From 866305ffa728cb6e90f16015b0b881ba6cb0362e Mon Sep 17 00:00:00 2001
From: Lei Yan
Date: Sat, 22 Feb 2014 21:57:13 -0600
Subject: On branch master

---
 .../datasampledir/load_genotypes/sample.geno       | 26 ++++++++++------------
 wqflask/maintenance/dataset/datastructure.py       | 10 +++++++++
 wqflask/maintenance/dataset/load_genotypes.py      | 12 +++++-----
 3 files changed, 29 insertions(+), 19 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/maintenance/dataset/datasampledir/load_genotypes/sample.geno b/wqflask/maintenance/dataset/datasampledir/load_genotypes/sample.geno
index 6dad9ace..618e4833 100644
--- a/wqflask/maintenance/dataset/datasampledir/load_genotypes/sample.geno
+++ b/wqflask/maintenance/dataset/datasampledir/load_genotypes/sample.geno
@@ -1,14 +1,12 @@
-@name:BXD
-@type:riset
-@mat:B
-@pat:D
-@het:H
-@unk:U
-Chr	Locus	cM	Mb	BXD1	BXD2	BXD5	BXD6	BXD8
-1	rs6269442	0	3.482275	B	B	D	D	D
-1	rs6365999	0	4.811062	B	B	D	D	D
-1	rs6376963	0.895	5.008089	B	B	D	D	D
-1	rs3677817	1.185	5.176058	B	B	D	D	D
-1	rs8236463	2.081	5.579193	B	B	D	D	D
-1	rs6333200	2.081	6.217921	B	B	D	D	D
-1	rs6298633	2.367	6.820241	B	B	D	D	D
+@name:BXD
+@type:riset
+@mat:B
+@pat:D
+@het:H
+@unk:U
+Chr	Locus	cM	Mb	BXD1	BXD2	BXD5	BXD6	BXD8
+1	rs6269442	0	3.482275	B	B	D	D	D
+2	rs6365999	0.3	4.811062	B	B	D	D	D
+3	rs6376963	0.895	5.008089	B	B	D	D	D
+4	rs3677817	1.185	5.176058	B	B	D	D	D
+5	rs8236463	2.081	5.579193	B	B	D	D	D
diff --git a/wqflask/maintenance/dataset/datastructure.py b/wqflask/maintenance/dataset/datastructure.py
index fd9386b3..0ee4b4ab 100644
--- a/wqflask/maintenance/dataset/datastructure.py
+++ b/wqflask/maintenance/dataset/datastructure.py
@@ -55,6 +55,16 @@ def get_species(inbredsetid):
         """
     cursor.execute(sql, (inbredsetid))
     return cursor.fetchone()
+    
+def get_genofreeze_byinbredsetid(inbredsetid):
+    cursor, con = utilities.get_cursor()
+    sql = """
+        SELECT GenoFreeze.`Id`, GenoFreeze.`Name`, GenoFreeze.`FullName`, GenoFreeze.`InbredSetId`
+        FROM GenoFreeze
+        WHERE GenoFreeze.`InbredSetId`=%s
+        """
+    cursor.execute(sql, (inbredsetid))
+    return cursor.fetchone()
 
 def get_nextdataid_phenotype():
     cursor, con = utilities.get_cursor()
diff --git a/wqflask/maintenance/dataset/load_genotypes.py b/wqflask/maintenance/dataset/load_genotypes.py
index 0ae2c5cd..bca99b95 100644
--- a/wqflask/maintenance/dataset/load_genotypes.py
+++ b/wqflask/maintenance/dataset/load_genotypes.py
@@ -38,12 +38,14 @@ def main(argv):
             strainnames = line.split()[4:]
             strains = datastructure.get_strains_bynames(speciesid, strainnames)
             continue
+        # geno line
         cells = line.split()
-        Chr = cells[0]
-        Locus = cells[1]
-        cM = cells[2]
-        Mb = cells[3]
-        print len(cells)
+        chr = cells[0]
+        locus = cells[1]
+        cm = cells[2]
+        mb = cells[3]
+        values = cells[4:]
+        print values
     return
 
     # open db
-- 
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