Fix and test EI-CoreBioinformatics#226

Mikado/subprograms/util/grep.py

@@ -8,6 +8,7 @@
 import functools
 from ...parsers import GFF, GTF
 from ...subprograms import to_gff
+import re
 
 
 __author__ = 'Luca Venturini'
@@ -21,6 +22,8 @@ def print_gff_gene(curr_gene, curr_transcripts, args):
     :return: None
     """
 
+    pat = re.compile("gene")
+
     if curr_gene is not None or len(curr_transcripts) > 0:
         starts, ends = [], []
         lines = []
@@ -35,11 +38,17 @@ def print_gff_gene(curr_gene, curr_transcripts, args):
             curr_gene.start = min(starts)
         if ends and curr_gene is not None:
             curr_gene.end = max(ends)
-        if curr_gene:
+
+        if curr_gene and not pat.search(curr_gene.feature) and not lines:
             print(curr_gene, file=args.out)
+            print("###", file=args.out)
+            return
+
         if lines:
+            if curr_gene:
+                print(curr_gene, file=args.out)
             print(*lines, sep="\n", file=args.out)
-        print("###", file=args.out)
+            print("###", file=args.out)
 
 
 def verify_storability(record, mrna_ids, gene_ids, args):

Mikado/tests/test_system_calls.py

@@ -1950,6 +1950,47 @@ def test_v_grep(self):
                 self.assertEqual(len(found), len(others))
                 self.assertEqual(found, set(_[0] for _ in others))
 
+    @mark.slow
+    def test_problem_grep(self):
+        fname = pkg_resources.resource_filename("Mikado.tests", "Chrysemys_picta_bellii_problematic.gff3")
+        flist = pkg_resources.resource_filename("Mikado.tests", "Chrysemys_picta_bellii_problematic.list.txt")
+
+        for flag in ("", "-v"):
+            with self.subTest(flag=flag):
+                form = os.path.splitext(fname)[1]
+                outfile = tempfile.NamedTemporaryFile("wt", suffix=form)
+                outfile.close()
+                self.assertFalse(os.path.exists(outfile.name))
+                if flag:
+                    sys.argv = ["mikado", "util", "grep", flag, flist, fname, outfile.name]
+                else:
+                    sys.argv = ["mikado", "util", "grep", flist, fname, outfile.name]
+                print(*sys.argv)
+                pkg_resources.load_entry_point("Mikado", "console_scripts", "mikado")()
+                self.assertTrue(os.path.exists(outfile.name))
+                found = set()
+
+                others = ["NC_023890.1:1..16875"]
+                if flag != "-v":
+                    for line in pkg_resources.resource_stream("Mikado.tests",
+                                                              "Chrysemys_picta_bellii_problematic.list.txt"):
+                        rec = line.decode().rstrip().split()[0]
+                        print(line, rec)
+                        others.append(rec)
+
+                with to_gff(outfile.name, input_format=form[1:]) as stream:
+                    for record in stream:
+                        if record.feature in ("exon", "CDS"):
+                            continue
+                        if record.is_transcript:
+                            found.add(record.transcript)
+                        elif record.feature in ("pseudogene", "region"):
+                            found.add(record.id)
+
+                self.assertEqual(len(found), len(others))
+                self.assertEqual(found, set(others))
+
+
 
 if __name__ == "__main__":
     unittest.main()