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')
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()