UNIX commands

# Make file with genes annotated with the source of JonathanStoltzfus
grep -E "JonathanStoltzfus" strongyloides_stercoralis.PRJEB528.WBPS14.annotations_JSadditions20230609.gff3 | grep "gene" | grep -vE "mRNA" > temp.gff3

# Make file with genes that are labeled "modified" or "split"
grep -E "JonathanStoltzfus" strongyloides_stercoralis.PRJEB528.WBPS14.annotations_JSadditions20230609.gff3 | grep "gene" | grep -vE "mRNA" | grep -E "_modified|_split" > JSadditions_modified.gff3


# Make file with genes that are not labeled "modified" or "split"
grep -E "JonathanStoltzfus" strongyloides_stercoralis.PRJEB528.WBPS14.annotations_JSadditions20230609.gff3 | grep "gene" | grep -vE "mRNA" | grep -vE "_modified|_split" > JSadditions_unmodified.gff3


# Count number of lines with modified genes (125)
grep -E "JonathanStoltzfus" strongyloides_stercoralis.PRJEB528.WBPS14.annotations_JSadditions20230609.gff3 | grep "gene" | grep -vE "mRNA" | grep -Ec "_modified|_split"

# Count number of lines with examined but unmodified genes (280)
grep -E "JonathanStoltzfus" strongyloides_stercoralis.PRJEB528.WBPS14.annotations_JSadditions20230609.gff3 | grep "gene" | grep -vE "mRNA" | grep -vEc "_modified|_split"