How to edit the fasta headers?

Question

[p]

Hi, pls, let me know how can i edit the fasta file header.

>LR99555.1 Avo, chromosome: 1 

I want this header like this.

>LR99555.1

[Mensur Dlakic]

A low-tech way of doing this is to open the file in any text editor and simply delete the part you don't need. This is not advised if you have a large number of sequences.

Answer 1

[Pierre Lindenbaum]

cut -d ' ' -f 1 < in.fa

[p]

hi, thanks for the reply, what is -f here?

[Carlo Yague]

according to the manual (man cut):

 -f list
         The list specifies fields, separated in the input by the field
         delimiter character (see the -d option).  Output fields are
         separated by a single occurrence of the field delimiter character.

Meaning that it keeps everything before the first space delimiter and removes the rest.

Answer 2

[cpad0112]

$ awk '/^>/ {print $1} !/>/' test.fa
$ sed '/^>/ s/\s.*//g' input.fa