Hello Danny,
Accessing the public mySQL database directly (no http queries) using perl with
the DBI module is an option. There is no set of tools provided for this, but
here is the access info: http://genome.ucsc.edu/FAQ/FAQdownloads#download29
However, a better may be to work with the data in flat file format from the
start. On our Downloads page, every mySQL table is represented in plain text
format (same name as in DB, .txt.gz is the data, .sql is the schema). Use the
Table browser to find out which tables/files are associated with which tracks
and the common keys to join on ("view schema" button). On Downloads there is
also data not contained in the database as a track (chromosome files, other
specially formatted data). The best way to understand this is to navigate the
web page and examine the REAME docs.
The Table browser could also be used to create your own flat files, but this
usually not a good solution if the data is dense and genome-wide. Using the
files on Downloads is both faster and would not require you to break up the
data (there is a 100k line limit on Table browser output, we normally recommend
breaking large data down by chromosome.
Here are some help pages about the Table browser and Downloads:
http://hgdownload.cse.ucsc.edu/downloads.html
http://genome.ucsc.edu/cgi-bin/hgTables
http://genome.ucsc.edu/FAQ/FAQdownloads#download32
Thanks,
Jennifer
------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group
----- "Nemesis" <black.neme...@gmail.com> wrote:
> From: "Nemesis" <black.neme...@gmail.com>
> To: gen...@soe.ucsc.edu
> Sent: Wednesday, October 14, 2009 6:03:27 AM GMT -08:00 US/Canada Pacific
> Subject: [Genome] Query UCSC via Perl software
>
> Dear UCSC Staff,
> I'm actually involved in a little research with my lab and I require
> to write a Perl program, to query your database, to get in some ways
> informations about hystones status at certain positions of the
> chromosome.
> How is it possible to do this? For example NCBI gives to programmers
> a
> set of E-Utils, do you provide something similiar? I need to
> manipulate or the HTTP queries or the MySQL one.
> Thanks you really
> Greetings
>
> Danny Incarnato
> _______________________________________________
> Genome maillist - Genome@lists.soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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