From 48af807b4d8eabb0fac53451333fe7e85d38855b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 21 Jul 2016 12:55:23 +0600
Subject: Doc: SNP handling

---
 doc/database.org | 50 +++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 49 insertions(+), 1 deletion(-)

(limited to 'doc/database.org')

diff --git a/doc/database.org b/doc/database.org
index 9c8c89f2..624174a4 100644
--- a/doc/database.org
+++ b/doc/database.org
@@ -945,7 +945,7 @@ INFO:base.data_set:.sql: get_trait_info:
 
 (that is a bug!).
 
-** Fetch phenotypes
+** Fetch phenotype information
 *** Through the trait page
 
 When hitting the trait page, e.g.
@@ -1165,3 +1165,51 @@ select * from ProbeSetData limit 5;
 5 rows in set (0.00 sec)
 
 linked by ProbeSetXRef.dataid.
+** Fetch genotype information
+
+*** SNPs
+
+The SNP count info for the BXD is calculated like this
+
+#+begin_src python
+        while startMb<endMb:
+            snp_count = g.db.execute("""
+                    select
+                            count(*) from BXDSnpPosition
+                    where
+                            Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
+                            StrainId1 = %d AND StrainId2 = %d
+                    """ % (chrName, startMb, startMb+stepMb, strainId1, strainId2)).fetchone()[0]
+            SNPCounts.append(snp_count)
+            startMb += stepMb
+#+end_src
+
+select * from BXDSnpPosition limit 5;
++------+-----------+-----------+----------+
+| Chr  | StrainId1 | StrainId2 | Mb       |
++------+-----------+-----------+----------+
+| 1    |         2 |         3 | 0.002477 |
+| 1    |         2 |         3 | 0.002592 |
+| 1    |         2 |         3 |  0.00283 |
+| 1    |         2 |         3 | 0.002994 |
+| 1    |         2 |         3 | 0.003299 |
++------+-----------+-----------+----------+
+
+Other SNP tables containing
+
+select * from SnpSource limit 5;
+Empty set (0.00 sec)
+
+select * from SnpAll limit 5;
+Empty set (0.00 sec)
+
+mysql> select * from SnpAll limit 5;
+Empty set (0.00 sec)
+
+mysql> select * from SnpPattern limit 5;
+Empty set (0.00 sec)
+
+mysql> select * from SnpSource limit 5;
+Empty set (0.00 sec)
+
+Hmmm. This is the test database. Then there are the plink files and VCF files.
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