How can I add an incremented value just after Accession no. ?

Question

[genious.kalia.141198]

I have a large csv file (1.7GB) containing sequences, and i have to provide a header to each sequence, so i did some thing like this with bash to do same:

*#/bin/bash

cat con_test.csv > out.out

for file in out.out; do

sed -e 's/^/>NZ_CP00000.1 volvox complete genome\n/' -i "$file" done*

my input files:

AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC

GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA

CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG

TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA

AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTAG

my output file after running this script. (NZ_CP00000.1)

NZ_CP00000.1 volvox complete genome AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC

NZ_CP00000.1 volvox complete genome GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA

NZ_CP00000.1 volvox complete genome CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG

NZ_CP00000.1 volvox complete genome TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA

NZ_CP00000.1 volvox complete genome AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTAG

Now i want to assign a different or unique value with the accession no. to all my sequences, so that the description line looks something like this: ( NZ_CP00000.1_000000001) and the unique value incremented for every time

>NZ_CP00000.1_000000001 volvox complete genome AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC

>NZ_CP00000.1_000000002 volvox complete genome GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA

>NZ_CP00000.1_000000003 volvox complete genome CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG

>NZ_CP00000.1_000000004 volvox complete genome TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA

>NZ_CP00000.1_000000005 volvox complete genome AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTAG

how can i achieve this?

Answer 1

[Pierre Lindenbaum]

awk '/^>/ {$1=sprintf("%s_%010d",$1,++N);} {print;}' input.fa

[genious.kalia.141198]

thank you so much it works..

[Pierre Lindenbaum]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Answer 2

[shenwei356]

$ seqkit replace -p '^(.+?) (.+)' -r '${1}_{nr} $2' --nr-width 9 -w 0 seq.fa
>NZ_CP00000.1_000000001 volvox complete genome
AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC
>NZ_CP00000.1_000000002 volvox complete genome
GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA
>NZ_CP00000.1_000000003 volvox complete genome
CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG
>NZ_CP00000.1_000000004 volvox complete genome
TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA
>NZ_CP00000.1_000000005 volvox complete genome
AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTA

[genious.kalia.141198]

i think seqkit is not installed thats why generating error. command not found.

[shenwei356]

oh, you can google it

Answer 3

[cpad0112]

nl -nrz   -bp">"   test.fa | sed "/>/ s/^\([0-9]\+\).*\(>\w\+\.[0-9]\)\(.*\)/\2_\1\3/g;s/^\s\+//g" 

>NZ_CP00000.1_000001 volvox complete genome
AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC
>NZ_CP00000.1_000002 volvox complete genome
GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCACGATGAGTTCAGCAGCAATGA
>NZ_CP00000.1_000003 volvox complete genome
CCAAGCCTGCGCGTGCCCTGCGTGGTTCTTCCCCACAGCAGCACACCGTGAGGGCAAACTG
>NZ_CP00000.1_000004 volvox complete genome
TCGCCGCACGTTCGGGCAAAAAAACCTGACGTGCGCGGTCTTGTAAAGCGGTTAGTCACCGA
>NZ_CP00000.1_000005 volvox complete genome
AGGGCACGCGGGGCCGATTCGCACCGGCCGAGGTCTGCCCAAGGCAACCCCTAGAGTCTAG