' | seqkit tab2fx > seqs2.fa

Example

$ echo -e ">seq\nacgtn\nACGTN"
>seq
acgtn
ACGTN

$ echo -e ">seq\nacgtn\nACGTN" | seqkit fx2tab --length | awk -F "\t" '{print $1"["$4"]\t"$2}' | seqkit tab2fx
>seq[10]
acgtnACGTN
• 0 views • link
written by shenwei356 shenwei356

Great, that's exactly what I was looking for. Thank you!

• 0 views • link
written by jan • jan

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