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From:Peter Brawley Date:December 3 2007 4:12pm
Subject:Re: Help with SQL query construction
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Marcus,

>I've managed to do this with a Perl-DBI script, but 
>would much prefer to do it completely with MySQL instead. 

You could port it to a recursive stored procedure. It would probably be 
slower, and what would you have gained?

PB

Marcus Claesson wrote:
> Hi!
>
> I have a "SQL query construction" question that I hope someone can help
> me with. After comparing a bunch of DNA fragments (see name below) with
> a larger reference sequence I get a ordered list ranked according to
> similarities, and with start/stop co-ordinates where the fragments map
> to the reference sequence:
>
> +------+------+-------+------+----------+
> | name | rank | start | stop | sub_rank |
> +------+------+-------+------+----------+
> | A    |    1 |     1 | 1000 |   NULL   |
> | B    |    2 |     2 |  998 |   NULL   |
> | C    |    4 |  1100 | 2000 |   NULL   |
> | D    |    3 |  3050 | 4100 |   NULL   |
> | E    |    5 |  2040 | 3000 |   NULL   | 
> | F    |    6 |  1102 | 2000 |   NULL   |
> | G    |    7 |  1098 | 1998 |   NULL   |
> | H    |    8 |  3048 | 4100 |   NULL   |
> | I    |    9 |  3051 | 4102 |   NULL   |
> +------+------+-------+------+----------+
>
> A graphical representation of fragments mapped to the ref sequence:
>
> ref========================================>
> 1  A------>
> 2  B---->
> 3                              D------>
> 4           C------>
> 5                     E---->
> 6           F------->
> 7          G------->
> 8                              H------->
> 9                               I------->
>
> Now, I want to group fragments in each overlapping position and sub-rank
> them according to their rank in that position. The final table would
> then look like:
> +------+------+-------+------+----------+
> | name | rank | start | stop | sub_rank |
> +------+------+-------+------+----------+
> | A    |    1 |     1 | 1000 |     1    |
> | B    |    2 |     2 |  998 |     2    |
> | C    |    4 |  1100 | 2000 |     1    |
> | D    |    3 |  3050 | 4100 |     1    |
> | E    |    5 |  2040 | 3000 |     1    |
> | F    |    6 |  1102 | 2000 |     2    |
> | G    |    7 |  1098 | 1998 |     3    |
> | H    |    8 |  3048 | 4100 |     2    |
> | I    |    9 |  3051 | 4102 |     3    |
> +------+------+-------+------+----------+
>
> Is this possible to achieve using SQL queries alone (perhaps with GROUP
> BY, nested SELECTs etc)?
>
> I've managed to do this with a Perl-DBI script, but would much prefer to
> do it completely with MySQL instead. The Perl code is below and below
> that is the MySQL-dump of the test data set...
>
> Many thanks in advance!
> Marcus
>
>
> while (@{$dbh->selectcol_arrayref("SELECT rank FROM test WHERE sub_rank
> IS NULL")}) {
>     @null_sub_ranks = @{$dbh->selectcol_arrayref("SELECT rank FROM test
> WHERE sub_rank IS NULL AND NOT (start>=(SELECT stop FROM test WHERE rank
> = (SELECT min(rank) FROM test WHERE sub_rank IS NULL)) OR stop <=
> (SELECT start FROM test WHERE rank = (SELECT min(rank) FROM test WHERE
> sub_rank IS NULL)))")};
>     for ($rank=0; $rank < scalar(@null_sub_ranks); $rank++ ) {
> 	$sub_rank = $rank + 1;
> 	$dbh->do("UPDATE test SET sub_rank=$sub_rank WHERE rank=
> $null_sub_ranks[$rank]");
>     }
> }
>
>
> -- MySQL dump 10.10
> --
> -- Host: localhost    Database: bxb
> -- ------------------------------------------------------
> -- Server version       5.0.22
>
> /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
> /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
> /*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
> /*!40101 SET NAMES utf8 */;
> /*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
> /*!40103 SET TIME_ZONE='+00:00' */;
> /*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
> /*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS,
> FOREIGN_KEY_CHECKS=0 */;
> /*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO'
> */;
> /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
>
> --
> -- Table structure for table `test`
> --
>
> DROP TABLE IF EXISTS `test`;
> CREATE TABLE `test` (
>   `name` text,
>   `rank` int(11) default NULL,
>   `start` int(11) default NULL,
>   `stop` int(11) default NULL,
>   `sub_rank` int(11) default NULL
> ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
>
> --
> -- Dumping data for table `test`
> --
>
>
> /*!40000 ALTER TABLE `test` DISABLE KEYS */;
> LOCK TABLES `test` WRITE;
> INSERT INTO `test` VALUES
>
> ('A',1,1,1000,NULL),('B',2,2,998,NULL),('C',4,1100,2000,NULL),('D',3,3050,4100,NULL),('E',5,2040,3000,NULL),('F',6,1102,2000,NULL),('G',7,1098,1998,NULL),('H',8,3048,4100,NULL),('I',9,3051,4102,NULL);
> UNLOCK TABLES;
> /*!40000 ALTER TABLE `test` ENABLE KEYS */;
> /*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
>
> /*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
> /*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */;
> /*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */;
> /*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
> /*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
> /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
> /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
>
>
>   
Thread
Help with SQL query constructionMarcus Claesson3 Dec
  • RE: Help with SQL query constructionJeff Mckeon3 Dec
  • Re: Help with SQL query constructionPeter Brawley3 Dec