[BioC] libraries or commands to help with parsing or handling web based database queries
ALAN SMITH
alansmith2 at gmail.com
Mon Feb 19 18:41:47 CET 2007
Hello Bioconductors
I am having a very hard time figuring out how to make web based
database query results into a nice neat table (if such a thing is
possible in R). I am constantly searching the metabolite database
METLIN by copying and pasting addresses. I have to search this
database with several hundred entries, often, and would like to
automate the process to remove the HUGE amount of time I spend doing
this carpel tunnel creating routine. I have found several ways to get
the pages source like.
library(RCurl)
test<-getURL("http://metlin.scripps.edu/metabo_list.php?mass_min=112.04885&mass_max=112.0555")
#OR
url.show("http://metlin.scripps.edu/metabo_list.php?mass_min=112.04885&mass_max=112.0555")
Once I get the URL info I notice that the data I am interested in is
between </form> and </table>.
Are there any packages or methods in R to remove the information I am
interested in? I am having problems manipulating STRINGS in R like
selecting all of the text between two strings. I am not a programmer.
Thanks,
Alan
Note I am able to use KEGGSOAP without any trouble.
More information about the Bioconductor
mailing list