Help with constructing a SQL query 2007-12-03 - By Marcus Claesson
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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 (@{$dbh->selectcol_arrayref("SELECT rank FROM test WHERE sub_rank
IS NULL")}) {
@(protected) = @{$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(@(protected)); $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 @(protected)=@@(protected) */;
/*!40101 SET @(protected)=@@(protected) */;
/*!40101 SET @(protected)=@@(protected) */;
/*!40101 SET NAMES utf8 */;
/*!40103 SET @(protected)=@@(protected) */;
/*!40103 SET TIME_ZONE='+00:00' */;
/*!40014 SET @(protected)=@@(protected), UNIQUE_CHECKS=0 */;
/*!40014 SET @(protected)=@@(protected),
FOREIGN_KEY_CHECKS=0 */;
/*!40101 SET @(protected)=@@(protected), SQL_MODE='NO_AUTO_VALUE_ON_ZERO'
*/;
/*!40111 SET @(protected)=@@(protected), 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=@(protected) */;
/*!40101 SET SQL_MODE=@(protected) */;
/*!40014 SET FOREIGN_KEY_CHECKS=@(protected) */;
/*!40014 SET UNIQUE_CHECKS=@(protected) */;
/*!40101 SET CHARACTER_SET_CLIENT=@(protected) */;
/*!40101 SET CHARACTER_SET_RESULTS=@(protected) */;
/*!40101 SET COLLATION_CONNECTION=@(protected) */;
/*!40111 SET SQL_NOTES=@(protected) */;
--
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