Rename the fasta file with the first sequence header

Suppose there are multiple fasta files with single sequence. We want to rename the fasta file with the header of the single sequence present in the fasta file. We can run the following command.

Place all the fasta files you want to change the file names in one directory and run the following command.

for i in *; do if [ ! -f $i ]; then echo "skipping $i"; else newname=`head -1 $i | sed 's/^\s*\([a-zA-Z0-9]\+\).*$/\1/'`; [ -n "$newname" ] ; mv -i $i $newname.fasta || echo "error at: $i"; fi; done | rename s/ // *.fasta