update unit test, use ensemble id if name is empty

agfusion/cli.py

@@ -111,15 +111,17 @@ def annotate(
 
     if batch_out_dir is not None:
 
+        gene1_name = fusion.gene5prime.gene.name
+        if gene1_name == "":
+            gene1_name = fusion.gene5prime.gene.id
+
+        gene2_name = fusion.gene3prime.gene.name
+        if gene2_name == "":
+            gene2_name = fusion.gene3prime.gene.id
+
         outdir = join(
             batch_out_dir,
-            fusion.gene5prime.gene.name
-            + "-"
-            + str(junction5prime)
-            + "_"
-            + fusion.gene3prime.gene.name
-            + "-"
-            + str(junction3prime),
+            gene1_name + "-" + str(junction5prime) + "_" + gene2_name + "-" + str(junction3prime),
         )
 
     fusion.save_transcript_cdna(out_dir=outdir, middlestar=args.middlestar)
@@ -155,8 +157,7 @@ def batch_mode(args, agfusion_db, pyensembl_data, rename, colors):
         agfusion_db.logger.warn(f"Output directory {args.out} already exists! Overwriting...")
 
     if not Path(args.file).exists():
-        FileNotFoundError(f"File not found {args.file}")
-        sys.exit(1)
+        raise FileNotFoundError(f"File not found {args.file}")
 
     if args.algorithm in parsers.parsers:
         for fusion in parsers.parsers[args.algorithm](args.file, agfusion_db.logger):

agfusion/model.py

@@ -1,6 +1,7 @@
 """
 Holds classes for containing information for Gene and Fusion exon and protein information.
 """
+
 import itertools
 import os
 import re
@@ -342,7 +343,15 @@ def __init__(
             noncanonical=noncanonical,
         )
 
-        self.name = self.gene5prime.gene.name + "_" + self.gene3prime.gene.name
+        gene1_name = self.gene5prime.gene.name
+        if gene1_name == "":
+            gene1_name = self.gene5prime.gene.id
+
+        gene2_name = self.gene3prime.gene.name
+        if gene2_name == "":
+            gene2_name = self.gene3prime.gene.id
+
+        self.name = gene1_name + "_" + gene2_name
         self.name = self.name.replace("/", "-")
 
         # construct all the fusion transcript combinations

test/test_parsers.py

@@ -16,9 +16,9 @@
 db_human = database.AGFusionDB(abspath(join(curdir, "agfusion.homo_sapiens.75.db")))
 db_human.build = "homo_sapiens_75"
 
-data_human95 = pyensembl.EnsemblRelease(111, "human")
-db_human95 = database.AGFusionDB(abspath(join(curdir, "agfusion.homo_sapiens.111.db")))
-db_human95.build = "homo_sapiens_111"
+data_human_hg38 = pyensembl.EnsemblRelease(111, "human")
+db_human_hg38 = database.AGFusionDB(abspath(join(curdir, "agfusion.homo_sapiens.111.db")))
+db_human_hg38.build = "homo_sapiens_111"
 
 
 BASEDIR = "./data/FusionsFindingAlgorithms"
@@ -112,15 +112,15 @@ def test_with_coding_effect(self):
         all_fusions = ["ARID3B_MYCNUT", "ARID3B_MYCN", "TVP23C_CDRT4"]
         for fusion in parsers.parsers["starfusion"](
             f"{BASEDIR}/STARFusion/" + "star-fusion.fusion_predictions.abridged.coding_effect.tsv",
-            db_human95.logger,
+            db_human_hg38.logger,
         ):
             fusion = model.Fusion(
                 gene5prime=fusion["gene5prime"],
                 gene5primejunction=fusion["gene5prime_junction"],
                 gene3prime=fusion["gene3prime"],
                 gene3primejunction=fusion["gene3prime_junction"],
-                db=db_human95,
-                pyensembl_data=data_human95,
+                db=db_human_hg38,
+                pyensembl_data=data_human_hg38,
                 protein_databases=["pfam"],
                 noncanonical=False,
             )
@@ -156,15 +156,15 @@ def test_parse_human(self):
         all_fusions = ["BCAS4_BCAS3", "HNRNPC_ACIN1"]
         for fusion in parsers.parsers["longgf"](
             f"{BASEDIR}/LongGF/fusions_hg38.log",
-            db_human95.logger,
+            db_human_hg38.logger,
         ):
             fusion = model.Fusion(
                 gene5prime=fusion["gene5prime"],
                 gene5primejunction=fusion["gene5prime_junction"],
                 gene3prime=fusion["gene3prime"],
                 gene3primejunction=fusion["gene3prime_junction"],
-                db=db_human95,
-                pyensembl_data=data_human95,
+                db=db_human_hg38,
+                pyensembl_data=data_human_hg38,
                 protein_databases=["pfam"],
                 noncanonical=False,
             )
@@ -177,35 +177,35 @@ class TestFusionInspector(unittest.TestCase):
     def test_parse_human(self):
         """Test basic parsing."""
 
-        all_fusions = ["AL627171.2_TPM3", "STAT3_AL627171.2"]
+        all_fusions = ["ENSG00000282885_TPM3", "STAT3_ENSG00000282885"]
 
         for fusion in parsers.parsers["fusioninspector"](
             f"{BASEDIR}/FusionInspector/test.FusionInspector.fusions.abridged.txt",
-            db_human95.logger,
+            db_human_hg38.logger,
         ):
             fusion = model.Fusion(
                 gene5prime=fusion["gene5prime"],
                 gene5primejunction=fusion["gene5prime_junction"],
                 gene3prime=fusion["gene3prime"],
                 gene3primejunction=fusion["gene3prime_junction"],
-                db=db_human95,
-                pyensembl_data=data_human95,
+                db=db_human_hg38,
+                pyensembl_data=data_human_hg38,
                 protein_databases=["pfam"],
                 noncanonical=False,
             )
             assert fusion.name in all_fusions, f"{fusion.name} not in list!"
 
         for fusion in parsers.parsers["fusioninspector"](
             f"{BASEDIR}/FusionInspector/test.FusionInspector.fusions.txt",
-            db_human95.logger,
+            db_human_hg38.logger,
         ):
             fusion = model.Fusion(
                 gene5prime=fusion["gene5prime"],
                 gene5primejunction=fusion["gene5prime_junction"],
                 gene3prime=fusion["gene3prime"],
                 gene3primejunction=fusion["gene3prime_junction"],
-                db=db_human95,
-                pyensembl_data=data_human95,
+                db=db_human_hg38,
+                pyensembl_data=data_human_hg38,
                 protein_databases=["pfam"],
                 noncanonical=False,
             )