Value Lookup from File without Slurping
The sqldf package can read a large file to a database without going through R followed by extracting it. The package makes it easier to use RSQLite by setting up the database for you and after extracting the portion you want removing the database automatically. You can specify all this in two lines: one to name the file and one to specify the extraction using SQL. See the examples in example 6 on the home page: http://sqldf.googecode.com#Example_6._File_Input On Fri, Jan 16, 2009 at 4:12 AM, Carlos J. Gil Bellosta
<cgb at datanalytics.com> wrote:
On Fri, 2009-01-16 at 18:02 +0900, Gundala Viswanath wrote:
Dear all, I have a repository file (let's call it repo.txt) that contain two columns like this: # tag value AAA 0.2 AAT 0.3 AAC 0.02 AAG 0.02 ATA 0.3 ATT 0.7 Given another query vector
qr <- c("AAC", "ATT")
I would like to find the corresponding value for each query above, yielding: 0.02 0.7 However, I want to avoid slurping whole repo.txt into an object (e.g. hash). Is there any ways to do that? The reason I want to do that because repo.txt is very2 large size (milions of lines, with tag length > 30 bp), and my PC memory is too small to keep it. - Gundala Viswanath Jakarta - Indonesia
Hello, You can always store your repo.txt into a database, say, SQLite, and select only the values you want via an SQL query. Thus, you will prevent loading the full file into memory. Best regards, Carlos J. Gil Bellosta http://www.datanalytics.com
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