A useful pure bash construct for dealing with FASTA files. Can be tweaked to perform all sorts of actions on the headers of sequences (e.g. rearrangement, regex, text matching)

Fiddling_with_fastas.sh

#!/bin/bash


#### Print out all fastas ending in a certain string. ####
# Change *"$string" to *"$string"* to find containing,
# or "$string"* to find starts with.

file="$1"
string="$2"

while read line ; do
	if [ ${line:0:1} == ">" ] ; then
		header="$line"
	else
		seq="$line"
	if [[ "$header" == *"$string" ]] ; then
	echo -e "$header""\n""$seq"
	fi
	fi
done < "$file"


#### Print out all fastas but custom re-order their headers based on delimiter. ####
# Alter the "$header[0,1,2,3...] order in echo to change the order the fields are output.

file="$1"
delimiter="$2"

while read line ; do
	if [ ${line:0:1} == ">" ] ; then
		IFS="$delimiter" read -a header <<< "$line"
	else
		seq="$line"
	echo -e "${header[0]}"\|"${header[2]}"\|"${header[1]}""\n""$seq"
	fi
done < "$file"