Manipulating fasta

fasta

#filter out fasta sequence by pattern in header
awk '/^>/ {P=index($0,"STRING")==0} {if(P) print} ' in.fasta > out.fasta

#keeping fasta sequence based on pattern in header
 awk '/^>/ {ok=index($0,"Escherichia coli");} {if(ok) print;}' in.fasta
 
# removing empty records (e.g. seq1 here)
#>seq1
#
#>seq2
#ATGCATGCATAGC
awk -v RS=">" -v FS="\n" -v ORS="" ' { if ($2) print ">"$0 } ' genome.fa > genome.ok.fa

# removing blank lines (e.g. blank line in seq1 here)
#>seq1
#ATGCATGCATAGC
#[[:BLANK:]]
#>seq2
#ATGCATGCATAGC
grep -v '^$' genome.fa > genome.ok.fa