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| author | Pjotr Prins | 2018-10-12 08:24:16 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2018-10-12 08:24:16 +0000 |
| commit | 5162d1484f01a51d65e7e70143146f018d96edb4 (patch) | |
| tree | 0ebcdab6a10a1d112dd5a36512352314219fcc56 /wqflask/maintenance | |
| parent | dd743c8311b26f6a786c346cf4deed144c6a9b61 (diff) | |
| parent | 261ba5e41408d212cc3c33df658b6be2431f68ad (diff) | |
| download | genenetwork2-5162d1484f01a51d65e7e70143146f018d96edb4.tar.gz | |
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into gn-testing
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 | 2 |
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) |