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)
