From bcbdf46ad35eda39f3b837719ab39bc5896f89dd Mon Sep 17 00:00:00 2001 From: e-sollier Date: Fri, 15 Nov 2024 09:40:57 +0100 Subject: [PATCH] gtf: use gene attribute for finding gene coords --- figeno/genes.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/figeno/genes.py b/figeno/genes.py index a6df458..7bd708d 100644 --- a/figeno/genes.py +++ b/figeno/genes.py @@ -347,7 +347,7 @@ def find_genecoord_gtf(gene_name,file): linesplit = line.split("\t") if linesplit[2] in ["gene","miRNA_gene","rRNA_gene"]: for x in linesplit[8].split(";"): - if x.lstrip(" ").startswith("gene_name"): + if x.lstrip(" ").startswith("gene_name") or x.lstrip(" ").startswith("gene"): x = x[x.find("\"")+1:] name = x[:x.find("\"")] if gene_name.upper()==name.upper(): @@ -362,7 +362,7 @@ def find_genecoord_gtf(gene_name,file): else: break if linesplit[2] in ["transcript"]: for x in linesplit[8].split(";"): - if x.lstrip(" ").startswith("gene_name"): + if x.lstrip(" ").startswith("gene_name") or x.lstrip(" ").startswith("gene"): x = x[x.find("\"")+1:] name = x[:x.find("\"")] if gene_name.upper()==name.upper():