diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 5 | ||||
| -rwxr-xr-x | wqflask/base/mrna_assay_tissue_data.py | 10 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfig.py | 2 |
3 files changed, 13 insertions, 4 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index d6a46c2e..5603fe2e 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -158,7 +158,10 @@ class Markers(object): """Todo: Build in cacheing so it saves us reading the same file more than once""" def __init__(self, name): json_data_fh = open(os.path.join(webqtlConfig.NEWGENODIR + name + '.json')) - markers = json.load(json_data_fh) + try: + markers = json.load(json_data_fh) + except: + markers = [] for marker in markers: if (marker['chr'] != "X") and (marker['chr'] != "Y"): diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 54a7ce8e..ba82057a 100755 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -19,7 +19,7 @@ class MrnaAssayTissueData(object): if self.gene_symbols == None: self.gene_symbols = [] - print("self.gene_symbols:", self.gene_symbols) + #print("self.gene_symbols:", self.gene_symbols) self.data = collections.defaultdict(Bunch) @@ -57,9 +57,15 @@ class MrnaAssayTissueData(object): results = g.db.execute(query).fetchall() + lower_symbols = [] + for gene_symbol in gene_symbols: + if gene_symbol != None: + lower_symbols.append(gene_symbol.lower()) + for result in results: symbol = result[0] - if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]: + #if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]: + if symbol.lower() in lower_symbols: #gene_symbols.append(symbol) symbol = symbol.lower() diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 330fec56..4f9b3af3 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -55,7 +55,7 @@ COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'genotype_files/' PYLMM_PATH = '/home/zas1024/plink_gemma/' SNP_PATH = '/home/zas1024/snps/' -IMGDIR = GNROOT + '/wqflask/wqflask/images/' +IMGDIR = GNROOT + '/wqflask/output/' IMAGESPATH = HTMLPATH + 'images/' UPLOADPATH = IMAGESPATH + 'upload/' TMPDIR = '/home/zas1024/tmp/' # Will remove this and dependent items later |