Re: SQLLDR question
Date: Tue, 23 Nov 2004 23:41:20 +0100
[Quoted] "Dinanath" <sulakhe_at_mcs.anl.gov> wrote in message
> I have file that contains PROTEIN sequences in it. I will show the
> format below. It has about 2million records in it. I wanted to know if
> someone can suggest a sqlldr control file that would help in uploading
> the data that I need to upload. I don't want all the data from this
> file but only some data. I tried to figure out on my own but i
> couldn't do it..
> First look at the example of this file: Looks complex but is very
> >gi|2695847|emb|CAA73704.1| immunoglobulin heavy chain
> >gi|2695851|emb|CAA73709.1| immunoglobulin heavy chain
> >gi|2695853|emb|CAA73712.1| immunoglobulin heavy chain
> ..........so on.. upto 2million records.
> There two things in this file for each record.
> One is Header: that starts with ">"
> Two is SEQUENCE: lines after header till the next header (letters in
> The next record again start with a ">". and so on..
> I am interested to pick only two fields out of each records:
> 1. GI number: that is the number between ">gi|" and "|emb|" eg:2695851
> (for firt record).
> 2. Sequence: example, line numbers 2,3, and 4 of the first record.
> Can anyone write an sqlldr control file that can extract this info and
> put in the following table:
> create table sequences
> gi_number NUMBER NOT NULL,
> sequence CLOB NOT NULL
> Please notice the second column is a clob. because the sequence might
> go beyond 4000 characters sometimes so i can't fit it into varchar.
> I would appreciate any help and sorry if its not the right place to
> post such messages. Please let me know where can post this message if
> not here.
> Thank you very much,
Which version of Oracle do you use ?
Maybe you could try to load the file with the external table feature (Oracle 9i and above).
See this page for examples :
Matthias Hoys Received on Tue Nov 23 2004 - 23:41:20 CET