Merge branch 'master' of https://github.com/zsloan/genenetwork2 into zsloan

1 files changed, 16 insertions, 2 deletions

diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index c9ec3872..b8397b47 100755
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -17,8 +17,13 @@ def process_genofiles(geno_dir=webqtlConfig.GENODIR):
             sample_list = get_samplelist(geno_file)
 
 
-def get_samplelist(geno_file):
-    genofilename = os.path.join(webqtlConfig.GENODIR, geno_file)
+def get_samplelist(file_type, geno_file):
+    if file_type == "geno":
+        return get_samplelist_from_geno(geno_file)
+    elif file_type == "plink":
+        return get_samplelist_from_plink(geno_file)
+
+def get_samplelist_from_geno(genofilename):
     if os.path.isfile(genofilename + '.gz'):
         genofilename += '.gz'
         genofile = gzip.open(genofilename)
@@ -41,3 +46,12 @@ def get_samplelist(geno_file):
         samplelist = headers[3:]
     return samplelist
 
+def get_samplelist_from_plink(genofilename):
+    genofile = open(genofilename)
+    
+    samplelist = []
+    for line in genofile:
+        line = line.split(" ")
+        samplelist.append(line[0])
+
+    return samplelist
\ No newline at end of file