def MGG_unpresent_Augustus_locate_in_pav_orthofinder( MGG_unpresent_Augustus_list_file_name, pav_orthofinder_file_name, gene_protein_mapping_table_file_name, pav_MGG_unpresent_Augustus_file_name, orthofinder_unassianed_tsv_file_name, MGG_unpresent_Augustus_unassianed_list_file_name): R_code = ''' MGG_unpresent_Augustus_locate_in_pav_orthofinder=function(MGG_unpresent_Augustus_list_file_name,pav_orthofinder_file_name,gene_protein_mapping_table_file_name,pav_MGG_unpresent_Augustus_file_name,orthofinder_unassianed_tsv_file_name,MGG_unpresent_Augustus_unassianed_list_file_name){ require(readxl) require(WriteXLS) require(dplyr) MGG_unpresent_Augustus_list=read.table(MGG_unpresent_Augustus_list_file_name,stringsAsFactors = F) pav_orthofinde=read_xlsx(pav_orthofinder_file_name) pav_orthofinde=pav_orthofinde[,-1] gene_protein_mapping_table=read.table(gene_protein_mapping_table_file_name) pav_orthofinde_protein=merge(MGG_unpresent_Augustus_list,gene_protein_mapping_table,by.x = 1,by.y = 1) pav_MGG_unpresent_Augustus =pav_orthofinde %>% filter(protein_id %in% pav_orthofinde_protein$V2) pav_MGG_unpresent_Augustus=pav_MGG_unpresent_Augustus[,c(158,1:157)] WriteXLS::WriteXLS(pav_MGG_unpresent_Augustus,pav_MGG_unpresent_Augustus_file_name) orthofinder_unassianed=read.table(orthofinder_unassianed_tsv_file_name,sep = "\t",header = T,check.names = F) MGG_unpresent_Augustus_unassianed_list=intersect(pav_MGG_unpresent_Augustus$protein_id,orthofinder_unassianed$`70-15_protein`) write.table(MGG_unpresent_Augustus_unassianed_list,MGG_unpresent_Augustus_unassianed_list_file_name,quote = F,row.names = F,col.names = F) } ''' R_MGG_unpresent_Augustus_locate_in_pav_orthofinder = SignatureTranslatedAnonymousPackage( R_code, "R_MGG_unpresent_Augustus_locate_in_pav_orthofinder") R_MGG_unpresent_Augustus_locate_in_pav_orthofinder.MGG_unpresent_Augustus_locate_in_pav_orthofinder( MGG_unpresent_Augustus_list_file_name, pav_orthofinder_file_name, gene_protein_mapping_table_file_name, pav_MGG_unpresent_Augustus_file_name, orthofinder_unassianed_tsv_file_name, MGG_unpresent_Augustus_unassianed_list_file_name)