aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
authorzsloan2017-02-08 18:27:13 +0000
committerzsloan2017-02-08 18:27:13 +0000
commitd015b37f863c69932072d4ecf9fa1c1cd7fd3ee0 (patch)
treecc515905822ac8e8118c614c9a34b07a5f02ddda /wqflask
parent160503c3c04ca19c9262d5c3b6100b7ac2242e0e (diff)
downloadgenenetwork2-d015b37f863c69932072d4ecf9fa1c1cd7fd3ee0.tar.gz
Changed the way .fam files are written/read, which fixes the issue with GEMMA mapping accuracy.
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/maintenance/get_group_samplelists.py2
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py2
2 files changed, 2 insertions, 2 deletions
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index 2d48ce78..04e94886 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -51,6 +51,6 @@ def get_samplelist_from_plink(genofilename):
samplelist = []
for line in genofile:
line = line.split(" ")
- samplelist.append(line[0])
+ samplelist.append(line[1])
return samplelist
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 66bed5a2..3bde61cd 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -41,7 +41,7 @@ def gen_pheno_txt_file(this_dataset, samples, vals):
this_val = -9
else:
this_val = vals[i]
- outfile.write(line[0] + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
+ outfile.write("0" + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
def parse_gemma_output(this_dataset):
included_markers = []