Gallery - Example 4

Below is the R code to reproduce the example:

Hide output

library(DECIPHER)
> library(RSQLite)
> 
> # import a GenBank sequence file
> gen <- system.file("extdata",
+    "Bacteria_175seqs.gen",
+    package="DECIPHER")
> dbConn <- dbConnect(SQLite(),
+    ":memory:")
> Seqs2DB(gen,
+    "GenBank",
+    dbConn,
+    "")
Reading GenBank file chunk 1


175 total sequences in table Seqs.
Time difference of 0.23 secs


> 
> # add rank information to the database
> ids <- IdentifyByRank(dbConn,
+    level=10,
+    add2tbl=TRUE)


Updating column: "identifier"...
Formed 72 distinct groups.
Added to table Seqs: "identifier".
Time difference of 0.03 secs


> 
> # add length information to the database
> lns <- IdLengths(dbConn,
+    add2tbl=TRUE)


Lengths counted for 175 sequences.
Added to Seqs:  "standard", "nonstandard", and "width".


> 
> # view the database table in a browser
> BrowseDB(dbConn,
+    maxChars=25)
> 
> dbDisconnect(dbConn)
[1] TRUE