for simple fasta format, sequence in one line:

$ head -n 2000 in.fa > first_1k.fa 
$ tail -n 1000 in.fa > last_500.fa

for fasta with multiple line sequence format, using bioawk: https://github.com/lh3/bioawk

$ bioawk -cfastx 'NR<=1000{print ">"$name"\n"$seq}' in.fa > first_1k.fa
$ bioawk -cfastx 'NR>1000{print ">"$name"\n"$seq}' in.fa > last_500.fa

If each raw sequence is in and only one line, then including the header it will be two lines, so you can use:

head  -n 2000 file.fasta > file1.fasta
tail  +2001 file.fasta > file2.fasta

+ before 2001 is necessary as it will output line 2001 and anything after that line.

Hii, This is my fasta file header

>hCoV-19/Country_name/1-27/2020|EPI_ISL_413522|2020-01-27

I have a merged fasta file.Can you suggest me a script or way to split my merged fasta file based on country_name? I want all the fasta sequences from one country in one separate fasta and same for others.Is it possible?

Try this:

  awk '{ if( $0 ~ /^>/){print prevID"\t"seq; prevID=$0; seq=""} else {gsub(/\W/, "", $0) ; seq=seq$0} } END {print prevID"\t"seq}' YOUR_FASTA_FILE |awk 'FNR >1'|head -1000|sed 's/\t/\n/g' > first1000seqs.fas

for the last 500 sequences substitute the head -1000 to tail -500.