it seems a db0 package can pass check but be wrong

[vjcitn]

[1] "/usr/local/lib/R/site-library/fly.db0/extdata/chipmapsrc_fly.sqlite"
[2] "/usr/local/lib/R/site-library/fly.db0/extdata/chipsrc_fly.sqlite"   
> con = dbConnect(SQLite(), pas[2])
> dbListTables(con)
 [1] "accessions"            "chrlengths"            "chromosome_locations" 
 [4] "chromosomes"           "cytogenetic_locations" "ec"                   
 [7] "flybase"               "flybase_cg"            "gene_info"            
[10] "gene_synonyms"         "genes"                 "genetype"             
[13] "go_bp"                 "go_bp_all"             "go_cc"                
[16] "go_cc_all"             "go_mf"                 "go_mf_all"            
[19] "kegg"                  "map_counts"            "map_metadata"         
[22] "metadata"              "pubmed"                "refseq"               
[25] "sqlite_stat1"          "uniprot" 

it should have some ensembl tables i think

[vjcitn]

> dbListTables(con)
 [1] "accessions"            "chrlengths"            "chromosome_locations" 
 [4] "chromosomes"           "cytogenetic_locations" "ec"                   
 [7] "ensembl"               "gene_info"             "gene_synonyms"        
[10] "genes"                 "genetype"              "go_bp"                
[13] "go_bp_all"             "go_cc"                 "go_cc_all"            
[16] "go_mf"                 "go_mf_all"             "kegg"                 
[19] "map_counts"            "map_metadata"          "metadata"             
[22] "ncbi2ensembl"          "pubmed"                "refseq"               
[25] "sqlite_stat1"          "uniprot"              

rat has an ensembl table

[vjcitn]

Zebrafish:

Appending Pfam
Error: no such table: anno.pfam
Execution halted

[vjcitn]

human failed at the same point as zebrafish

[vjcitn]

re running the uniprot script rectified the human and zebrafish problems

[vjcitn]

BUT -- ```
Appending Flybase Protein IDs
Error: no such table: anno.flybase_prot

when trying Dm again.

[vjcitn]

for flybase_prot, need to run the code in inparanoid