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

1 files changed, 43 insertions, 0 deletions

diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
new file mode 100644
index 00000000..c9ec3872
--- /dev/null
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -0,0 +1,43 @@
+from __future__ import absolute_import, print_function, division
+
+import os
+import glob
+import gzip
+
+from base import webqtlConfig
+
+
+def process_genofiles(geno_dir=webqtlConfig.GENODIR):
+    print("Yabba")
+    #sys.exit("Dabba")
+    os.chdir(geno_dir)
+    for geno_file in glob.glob("*"):
+        if geno_file.lower().endswith(('.geno', '.geno.gz')):
+            #group_name = genofilename.split('.')[0]
+            sample_list = get_samplelist(geno_file)
+
+
+def get_samplelist(geno_file):
+    genofilename = os.path.join(webqtlConfig.GENODIR, geno_file)
+    if os.path.isfile(genofilename + '.gz'):
+        genofilename += '.gz'
+        genofile = gzip.open(genofilename)
+    else:
+        genofile = open(genofilename)
+        
+    for line in genofile:
+        line = line.strip()
+        if not line:
+            continue
+        if line.startswith(("#", "@")):
+            continue
+        break
+    
+    headers = line.split()
+    
+    if headers[3] == "Mb":
+        samplelist = headers[4:]
+    else:
+        samplelist = headers[3:]
+    return samplelist
+