convert_to_gff.sh

#!/bin/bash
FILE='./Supp_miRNA_Annotation_Table.xlsx - miRNA_annotated.csv'
OUT_FILE='./miRNA.gff'
echo "##gff-version 3" > $OUT_FILE
tail -n +2 "$FILE" | awk -F ',' '!($5 == "")' | cut -d',' -f 1,5,9 | sed -E -e 's/(:|\.\.)/,/g' | \
 awk 'BEGIN {FS=","; OFS="\t"} {print $2, MirDeep2, miRNA, $3, $4, $6, $5, ".", "gene_name=\""$1"\""}' >> $OUT_FILE