#Script to download and make named lists of GO annotations for use in Metaneighbor

Grabbed .gaf file from http://geneontology.org/gene-associations/goa_human.gaf.gz
http://geneontology.org/gene-associations/goa_human_rna.gaf.gz



Named character vector of all go terms, mapping to GO ids
```{r}
#To convert GO ids to their related terms
library(GO.db)
goterms = Term(GOTERM)
write.table(goterms, sep = "\t", file = '/home/werner/tools/metaneighbor_go_annot/goterms.txt' )
```


```{r}
#41 lines of header for the full protien annotations
go_metadata = read.table(file = '/home/werner/tools/metaneighbor_go_annot/goa_human.gaf', skip = 41, sep="\t", fill = T, quote = "")
dim(go_metadata)
```

```{r}
head(go_metadata)

```

Get all the unique GO IDs
make a named list, 
```{r}

go_id = unique(as.character(go_metadata$V5))
length(go_id)
go_human_annots = vector(mode = 'list', length = length(go_id) )

names(go_human_annots) = go_id
for(i in 1:length(go_id)){
  gene_names = c(unique(as.character(go_metadata$V3[as.character(go_metadata$V5) == go_id[i]])))
  go_human_annots[[i]] = gene_names
  
}



```





```{r}

save(go_human_annots, file = '/home/werner/tools/metaneighbor_go_annot/GO_human_annot')

```