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| author | zsloan | 2018-10-11 15:43:41 +0000 |
|---|---|---|
| committer | zsloan | 2018-10-11 15:43:41 +0000 |
| commit | 261ba5e41408d212cc3c33df658b6be2431f68ad (patch) | |
| tree | 0ebcdab6a10a1d112dd5a36512352314219fcc56 /wqflask/maintenance/convert_geno_to_bimbam.py | |
| parent | 65eff561d9527d10a32bea36b660135422e8cce9 (diff) | |
| download | genenetwork2-261ba5e41408d212cc3c33df658b6be2431f68ad.tar.gz | |
- Added fix for GEMMA LOCO
- Added all current SNP browser code (not complete yet)
- Added change to convert_geno_to_bimbam that makes it ignore .geno files marked as "filler" (so ones where the .geno file is fake and we sometimes directly receive the genotypes as BIMBAM)
- Changes TheSpecies object in species.py to accept species name as well as dataset name
Diffstat (limited to 'wqflask/maintenance/convert_geno_to_bimbam.py')
| -rw-r--r-- | wqflask/maintenance/convert_geno_to_bimbam.py | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py index a5d2d12a..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 |