python16

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

import os
import sys
import argparse

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()
    headlines = inputlines[0].strip().split('\t')
    headcon = ''
    for headeri in headlines:
        headcon = headcon+str(headeri)+ "\t"
    outcon.write(str(headcon)+"\n")
    for inputline in inputlines[1:]:
        inputlin = inputline.strip().split("\t")
        geneid = inputlin[0].strip().split("_")[0]
        con = ''
        for inputli in inputlin[1:]:
            con = con + str(inputli)+"\t"
        outcon.write(str(idname[geneid])+"\t"+str(con)+"\n")