Hacky script for converting fasta files munged by some other program into RTF files back to fasta format (used for frog data). Probably output file will need some additional corrections by hand.

clean_rtf_to_fasta.sh

#!/bin/sh
#
if [ -z "$1" ] || [ -z "$2" ] ; then
  echo "Usage: $0 IN.rtf OUT.fasta"
  exit 1
fi
if [ ! -e "$1" ] ; then
  echo "Input file $1 not found"
  exit 1
fi
sed 's/.*>/>/g' "$1"  | sed 's/^\\f[0-9]/>/g' | sed 's/^\\//g' | sed 's/\\$//g' | sed 's/\t$//g' | sed 's/^> />/g' | sed 's/^>$//g' | sed 's/\t//g' | sed 's/^[^ACGT>]*//g' | grep -v "^$" > $2
##
#