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| author | zsloan | 2018-10-01 16:09:47 +0000 |
|---|---|---|
| committer | zsloan | 2018-10-01 16:09:47 +0000 |
| commit | a3365dae23f204e489939d3defc55edc1b4872d8 (patch) | |
| tree | d4b06818cd0af291cfa34a484e25a6c07621f1ea /wqflask/maintenance | |
| parent | ee8e1eacd88399609f530a33e2d91cf7895da5b0 (diff) | |
| download | genenetwork2-a3365dae23f204e489939d3defc55edc1b4872d8.tar.gz | |
- Can now remove cofactors from correlation scatterplot and select them by just clicking their row in collection
- Cofactor color picker now works in Safari/Macs
- Displays N for relevant samples in trait page sample table
- Don't show bar chart when N>256
- Mapping loading page contents better centered
- Anonymous collections timeout correctly listed as 30 days now
- Minor allele frequency can actually be changed for GEMMA now (previously didn't work)
- Fixed transcript position marker location for mapping results
- Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password
- Users can now map with submitted traits
- Histogram width changes depending upon number of bins (need to improve this still)
- Improved Q-q plot (previously called "probability plot")
Diffstat (limited to 'wqflask/maintenance')
| -rw-r--r-- | wqflask/maintenance/convert_geno_to_bimbam.py | 2 | ||||
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 2 | ||||
| -rw-r--r-- | wqflask/maintenance/generate_kinship_from_bimbam.py | 2 |
3 files changed, 5 insertions, 1 deletions
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index 45522705..a5d2d12a 100644 --- a/wqflask/maintenance/convert_geno_to_bimbam.py +++ b/wqflask/maintenance/convert_geno_to_bimbam.py @@ -154,6 +154,8 @@ 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) |