def getGeneInfo(self, plot_type_id=None):
"""
2008-10-17
return data structure containing sorted gene list and its info
"""
SNPRegionPlot = model.Stock_250kDB.SNPRegionPlot
SNPRegionPlotToGene = model.Stock_250kDB.SNPRegionPlotToGene
rows = model.db.metadata.bind.execute("select g.gene_id, count(distinct s.phenotype_method_id) as count from %s g, %s s\
where s.id=g.plot_id and s.plot_type_id=%s group by g.gene_id order by count desc, gene_id"\
%(SNPRegionPlotToGene.table.name, SNPRegionPlot.table.name, plot_type_id))
gene_ls = []
gene_id2index = {}
gene_label_ls = []
gene_desc_names = ['gene_id', 'gene_symbol', 'type_of_gene', 'chr', 'start', 'stop', 'protein_label', 'protein_comment', 'protein_text']
for row in rows:
gene_id2index[row.gene_id] = len(gene_ls)
matrix_of_gene_descriptions = hc.returnGeneDescLs(model.gene_annotation, gene_id_ls=[row.gene_id])
if len(matrix_of_gene_descriptions)>0:
gene_desc_ls = matrix_of_gene_descriptions[0]
gene = PassingData(gene_id=row.gene_id, gene_symbol=gene_desc_ls[1], type_of_gene=gene_desc_ls[2], chr=gene_desc_ls[3],\
start=gene_desc_ls[4], stop=gene_desc_ls[5], protein_label=gene_desc_ls[6], protein_comment=gene_desc_ls[7], \
protein_text=gene_desc_ls[8])
else:
gene = PassingData(gene_id=row.gene_id)
gene.count = row.count
gene.snp_region_plot_ls = []
gene_ls.append(gene)
gene_label_ls.append(getattr(gene, 'gene_symbol', row.gene_id))
gene_info = PassingData()
gene_info.gene_id2index = gene_id2index
gene_info.gene_ls = gene_ls
gene_info.gene_label_ls = gene_label_ls
return gene_info
def show_plot(self, id=None, snp_region_plot_ids=None):
"""
2008-10-30
add option snp_region_plot_ids for display_results_gene_one.html to call but not necessary. request.params is good enough.
2008-10-17
get request params: get_other_phenotypes, snp_region_plot_ids
2008-10-06
"""
SNPRegionPlot = model.Stock_250kDB.SNPRegionPlot
if id:
c.snp_region_plot = SNPRegionPlot.get(id)
else:
c.snp_region_plot = None
get_other_phenotypes = request.params.get('get_other_phenotypes', False)
snp_region_plot_ids = request.params.get('snp_region_plot_ids', snp_region_plot_ids)
if get_other_phenotypes:
c.snp_region_plot_ls = SNPRegionPlot.query.filter_by(chromosome=c.snp_region_plot.chromosome).\
filter_by(start=c.snp_region_plot.start).\
filter_by(stop=c.snp_region_plot.stop).\
filter_by(plot_type_id=c.snp_region_plot.plot_type_id).order_by(SNPRegionPlot.phenotype_method_id).all()
elif snp_region_plot_ids:
snp_region_plot_id_ls = snp_region_plot_ids.split(',')
#snp_region_plot_id_ls = map(int, snp_region_plot_id_ls)
c.snp_region_plot_ls = [SNPRegionPlot.get(int(snp_region_plot_id)) for snp_region_plot_id in snp_region_plot_id_ls]
else:
c.snp_region_plot_ls = []
if c.snp_region_plot is None and len(c.snp_region_plot_ls)>0:
c.snp_region_plot = c.snp_region_plot_ls[0]
#plot_file_path = os.path.join(config['app_conf']['plots_store'], 'snp_region_plot_%s.png'%c.snp_region_plot.id)
#if not os.path.isfile(plot_file_path):
# self.savePlot(c.snp_region_plot, plot_file_path)
gene_annotation = model.gene_annotation
gene_id_ls = [plot2gene.gene_id for plot2gene in c.snp_region_plot.plot2gene_ls]
c.matrix_of_gene_descriptions = hc.returnGeneDescLs(gene_annotation, gene_id_ls)
#print abc
#raise Exception('Just testing the interactive debugger!')
#c.matrix_of_gene_descriptions = []
return render('/snp_region_plot_single.html')
