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-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py4
-rw-r--r--wqflask/maintenance/geno_to_json.py6
2 files changed, 6 insertions, 4 deletions
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index ad0eb036..b53f5dda 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -54,8 +54,8 @@ class GenerateKinshipMatrices(object):
if __name__=="__main__":
- Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
- Bimbam_Directory = """/home/zas1024/genotype_files/genotype/bimbam/"""
+ Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/"""
+ Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
#./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD \ No newline at end of file
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 789a1691..9579812a 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -24,6 +24,8 @@ import simplejson as json
from pprint import pformat as pf
+#from utility.tools import flat_files
+
class EmptyConfigurations(Exception): pass
@@ -183,8 +185,8 @@ class ConvertGenoFile(object):
if __name__=="__main__":
- Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
- New_Geno_Directory = """/home/zas1024/genotype_files/genotype/json/"""
+ Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
+ New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json"""
#Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
#Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
#convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")