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)
