diff options
| -rw-r--r-- | wqflask/wqflask/snp_browser/snp_browser.py | 26 |
1 files changed, 23 insertions, 3 deletions
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 360e6b28..9a980cb1 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -300,7 +300,7 @@ class SnpBrowser(object): gene_id = get_gene_id(self.species_id, self.gene_name) gene = [gene_id, self.gene_name] else: - gene = "" + gene = check_if_in_gene(species_id, chr, mb) transcript = exon = function = function_details = '' if self.redundant == "false" or last_mb != mb: # filter redundant if self.include_record(domain, function, snp_source, conservation_score): @@ -444,8 +444,8 @@ class SnpBrowser(object): if domain: domain_1 = domain[0] domain_2 = domain[1] - if domain_1 == "Intergenic" and self.gene_name != "": - domain_1 = self.gene_name + if domain_1 == "Intergenic" and gene != "": + domain_1 = gene_name else: if domain_1 == "Exon": domain_1 = domain_1 + " " + exon @@ -874,3 +874,23 @@ def get_gene_id_name_dict(species_id, gene_name_list): pass return gene_id_name_dict + +def check_if_in_gene(species_id, chr, mb): + if species_id != 0: #ZS: Check if this is necessary + query = """SELECT geneId, geneSymbol + FROM GeneList + WHERE SpeciesId = {0} AND chromosome = '{1}' AND + (txStart < {2} AND txEnd > {2}); """.format(species_id, chr, mb) + else: + query = """SELECT geneId,geneSymbol + FROM GeneList + WHERE chromosome = '{0}' AND + (txStart < {1} AND txEnd > {1}); """.format(species_id, chr, mb) + + result = g.db.execute(query).fetchone() + + if result: + return [result[0], result[1]] + else: + return "" + |