splitFasta.fa

#!/usr/bin/env bash

# DETAILS: Functions by setting the field separator to a regular expression capturing ">", tab, and space.
# For each row in the file, if it is a header (begins with ">"), update the value of variable s
# to be equal to the first word in the header, and write a header line only containing that first word.
# Every line is written to a file <first_word_in_header>.fa, splitting the file into separate contigs.

awk -F "(^>|\t| )" '{if($0 ~ /^>/) {s=$2".fa";  print ">"$2 > s} else print > s}' ${inFasta}