merge changes

1 files changed, 47 insertions, 0 deletions

diff --git a/gn2/maintenance/get_group_samplelists.py b/gn2/maintenance/get_group_samplelists.py
new file mode 100644
index 00000000..6af637ea
--- /dev/null
+++ b/gn2/maintenance/get_group_samplelists.py
@@ -0,0 +1,47 @@
+import os
+import glob
+import gzip
+
+from gn2.base import webqtlConfig
+
+
+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)
+    else:
+        genofile = open(genofilename)
+
+    for line in genofile:
+        line = line.strip()
+        if not line:
+            continue
+        if line.startswith(("#", "@")):
+            continue
+        break
+
+    headers = line.split("\t")
+
+    if headers[3] == "Mb":
+        samplelist = headers[4:]
+    else:
+        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[1])
+
+    return samplelist