python 将GFF文件拆分为单独的轨道#gff #bash

Posted 2021-05-10

gunzip -kfc <GFF> | grep -v ^"#" | sort -k3,3 | python process_gff.py

for i in `ls *.gff`; do
    (grep ^"#" $i.gff; grep -v ^"#" $i.gff | sort -k1,1 -k4,4n) | bgzip > $i.sorted.gff.gz;
    tabix $i.sorted.gff.gz
    rm $i.gff
done

import sys

current_feature = ""

for line in sys.stdin:
    feature = line.split("\t")[2]
    if feature != current_feature:
        f = file(feature + ".gff", "a+")
    f.write(line)