seqkit replace multifasta file

the headers in my multifasta files are of different formats and names, the only thing in common among all of them is the order of headers. I have provided a list of names that should be replaced according to the orders. I was thinking of using seqkit but I can't find the correct syntax for it

>EOG09150JA6_/storage/home/users/Dlittoralis_73_scf.fasta_jcf7180000720927_64871-66017 117 bp
MRRNNYPYQPLNQHPAPSGPAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK
LLRGIDDDMDRTGGFLGNTMTRVVRLAKQGGGSKQMCYMFLFVLFVFVLLWLTLKFK
>EOG09150JA6_/storage/home/users/Dlummei_81_scf.fasta_jcf7180000898911_4133-4655 117 bp
MRRNNYPYQPLNQHPAPSGQAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK
LLRGIDDDMDRTGGFLGNTMTRVVRLAKQGGGSKQMCYMFLFVLFVFVLLWLTLKFK
>dmoj37yC5.fa_scf7180000237413_9322-9672 117 bp
MRRNNYPYQPLNQHPAPSGPAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK

so far this is what I came up with

seqkit replace -p "^(\S+)"

but symbol -r "{kv}" needs a tab delimited file, while in my case the headers are variable so I can only provide the new names based on order

seqkit multifasta

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updated 4.5 years ago by shenwei356

• written 4.5 years ago by mthm •

you need to be more specific, what do you want to rename it as? Give a full example of one record, input/output.

Once tasks are more complicated writing a very simply Python script is usually the way to go.

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written 4.5 years ago by Istvan Albert

In BioPython the solution would be like so

from Bio import SeqIO

mapping = {}
for line in open('names.txt'):
    oldname, newname = line.strip().split()
    mapping[oldname] = newname

recs = SeqIO.parse("input.fa", 'fasta')
recs = list(recs)

# Rename the records
for rec in recs:
    rec.id = mapping[rec.id]

SeqIO.write(recs, "output.fa", 'fasta')

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written 4.5 years ago by Istvan Albert

2 answers

use paste:

$ cat names.txt 
seq1
seq2
seq3

$ seqkit seq -n  test.fasta
EOG09150JA6 _/storage/home/users/Dlittoralis_73_scf.fasta_jcf7180000720927_64871-66017 117 bp
EOG09150JA6 _/storage/home/users/Dlummei_81_scf.fasta_jcf7180000898911_4133-4655 117 bp
dmoj37yC5.fa _scf7180000237413_9322-9672 117 bp

# or 
#   paste names.txt <(seqkit fx2tab test.fasta | cut -f 2) | seqkit tab2fx 
$ seqkit fx2tab test.fasta | cut -f 2 | paste names.txt - | seqkit tab2fx

>seq1
MRRNNYPYQPLNQHPAPSGPAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK
LLRGIDDDMDRTGGFLGNTMTRVVRLAKQGGGSKQMCYMFLFVLFVFVLLWLTLKFK
>seq2
MRRNNYPYQPLNQHPAPSGQAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK
LLRGIDDDMDRTGGFLGNTMTRVVRLAKQGGGSKQMCYMFLFVLFVFVLLWLTLKFK
>seq3
MRRNNYPYQPLNQHPAPSGPAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK

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written 4.5 years ago by shenwei356

$ seqkit replace -p '.*' -r 'seq' test.fa | seqkit -w 0 rename | sed '1s/$/_1/'

>seq_1
MRRNNYPYQPLNQHPAPSGPAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDKLLRGIDDDMDRTGGFLGNTMTRVVRLAKQGGGSKQMCYMFLFVLFVFVLLWLTLKFK
>seq_2 
MRRNNYPYQPLNQHPAPSGQAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDKLLRGIDDDMDRTGGFLGNTMTRVVRLAKQGGGSKQMCYMFLFVLFVFVLLWLTLKFK
>seq_3 
MRRNNYPYQPLNQHPAPSGPAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK


$ awk  -v RS=">" 'NR > 1 {print ">seq_"NR-1,$0}' test.fa  | awk 'NF {print $1}'

>seq_1
MRRNNYPYQPLNQHPAPSGPAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK
LLRGIDDDMDRTGGFLGNTMTRVVRLAKQGGGSKQMCYMFLFVLFVFVLLWLTLKFK
>seq_2
MRRNNYPYQPLNQHPAPSGQAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK
LLRGIDDDMDRTGGFLGNTMTRVVRLAKQGGGSKQMCYMFLFVLFVFVLLWLTLKFK
>seq_3
MRRNNYPYQPLNQHPAPSGPAGHDALEAENERAAEELQQKIGALKSLTIDIGNEVRYQDK

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written 4.5 years ago by cpad0112