support old isoquant runs

src/post_process.py

@@ -224,7 +224,22 @@ def parse_input_gtf(self):
  """Parses the GTF file using gffutils to build a detailed dictionary of genes, transcripts, and exons."""
  gene_dict = {}
  if not self.config.genedb_filename:
- raise FileNotFoundError("IsoQuant annotation DB file is missing.")
+ # convert GFT to DB if we use previous IsoQuant runs
+ # remove this functionality later
+ tmp_file = tempfile.NamedTemporaryFile(suffix=".db")
+ self.config.genedb_filename = tmp_file.name
+ input_gtf_path = self.config.input_gtf
+ gffutils.create_db(
+ input_gtf_path,
+ dbfn=self.config.genedb_filename,
+ force=True,
+ keep_order=True,
+ merge_strategy="merge",
+ sort_attribute_values=True,
+ disable_infer_genes=True,
+ disable_infer_transcripts=True,
+ )
+ # raise FileNotFoundError("IsoQuant annotation DB file is missing.")
 
  try:
  # Create a temporary database