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fast way to change the title name

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

genome
• 4,645 views • link
updated by sacha sacha • written by wu.zhiqiang.1020 • wu.zhiqiang.1020

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 :)

• 0 views • link
written by GenoMax GenoMax

2 answers 

cut -d ' ' -f 1 in.fa > out.fa
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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

• 0 views • link
written by GenoMax GenoMax

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

• 0 views • link
written by Farbod Farbod 
  seqtk rename file.fasta

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

• 0 views • link
written by sacha sacha

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