ex-289 (cgates): adjusted varscan validation to allow empty HC files.…

… Some pep8 cleanup.
umich-brcf-bioinf · Sep 2, 2015 · 08af4ca · 08af4ca
1 parent c0d6f2e
commit 08af4ca
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Showing 3 changed files with 33 additions and 35 deletions.
diff --git a/jacquard/variant_caller_transforms/varscan.py b/jacquard/variant_caller_transforms/varscan.py
@@ -35,6 +35,9 @@
 VARSCAN_ABBREVIATION = "VS"
 VERSION = "v2.3"
 
+def _varscan_hc_fileheader(line):
+    return line.startswith("chrom\tposition")
+
 class _GenotypeTag(common_tags.AbstractJacquardTag):
     #pylint: disable=too-few-public-methods
     def __init__(self):
@@ -143,23 +146,14 @@ def __init__(self, file_reader):
 
     @staticmethod
     def _parse_file_reader(file_reader):
-        column_header = None
         hc_loci = set()
         file_reader.open()
         for line in file_reader.read_lines():
-            if line.startswith("chrom\tposition"):
-                column_header = line
-            else:
+            if not _varscan_hc_fileheader(line):
                 split_line = line.split("\t")
                 hc_loci.add((split_line[0], split_line[1]))
         file_reader.close()
 
-        #TODO : (cgates): Please test this
-        if not column_header:
-            raise utils.JQException("Error. The hc file {} is in an incorrect"
-                                    "format. Review inputs and try"
-                                    "again.".format(file_reader.file_name))
-
         return hc_loci
 
     def add_tag_values(self, vcf_record):
@@ -199,18 +193,19 @@ def _get_hc_file_pattern(args):
 
     @staticmethod
     def _validate_filter_file(file_reader):
-        column_header = 0
-        file_reader.open()
+        header_is_valid = False
         file_is_empty = True
+        file_reader.open()
         for line in file_reader.read_lines():
             file_is_empty = False
-            if line.startswith("chrom\tposition"):
-                column_header = line
+            if _varscan_hc_fileheader(line):
+                header_is_valid = True
                 break
         file_reader.close()
 
-        if column_header or file_is_empty:
+        if file_is_empty or header_is_valid:
             return file_reader
+        return None
 
     @staticmethod
     def _is_varscan_vcf(file_reader):
@@ -219,8 +214,7 @@ def _is_varscan_vcf(file_reader):
             return "##source=VarScan2" in vcf_reader.metaheaders
         return False
 
-#TODO: (cgates) Add check of header line - extract constant from HCTag?
-    def _is_varscan_hc_file(self, file_reader):
+    def _is_varscan_hc_filename(self, file_reader):
         return self.hc_file_pattern.search(file_reader.file_name)
 
     @staticmethod
@@ -240,26 +234,30 @@ def _raise_invalid_filter_exception(invalid_filter_files):
                                 omitted_files)
 
