From 80652cd7bdc6fecd46d70c754011b9e35df6bf08 Mon Sep 17 00:00:00 2001 From: Kevin Ha Date: Fri, 18 May 2018 12:53:01 -0400 Subject: [PATCH] Deprecate set_gene() --- qapa/collapse.py | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/qapa/collapse.py b/qapa/collapse.py index 8c4220b..a93f461 100644 --- a/qapa/collapse.py +++ b/qapa/collapse.py @@ -58,16 +58,6 @@ def finalize(self): return [self.chrom, self.start, self.end, new_name, self.score, self.strand, self.gene_id] - def set_gene(self, conn): - '''Query for Ensembl Gene ID''' - query = 'select gene_id from ensembl_id where transcript_id = ?' - cur = conn.execute(query, (self.name,)) - r = cur.fetchone() - if r: - self.gene_id = r[0] - else: - self.gene_id = None - def _guess_species(self): if re.match(r'ENST\d+', self.name): return 'hg19'