Changeset: ec60d67107d2 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=ec60d67107d2
Added Files:
sql/test/sciql/Tests/smith_waterman.sql
Branch: sciql
Log Message:
A use case of SciQL in sequence alignment
The query doesn't work yet, hence, no stable.{out,err}
diffs (61 lines):
diff --git a/sql/test/sciql/Tests/smith_waterman.sql
b/sql/test/sciql/Tests/smith_waterman.sql
new file mode 100644
--- /dev/null
+++ b/sql/test/sciql/Tests/smith_waterman.sql
@@ -0,0 +1,56 @@
+-- Trying to implement the local sequence alignment algorithm Smith-Waterman
using SciQL
+
+-- An array to store the score table
+CREATE ARRAY blosum50 (x CHAR(1) DIMENSION, y char(1) dimension, score int);
+INSERT INTO blosum50 VALUES ('A', 'A', 5), ('A', 'R', -1), ..., ('V', 'Y',
-1), ('V', 'V', 5);
+
+-- The left-hand-side sequence to be aligned, y-axis
+CREATE ARRAY seq1 (idx INT DIMENSION[$len1], v CHAR(1));
+INSERT INTO seq1 VALUES ('P'), ('A'), ..., ('E');
+-- The right-hand-side sequence to be aligned, x-axis
+CREATE ARRAY seq2 (idx INT DIMENSION[$len2], v CHAR(1));
+INSERT INTO seq1 VALUES ('H'), ('E'), ..., ('E');
+
+-- The cost of a gap
+DECLARE d INT; SET d = ???;
+
+-- An array to store the scores of aligning the two sequences,
+-- 'ancst' denotes the ancestor of this score: 0 - none; 1 - upper left; 2 -
left; 3 - upper
+CREATE ARRAY scores (x INT DIMENSION[$len2], y INT DIMENSION[$len1], score INT
DEFAULT 0, ancst INT);
+INSERT INTO scores (
+ SELECT x, y,
+ max4 (0, scores[x-1][y-1].score + blosum50[][].score,
scores[x-1][y].score - d, scores[x][y-1].score - d),
+ -- returns which of the input parameters has the max value
+ max4_pos(0, scores[x-1][y-1].score + blosum50[][].score,
scores[x-1][y].score - d, scores[x][y-1].score - d),
+ FROM scores, blosum50
+ -- the first row+column are already initialised with 0 and need no more
computations
+ WHERE scores.x > 0 AND scores.y > 0;
+
+-- Table to store the alignment result, assuming only one best alignment, but
+-- should be easy to be extended for multiple best alignments
+-- Need to store (x, y) to denote the position of the letters
+CREATE TABLE alignment(x INT, y INT, c1 CHAR(1), c2 CHAR(1), score INT);
+
+DECLARE cur_x INT, cur_y INT, cur_scr INT;
+SET cur_scr = SELECT MAX(score) FROM scores;
+SET cur_x = SELECT x FROM scores WHERE score = cur_scr;
+SET cur_y = SELECT y FROM scores WHERE score = cur_scr;
+
+-- FIXME: forgot to deal with the gaps
+WHILE cur_scr > 0 DO
+ INSERT INTO alignment VALUES (cur_x, cur_y, seq1[cur_y].v,
seq2[cur_x].v, cur_scr);
+ IF (scores[cur_x][cur_y].ancst = 1) THEN
+ SET cur_x = cur_x -1;
+ SET cur_y = cur_y -1;
+ ELSEIF (scores[cur_x][cur_y].ancst = 2) THEN
+ SET cur_x = cur_x -1;
+ ELSEIF (scores[cur_x][cur_y].ancst = 3) THEN
+ SET cur_y = cur_y -1;
+ END IF;
+
+ IF (scores[cur_x][cur_y].ancst = 0) THEN
+ SET cur_scr = 0;
+ ELSE
+ SET cur_scr = scores[cur_x][cur_y].score;
+ END IF;
+END WHILE;
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