Shuffle fasta output from Polyester

# Polyester (https://github.com/alyssafrazee/polyester) simulates RNA-Seq reads
# Output is FASTA and sorted by input transcript ID
# Some tools don't like this e.g. Salmon, and want a more random order

# Here is a one-liner for shuffling the reads from sample 1 in output directory test.out

cat test.out/sample_01.fasta | paste - - | shuf | awk '{print $1"\n"$2}' > test.out/sample_01.shuf.fasta