python17

./cufflinks-2.2.1/gffread GCF_000331145.1_ASM33114v1_genomic.gff -T -F -o GCF_000331145.1_ASM33114v1_genomic.gtf
./cufflinks-2.2.1/gffread GCF_000331145.1_ASM33114v1_genomic.gtf -F -o- >GCF_000331145.1_ASM33114v1_genomic.gff3

# -*- coding: utf-8 -*-
#!/usr/bin/env python

import os
import sys
import argparse
import numpy as np

parser = argparse.ArgumentParser(description="trim data , change geneid to genename")
parser.add_argument('--infile',help=" inputfile ",required=True)
parser.add_argument('--outfile',help="output file",required=True)
argv = vars(parser.parse_args())
infile = argv['infile'] 
outfile =argv['outfile']

idname = {}
with open('genename',"r") as nameliness:
    namelines = nameliness.readlines()
    for nameline in namelines:
        namelin = nameline.strip().split("\t")
        idname[namelin[0]]=namelin[1]

outcon = open(outfile,"w")
with open(infile,"r") as inputliness:
    inputlines = inputliness.readlines()
    header = inputlines[0].strip().split("\t")
    outcon.write(header[0]+"\tgenename\t"+header[2]+"\t"+header[3]+"\tlog2FoldChange\t"+header[5]+"\tpadj\n")
    for inputline in inputlines[1:]:
        inputlin = inputline.strip().split("\t")
        geneid = inputlin[0]
        genename = idname[geneid]
        controlvalue = inputlin[2]
        treatvalue = inputlin[3]
        FCvalue = float(inputlin[4])
#        print(FCvalue)
#        print(type(FCvalue))
        Pvalue = inputlin[5]
        padj = inputlin[6]        
        if FCvalue == 0:
            log2FCvalue == 0
        elif FCvalue > 0:
            log2FCvalue = np.log2(FCvalue) 
        elif FCvalue < 0:
            FCvalue1= -FCvalue
            log2FCvalue = -np.log2(FCvalue1)
        outcon.write(str(geneid)+"\t"+str(genename)+"\t"+str(controlvalue)+"\t"+str(treatvalue)+"\t"+str(log2FCvalue)+"\t"+str(Pvalue)+"\t"+str(padj)+"\n")

完美，半个小时搞定