diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 12 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 2 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfig.py | 2 |
3 files changed, 8 insertions, 8 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 07fe9cd9..1668940c 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -779,14 +779,14 @@ class MrnaAssayDataSet(DataSet): #Max LRS and its Locus location if this_trait.lrs and this_trait.locus: - self.cursor.execute(""" + query = """ select Geno.Chr, Geno.Mb from Geno, Species - where Species.Name = '%s' and - Geno.Name = '%s' and + where Species.Name = '{}' and + Geno.Name = '{}' and Geno.SpeciesId = Species.Id - """ % (species, this_trait.locus)) - result = self.cursor.fetchone() - + """.format(species, this_trait.locus) + result = g.db.execute(query).fetchone() + if result: #if result[0] and result[1]: # lrs_chr = result[0] diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 3429d9c1..401b729c 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -30,7 +30,7 @@ class GeneralTrait(object): def __init__(self, get_qtl_info=False, **kw): # xor assertion - assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. xor name"; + assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; if kw.get('dataset_name'): self.dataset = create_dataset(kw.get('dataset_name')) else: diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 49afb631..a811c3cd 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -52,7 +52,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'web/' -PYLMM_PATH = HTMLPATH + 'plink/' +PYLMM_PATH = '/home/zas1024/' SNP_PATH = '/mnt/xvdf1/snps/' IMGDIR = HTMLPATH +'image/' IMAGESPATH = HTMLPATH + 'images/' |