From 6aaefdaae3a9fb068278d9b94d8cdf25d4f8d852 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 19 Jul 2013 16:13:47 -0500
Subject: Created file gen_group_samplelists that iterates through all
genofiles and builds each groups' samplelist
---
wqflask/maintenance/gen_select_dataset.py | 4 ++-
wqflask/maintenance/get_group_samplelists.py | 43 ++++++++++++++++++++++++++++
2 files changed, 46 insertions(+), 1 deletion(-)
create mode 100644 wqflask/maintenance/get_group_samplelists.py
(limited to 'wqflask/maintenance')
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 8cb94f20..d4e47327 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -115,7 +115,7 @@ def build_types(species, group):
(all types except phenotype/genotype are tissues)
"""
- Cursor.execute("""select distinct Tissue.Name, Tissue.Name
+ Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
InbredSet.Name = %s and
@@ -192,6 +192,8 @@ def main():
datasets=datasets,
)
+ print("data:", data)
+
output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json"""
with open(output_file, 'w') as fh:
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
new file mode 100644
index 00000000..2434038e
--- /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 get_sample_list_dir(geno_dir="/home/zas1024/gene/web/genotypes/"):
+ os.chdir(geno_dir)
+
+ for group_file in glob.glob("*"):
+ if group_file.lower().endswith(('.geno', '.geno.gz')):
+ #group_name = genofilename.split('.')[0]
+ sample_list = get_sample_list(group_file)
+ print("\n\n{}\n\n".format(sample_list))
+
+
+def get_sample_list(group_file):
+ print(group_file)
+ genofilename = str(os.path.join(webqtlConfig.GENODIR, group_file))
+ if genofilename.lower().endswith('.geno.gz'):
+ genofile = gzip.open(genofilename)
+ else:
+ genofile = open(genofilename)
+ for line in genofile:
+ line = line.strip()
+ if not line:
+ continue
+ if line.startswith(("#", "@")):
+ continue
+ headline = line
+ break
+ headers = headline.split("\t")
+ if headers[3] == "Mb":
+ samplelist = headers[4:]
+ else:
+ samplelist = headers[3:]
+ return samplelist
+
+if __name__ == '__main__':
+ get_sample_list_dir()
--
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