diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 8 | ||||
| -rwxr-xr-x | wqflask/base/mrna_assay_tissue_data.py | 6 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 2 |
3 files changed, 9 insertions, 7 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 706b193d..acfee3d4 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -789,7 +789,7 @@ class PhenotypeDataSet(DataSet): this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_score_value = LRS_score_value = this_trait.lrs - this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb)) + this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.6f Mb' % (LRS_Chr, float(LRS_Mb)) def retrieve_sample_data(self, trait): query = """ @@ -880,7 +880,7 @@ class GenotypeDataSet(DataSet): else: trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb - this_trait.location_repr = 'Chr%s: %.4f' % (this_trait.chr, float(this_trait.mb) ) + this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) ) this_trait.location_value = trait_location_value def retrieve_sample_data(self, trait): @@ -1107,7 +1107,7 @@ class MrnaAssayDataSet(DataSet): # this_trait.mb) #ZS: Put this in function currently called "convert_location_to_value" - this_trait.location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr, + this_trait.location_repr = 'Chr %s: %.6f Mb' % (this_trait.chr, float(this_trait.mb)) this_trait.location_value = trait_location_value @@ -1163,7 +1163,7 @@ class MrnaAssayDataSet(DataSet): this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_score_value = this_trait.lrs - this_trait.LRS_location_repr = 'Chr %s: %.4f Mb' % (lrs_chr, float(lrs_mb)) + this_trait.LRS_location_repr = 'Chr %s: %.6f' % (lrs_chr, float(lrs_mb)) def convert_location_to_value(self, chromosome, mb): diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 1a05fce7..b2c0448a 100755 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -51,15 +51,15 @@ class MrnaAssayTissueData(object): query += ''' Symbol in {} group by Symbol) as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol - and t.Mean = x.maxmean; + and t.Mean = x.maxmean;http://docs.python.org/2/library/string.html?highlight=lower#string.lower '''.format(in_clause) results = g.db.execute(query).fetchall() for result in results: symbol = result[0] - if symbol in gene_symbols: - #gene_symbols.append(symbol) + if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]: + #gene_symbols.append(symbol) symbol = symbol.lower() self.data[symbol].gene_id = result.GeneId diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 8930c917..7f1170a9 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -423,6 +423,8 @@ class GeneralTrait(object): if result: self.locus_chr = result[0] self.locus_mb = result[1] + else: + self.locus = self.locus_chr = self.locus_mb = "" else: self.locus = self.locus_chr = self.locus_mb = "" else: |