Merge pull request #17 from sanogenetics/hotfix/revert-nebula-dante

revert nebula dante

Author: willgdjones

src/snps/io/reader.py

@@ -156,14 +156,15 @@ def __call__(self):
         elif re.match("^rs[0-9]*[, \t]{1}[1]", first_line):
             d = self.read_generic(file, compression, skip=0)
         elif "vcf" in comments.lower() or "##contig" in comments.lower():
-            dante_comments = ["hwfssz1", "BIGDATA_COMPUTING", "bigdata_autoanalysis"]
-            if "/scratch/" in comments.lower():
-                provider = "Nebula"
-            elif any(x in comments.lower() for x in dante_comments):
-                provider = "Dante"
-            else:
-                provider = "vcf"
-            d = self.read_vcf(file, compression, provider, self._rsids)
+            # Commented out because we need to have a better think through how to discriminate between them.
+            # dante_comments = ["hwfssz1", "BIGDATA_COMPUTING", "bigdata_autoanalysis"]
+            # if "/scratch/" in comments.lower():
+            #     provider = "Nebula"
+            # elif any(x in comments.lower() for x in dante_comments):
+            #     provider = "Dante"
+            # else:
+            #     provider = "vcf"
+            d = self.read_vcf(file, compression, "vcf", self._rsids)
         elif ("Genes for Good" in comments) | ("PLINK" in comments):
             d = self.read_genes_for_good(file, compression)
         elif "DNA.Land" in comments:

tests/io/test_reader.py

@@ -311,8 +311,8 @@ def test_read_unannotated_vcf(self):
             "tests/input/unannotated_testvcf.vcf", "vcf", unannotated=True, build=0
         )
 
-    def test_read_vcf_Dante(self):
-        self.run_parsing_tests_vcf("tests/input/testvcf_Dante.vcf", "Dante")
+    # def test_read_vcf_Dante(self):
+    #     self.run_parsing_tests_vcf("tests/input/testvcf_Dante.vcf", "Dante")
 
-    def test_read_vcf_Nebula(self):
-        self.run_parsing_tests_vcf("tests/input/testvcf_Nebula.vcf", "Nebula")
+    # def test_read_vcf_Nebula(self):
+    #     self.run_parsing_tests_vcf("tests/input/testvcf_Nebula.vcf", "Nebula")