if type_id==8: primer="'complete'" elif type_id==5: primer="'3primer_partial'" elif type_id==3: primer="'5primer_partial'" elif type_id==0: primer="'internal'" else: print "error,",line sys.exit(1) # strand_value=r"'%s'" %(strand) insert_value='('+','.join([transcript_id,cds_start,cds_end,longest_start,longest_end,primer,strand_value])+')' insert_value_list.append(insert_value) if len(insert_value_list)>=300: insert_value_multi=",".join(insert_value_list) insert_field_list=['transcript_id','cds_start','cds_end','longest_cds_start','longest_cds_end','primer_style','strand'] db_operation.bed_2_mysql(connection,"orf_find",insert_field_list,insert_value_multi) insert_value_list=[] if len(insert_value_list)>0: insert_value_multi=",".join(insert_value_list) insert_field_list=['transcript_id','cds_start','cds_end','longest_cds_start','longest_cds_end','primer_style','strand'] db_operation.bed_2_mysql(connection,"orf_find",insert_field_list,insert_value_multi) #updata main_table cursor=connection.cursor() for trans_id in set(select_list): sql_update_main_table='update main_table SET cds_select=1 WHERE transcript_id=%d' %(int(trans_id)) cursor.execute(sql_update_main_table) connection.commit()
pool.join() if len(usearch_result_file_path_list)==0: print "Error, homology search failure." os.exit(1) for output_file_path in usearch_result_file_path_list: value_list=[] result_list_line=linecache.getlines(output_file_path) if len(result_list_line)==0: continue for line in result_list_line: line=line.replace(r"'",r"\'") line=line.replace(r'"',r'\"') line_list=line.split() # query_info_list=line_list[0].split('_') annotation_id=query_info_list[0] transcript_id=query_info_list[1].split('.')[0] sql_main_aahomo="update main_table SET aa_homology=1 WHERE transcript_id=%d" %(int(transcript_id)) cursor.execute(sql_main_aahomo) # db_info=line_list[1].replace("~"," ") # indent=line_list[2] query_coverage=line_list[3] taget_coverage=line_list[4] insert_value_list=[annotation_id,transcript_id,"'"+db_info+"'",indent,query_coverage,taget_coverage] insert_value="("+','.join(insert_value_list)+")" value_list.append(insert_value) sql_value=','.join(value_list) db_operation.bed_2_mysql(connection,'usearch',insert_field,sql_value)