an instructive shell scripts - filtering FASTA sequences

filtering FASTA sequences by chromosomes names from a big fasta file

You can do the following:

chr=$(seq 1 1 22)" X Y"
for i in $chr ; do 
    grep ">" input.fa | grep "|$i|" | awk 'BEGIN {FS=">"} {print $2}' > selection_$i
    samtools faidx input.fa `cat selection_$i` > output_$i.fa
done