Following is an example and code to append “>” on every second line (from start) including very first line.

input

$ cat test.fa

Gene1
AAAGTTGTTGCAG
Gene2
ACATACGATTCCGGAGAGG

output

$ awk '{ if ((NR % 2) == 1) printf(">")}1' test.fa

>Gene1
AAAGTTGTTGCAG
>Gene2
ACATACGATTCCGGAGAGG

$ sed  '1~2 s/^/>/' test.fa
>Gene1
AAAGTTGTTGCAG
>Gene2
ACATACGATTCCGGAGAGG

Now let us do some thing else. User wants

• Remove all headers in a file
• Use file name as fasta header
• Print only the sequences

Confused? Look at the input and expected output:

input

$ cat test.fa

>gene1
ATGCTA
>gene2
TGATGCT
>gene3
TAGTATG 

Expected output

 >test.fa
ATGCTA
TGATGCT
TAGTATG

Code

 $  awk 'BEGIN {print ">"ARGV[1]};!/^>/{print}' test.fa

>test.fa
ATGCTA
TGATGCT
TAGTATG

$ cat <(echo ">"$basename test.fa) <(grep -v ">" test.fa) 
> test.fa
ATGCTA
TGATGCT
TAGTATG

(Note: There is an extra space in later code)