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-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py4
-rw-r--r--wqflask/maintenance/gen_select_dataset.py2
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py2
3 files changed, 7 insertions, 1 deletions
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 45522705..8f331a06 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -140,6 +140,8 @@ class ConvertGenoFile(object):
key, _separater, value = row.partition(':')
key = key.strip()
value = value.strip()
+ if key == "@filler":
+ raise EmptyConfigurations
if key in self.haplotype_notation:
self.configurations[value] = self.haplotype_notation[key]
continue
@@ -154,6 +156,8 @@ class ConvertGenoFile(object):
if not input_file.endswith(('geno', '.geno.gz')):
continue
group_name = ".".join(input_file.split('.')[:-1])
+ if group_name == "HSNIH-Palmer":
+ continue
geno_output_file = os.path.join(new_directory, group_name + "_geno.txt")
pheno_output_file = os.path.join(new_directory, group_name + "_pheno.txt")
snp_output_file = os.path.join(new_directory, group_name + "_snps.txt")
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 18b2dac9..55c642a4 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -219,7 +219,7 @@ def build_datasets(species, group, type_name):
if group == 'MDP':
dataset_text = "Mouse Phenome Database"
else:
- dataset_text = "%s Published Phenotypes" % group
+ dataset_text = "%s Phenotypes" % group
elif type_name == "Genotypes":
Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index f322341d..ad0eb036 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -32,6 +32,8 @@ class GenerateKinshipMatrices(object):
if not input_file.endswith(('geno', '.geno.gz')):
continue
group_name = ".".join(input_file.split('.')[:-1])
+ if group_name == "HSNIH-Palmer":
+ continue
geno_input_file = os.path.join(bimbam_dir, group_name + "_geno.txt")
pheno_input_file = os.path.join(bimbam_dir, group_name + "_pheno.txt")
convertob = GenerateKinshipMatrices(group_name, geno_input_file, pheno_input_file)