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TAXIDs and NCBI genome?
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#Won't work by cross linking | |
```r | |
tax_search <- entrez_search(db="taxonomy", term="Acetobacter[ORGN] AND genus[RANK]") | |
linked_recs <- entrez_link(dbfrom="taxonomy", db="genome", id=tax_search$ids) | |
linked_recs$links$taxonomy_genome | |
``` | |
``` | |
#[1] "18005" | |
``` | |
```r | |
summ$scaffold_assemblies | |
``` | |
``` | |
[1] "2" | |
``` | |
##Might work by searching taxon names? | |
```r | |
gsearch <- entrez_search(db="genome", term="Acetobacter[ORGN]") | |
summ <- entrez_summary(db="genome", id=gsearch$ids) | |
extract_from_esummary(summ, "organism_name") | |
``` | |
``` | |
42306 42303 | |
"Acetobacter ghanensis" "Acetobacter senegalensis" | |
36731 36730 | |
"Acetobacter syzygii" "Acetobacter orleanensis" | |
36728 36727 | |
"Acetobacter orientalis" "Acetobacter indonesiensis" | |
36726 33022 | |
"Acetobacter cibinongensis" "Acetobacter malorum" | |
31752 31751 | |
"Acetobacter persici" "Acetobacter okinawensis" | |
31749 18005 | |
"Acetobacter papayae" "Acetobacter" | |
16085 10668 | |
"Acetobacter nitrogenifigens" "Acetobacter tropicalis" | |
3440 3150 | |
"Acetobacter pomorum" "Acetobacter aceti" | |
904 | |
"Acetobacter pasteurianus" | |
``` |
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