fast way to change the title name

Question

[wu.zhiqiang.1020]

Dear all,

I want to change the header of big fasta file as this:

>JH208680.1 dna:scaffold scaffold:PelSin_1.0:JH208680.1:1:16024077:1 REF

CTACCCATTCCTTTCCTTTGGTGTACTGTAGTCCTTCTATTAGGGGAACTAATGGGGAAC
TTTTCTTTATGCACCCTCTCCACACCACTCTTGCTTTTATAGACCTCTATCATATCCCCC
CTCCGTCTCCTCTTCTCTAAGCTGAAAAGTCCCAGTCTCTTTAGCCTCTCTTCATATGGG
ACCTGTTCCAAACCC

And change it to

>JH208680.1 

CTACCCATTCCTTTCCTTTGGTGTACTGTAGTCCTTCTATTAGGGGAACTAATGGGGAAC
TTTTCTTTATGCACCCTCTCCACACCACTCTTGCTTTTATAGACCTCTATCATATCCCCC
CTCCGTCTCCTCTTCTCTAAGCTGAAAAGTCCCAGTCTCTTTAGCCTCTCTTCATATGGG
ACCTGTTCCAAACCC

I use this command, but take a little time as:

awk '{if($1 ~ /^>/){split($1,a,"\s"); print a[1]}else{print}}' input.fasta > input.rename.fasta

Did this fast or not? did any one have better solution for faster?

thanks

P.S. the ">" was not shown here, but it is as fasta file ZQ

[GenoMax]

Did this fast or not? did any one have better solution for faster?

Are you losing money on this. Why worry if it is working :)

[wu.zhiqiang.1020]

it is working, but slow. so I want some better one.

Answer 1

[Pierre Lindenbaum]

cut -d ' ' -f 1 in.fa > out.fa

[GenoMax]

This would be fast. Send some of that money @Pierre's way.

[Farbod]

Hi dear Genomax2 and Pierre, As I helped in this post, please send me the rest of money :- )

By the way, we (me and @Goutham Atla) suggested awk in that post because the header has different orders.

Take care

[wu.zhiqiang.1020]

thanks, this one is more faster than I used.

Answer 2

[sacha]

  seqtk rename file.fasta

Or you can use http://bioinf.shenwei.me/seqkit/