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authorLei Yan2014-02-21 17:04:51 -0600
committerLei Yan2014-02-21 17:04:51 -0600
commit1014d09efced9c36274aec0d2486469648569721 (patch)
tree152d489c8b56349c6f3680ee7cf5554c95df90c0
parentff6224c23ff0894012297dc569de0bfdbb0da1c3 (diff)
downloadgenenetwork2-1014d09efced9c36274aec0d2486469648569721.tar.gz
On branch master
-rw-r--r--wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini8
-rw-r--r--wqflask/maintenance/dataset/load_genotypes.py17
2 files changed, 15 insertions, 10 deletions
diff --git a/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini b/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini
index 638c3bd8..1f977cf8 100644
--- a/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini
+++ b/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini
@@ -1,4 +1,6 @@
 [config]
-inbredsetid = 1
-datafile = datasampledir/load_phenotypes/sample_data.txt
-metafile = datasampledir/load_phenotypes/sample_meta.txt
+genofile = datasampledir/load_genotypes/sample.geno
+U = x
+H = 0
+B = -1
+D = 1
diff --git a/wqflask/maintenance/dataset/load_genotypes.py b/wqflask/maintenance/dataset/load_genotypes.py
index d309a903..204fb926 100644
--- a/wqflask/maintenance/dataset/load_genotypes.py
+++ b/wqflask/maintenance/dataset/load_genotypes.py
@@ -1,3 +1,8 @@
+import sys
+import re
+
+import utilities
+
 def main(argv):
     # config
     config = utilities.get_config(argv[1])
@@ -21,11 +26,10 @@ def main(argv):
                 kv = re.split(':|=', item)
                 metadic[kv[0].strip()] = kv[1].strip()
             continue
-        if line.startswith("Chr"):
-            print "[meta dictionary]"
-            for k,v in metadic.items():
-                print "%s: %s" % (k, v)
-            print
+        if line.lower().startswith("chr"):
+            print "geno meta:"
+            for k, v in metadic.items():
+                print "\t%s: %s" % (k, v)
             continue
         cells = line.split()
         Chr = cells[0]
@@ -33,7 +37,6 @@ def main(argv):
         cM = cells[2]
         Mb = cells[3]
         print len(cells)
-        ?
     return
 
     # open db
@@ -183,7 +186,7 @@ def main(argv):
     file_geno.close()
     con.close()
 
-# main
 if __name__ == "__main__":
+    print "command line arguments:\n\t%s" % sys.argv
     main(sys.argv)
     print "exit successfully"