kill the pipeline with no coding genes

Author: ifiddes

cat/__init__.py

@@ -942,7 +942,7 @@ def run(self):
         pipeline_args = self.get_pipeline_args()
         df = tools.gff3.parse_gff3(self.annotation_attrs, self.annotation_gp, self.genome != self.ref_genome)
         if 'protein_coding' not in set(df.GeneBiotype) or 'protein_coding' not in set(df.TranscriptBiotype):
-            logger.critical('No protein_coding annotations found!')
+            raise InvalidInputException('No genes or transcripts with biotype protein_coding found!')
         # validate number parsed
         tot_genes = len(open(self.annotation_gp).readlines())
         if tot_genes != len(df):