exon_num = int(options.exon_num)
start_time = time.time()
print "Run start:"
#######################################
make_dir(out_dir)
#gtf_outdir=out_dir+'/'+'gtf'
#tid_gid_file=gtf_outdir+"/"+"tid_gid"
#make_dir(gtf_outdir)
snc_gtf = out_dir + "/" + 'filter_out_noncoding.gtf'
lnc_gtf = out_dir + "/" + 'novel_lincRNA.gtf'
coding_gtf = out_dir + "/" + 'novel_coding.gtf'
cnc_gtf = out_dir + "/" + 'ambiguous_genes.gtf'
Gene_Info = out_dir + '/compare_2_infor.txt'
###################################
gtf = Gtf(gtf_input)
tid_gid = gtf.get_tid_gid()
#index_content=Table(index_file,0,False)
#index_content.write_to_file('index_content')
#transform_index_content=index_content.cal(index_transform,'row')
#transform_index=Table.build_table(1,['tid','cnc_type','score','start','end','length'],transform_index_content)
transform_index = Table(index_file, 1, True)
transform_index.left_join(1, tid_gid, 1)
gid_cnctype = transform_index.get_col('gid', 'index')
gid_cnctype = gid_cnctype.de_redundency()
gid_cnctype = gid_cnctype.key_by('gid', 'index')