     @staticmethod
-    def _raise_error_for_unpaired_files(unpaired_files, found_orphan, missing_counterpart):
-        _SINGLETON_ERROR_MSG = ("The VarScan {0} [{{}}] has no "
-                                "matching {1}.").format(found_orphan,
-                                                        missing_counterpart)
-        _MULTIPLE_ERROR_MSG = ("[{{1}}] VarScan {0}s [{{}}] did "
-                               "not have a matching {1}. See log for more "
-                               "details. Review inputs and try "
-                               "again.").format(found_orphan, 
-                                                missing_counterpart)
+    def _raise_error_for_unpaired_files(unpaired_files,
+                                        found_orphan,
+                                        missing_counterpart):
+        singleton_error_msg = ("The VarScan {0} [{{}}] has no "
+                               "matching {1}.").format(found_orphan,
+                                                       missing_counterpart)
+        multiple_error_msg = ("[{{1}}] VarScan {0}s [{{}}] did "
+                              "not have a matching {1}. See log for more "
+                              "details. Review inputs and try "
+                              "again.").format(found_orphan,
+                                               missing_counterpart)
         total_unpaired_files = len(unpaired_files)
         msg = None
         if total_unpaired_files == 1:
-            msg = _SINGLETON_ERROR_MSG.format(unpaired_files[0])
+            msg = singleton_error_msg.format(unpaired_files[0])
         else:
             cutoff = 5
-            unpaired_hc_files_list = ", ".join(unpaired_files[0:min(cutoff, total_unpaired_files)])
+            files = unpaired_files[0:min(cutoff, total_unpaired_files)]
+            unpaired_hc_files_list = ", ".join(files)
             if total_unpaired_files > cutoff:
                 omitted = total_unpaired_files - cutoff
-                unpaired_hc_files_list += ", ...({} file(s) omitted)".format(omitted)
-            msg = _MULTIPLE_ERROR_MSG.format(total_unpaired_files,
+                unpaired_hc_files_list += ", ...({} file(s) omitted)".\
+                        format(omitted)
+            msg = multiple_error_msg.format(total_unpaired_files,
                                              unpaired_hc_files_list)
         raise utils.UsageError(msg)
 
@@ -272,7 +270,7 @@ def _find_varscan_files(self, file_readers):
             if self._is_varscan_vcf(file_reader):
                 prefix, _ = os.path.splitext(file_reader.file_name)
                 prefix_file_readers[prefix] = file_reader
-            elif self._is_varscan_hc_file(file_reader):
+            elif self._is_varscan_hc_filename(file_reader):
                 filter_files.add(file_reader)
             else:
                 unclaimed_set.add(file_reader)
@@ -359,7 +357,7 @@ def _pair_files(self, prefixes, filter_files):
     def _validate_vcf_hc_pairs(self, vcf_hc_pairs):
         hc_files = [i[1] for i in vcf_hc_pairs if i[1]]
         if not hc_files:
-            return 
+            return
 
         unpaired_vcf_files = []
         unpaired_hc_files = []

diff --git a/test/expand_test.py b/test/expand_test.py
@@ -297,7 +297,7 @@ def test_validate_args_checkInputIfVCF(self):
             self.assertRaisesRegexp(utils.UsageError,
                                     ("The expand command requires a VCF file "
                                      "as an input, but the specified input "
-                                     "\[.*input.vcf\] contains no VCF "
+                                     r"\[.*input.vcf\] contains no VCF "
                                      "metaheaders. Review inputs and try "
                                      "again."),
                                     expand.validate_args,

diff --git a/test/variant_caller_transforms/varscan_test.py b/test/variant_caller_transforms/varscan_test.py
@@ -207,15 +207,15 @@ def test_validate_vcf_hc_pairs_raisesIfMissingHcFiles(self):
         vcf_hc_pairs = [(MockFileReader("A.vcf"), MockFileReader("A.hc")),
                         (MockFileReader("B.vcf"), None)]
         self.assertRaisesRegexp(utils.UsageError,
-                                "The VarScan VCF file \[B.vcf\] has no matching high-confidence file.",
+                                r"The VarScan VCF file \[B.vcf\] has no matching high-confidence file.",
                                 self.caller._validate_vcf_hc_pairs,
                                 vcf_hc_pairs)
 
     def test_validate_vcf_hc_pairs_raisesIfNoMissingVcfFiles(self):
         vcf_hc_pairs = [(MockFileReader("A.vcf"), MockFileReader("A.hc")),
                         (None, MockFileReader("B.hc"))]
         self.assertRaisesRegexp(utils.UsageError,
-                                "The VarScan high-confidence file \[B.hc\] has no matching VCF file.",
+                                r"The VarScan high-confidence file \[B.hc\] has no matching VCF file.",
                                 self.caller._validate_vcf_hc_pairs,
                                 vcf_hc_pairs)