AnnotationForge and Error in FUN(X[[i]], ...) : data.frames in '...' cannot contain duplicated rows

Question

[najibveto]

hello, I am trying to make the gene ontology and kegg database for my non model specie, for that purpose i am using the AnnotationForge package using the following this code:

library(tidyverse)
library(clusterProfiler)
library(AnnotationHub)
library(AnnotationForge)
egg <- rio::import('fatheadminnow-annotation.tsv')
egg[egg==""] <- NA 
colnames(egg)
gene_info <- egg %>% dplyr::select(GID = query_name, GENENAME = seed_ortholog) %>% na.omit()
gterms <- egg %>%
  dplyr::select(query_name, GOs) %>% na.omit()
gterms<- gterms[!grepl("-", gterms$GOs),]
library(stringr)
all_go_list=str_split(gterms$GOs,",")
gene2go <- data.frame(GID = rep(gterms$query_name,
                                times = sapply(all_go_list, length)),
                      GO = unlist(all_go_list),
                      EVIDENCE = "IEA")
gene2go<- gene2go[!grepl("-", gene2go$GO),]
gene2ko <- egg %>%
  dplyr::select(GID = query_name, KO = KEGG_ko) %>%
  na.omit()
load("kegg_info.RData")
colnames(ko2pathway)=c("KO",'Pathway')
library(stringr)
gene2ko$KO=str_replace(gene2ko$KO,"ko:","")
gene2ko<- gene2ko[!grepl("-", gene2ko$KO),]
gene2pathway <- gene2ko %>% left_join(ko2pathway, by = "KO") %>% 
  dplyr::select(GID, Pathway) %>%
  na.omit()
library(dplyr)
gene2go <- dplyr::distinct(gene2go)
gene2ko <- dplyr::distinct(gene2ko)
makeOrgPackage(gene_info=gene_info,
               go=gene2go,
               ko=gene2ko,
               maintainer='gmail.com>',
               author='gmail.com>',
               pathway=gene2pathway,
               version="0.0.1",
               outputDir = "C:/Users/Documents",
               tax_id=90988,
               genus="pimephales",
               species="promelas",
               goTable="go") 

the table gene2go is a fellow:

the table gene2ko is a fellow:

when i run, i got this error :

Error in FUN(X[[i]], ...) : 
  data.frames in '...' cannot contain duplicated rows

i already used the AnnotationForge for making database for another specie aspergillus niger and it worked fine. what could the problem? and how to solve it? thank you for your help.

[kashiff007]

As you already mentioned "data.frames in '...' cannot contain duplicated rows"

Your df gene2go has multiple duplications. Make a file with one gene correspond to multiple GO terms per line:

cep41   GO:0000086,GO:0000226,GO:0000278...

[najibveto]

thank you for your answer, I already used the same package with a different species:

and as u can see that here is duplicate for the same transcript and when I run the same code, I could make the database:

egg <- rio::import('KCN5-annotation.tsv')
egg[egg==""] <- NA 
colnames(egg)
gene_info <- egg %>% dplyr::select(GID = query_name, GENENAME = seed_ortholog) %>% na.omit()
gterms <- egg %>%
  dplyr::select(query_name, GOs) %>% na.omit()
library(stringr)
all_go_list=str_split(gterms$GOs,",")
gene2go <- data.frame(GID = rep(gterms$query_name,
                                times = sapply(all_go_list, length)),
                      GO = unlist(all_go_list),
                      EVIDENCE = "IEA")
gene2go<- gene2go[!grepl("-", gene2go$GO),]
gene2ko <- egg %>%
  dplyr::select(GID = query_name, KO = KEGG_ko) %>%
  na.omit()
load("kegg_info.RData")
colnames(ko2pathway)=c("KO",'Pathway')
library(stringr)
gene2ko$KO=str_replace(gene2ko$KO,"ko:","")
gene2pathway <- gene2ko %>% left_join(ko2pathway, by = "KO") %>% 
  dplyr::select(GID, Pathway) %>%
  na.omit()
makeOrgPackage(gene_info=gene_info,
               go=gene2go,
               ko=gene2ko,
               maintainer='@gmail.com>',
               author='@gmail.com>',
               pathway=gene2pathway,
               version="0.0.1",
               outputDir = "C:/Project05",
               tax_id=5061,
               genus="Aspergillus",
               species="nigerKCN5",
               goTable="go")

and i got the database made:

Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating go table:
go table filled
Populating ko table:
ko table filled
Populating pathway table:
pathway table filled
table metadata filled
'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled

so that is why it is intriguing to work for one specie and not for the other one.