diff options
Diffstat (limited to 'wqflask/maintenance')
| -rw-r--r-- | wqflask/maintenance/convert_geno_to_bimbam.py | 4 | ||||
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 2 | ||||
| -rw-r--r-- | wqflask/maintenance/generate_kinship_from_bimbam.py | 4 | ||||
| -rw-r--r-- | wqflask/maintenance/geno_to_json.py | 6 |
4 files changed, 9 insertions, 7 deletions
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index 8f331a06..528b98cf 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -180,8 +180,8 @@ class ConvertGenoFile(object): break if __name__=="__main__": - Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/""" - New_Geno_Directory = """/home/zas1024/genotype_files/genotype/bimbam/""" + Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype""" + New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam""" #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") diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 55c642a4..4ad921a2 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -248,7 +248,7 @@ def build_datasets(species, group, type_name): ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '%s' and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 order by - ProbeSetFreeze.OrderList asc""" % (species, group, type_name)) + ProbeSetFreeze.CreateTime desc""" % (species, group, type_name)) dataset_results = Cursor.fetchall() datasets = [] 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") |