(jebene) minor changes to cleanup pylint

jacquard/merge.py

@@ -114,7 +114,7 @@ def _get_desired_format_tags(self):
         format_tag_list = []
         regexes_used = set()
 
-        for tag in self.format_metaheaders: 
+        for tag in self.format_metaheaders:
             for regex in self.format_tag_regexes:
                 if re.match(regex, tag):
                     format_tag_list.append(tag)
@@ -126,14 +126,15 @@ def _get_desired_format_tags(self):
             for unused_regex in unused_regexes:
                 msg = ("In the specified list of regexes {}, the regex [{}] "
                        "does not match any format tags; this expression may be "
-                       "irrelevant.")
-            logger.warning(msg, self.format_tag_regexes, unused_regex)
+                       "irrelevant.").format(self.format_tag_regexes,
+                                             unused_regex)
+            logger.warning(msg)
 
         if len(format_tag_list)==0:
             msg = ("The specified format tag regex [{}] would exclude all "
                    "format tags. Review inputs/usage and try again")
             raise utils.UsageError(msg, self.format_tag_regexes)
-                       
+
         return sorted(format_tag_list)
 
     def _get_metaheader_subset(self):
@@ -236,6 +237,7 @@ def __init__(self, args):
                              "at_least_one_somatic": _Filter.\
                                                     _include_row_if_any_somatic}
         self._args = args
+
         if args.include_all and (args.include_cells or args.include_rows):
             msg = ('Unable to process command-line arguments. Neither '
                    '--include_cells nor --include_rows can be specified if '
@@ -718,14 +720,14 @@ def _validate_consistent_input(vcf_readers, include_all):
         untranslated_readers = []
         translated = False
         untranslated = False
-    
+
         for vcf_reader in vcf_readers:
             if '##jacquard.translate.caller' in vcf_reader.metaheaders:
                 translated = True
             else:
                 untranslated = True
                 untranslated_readers.append(vcf_reader)
-    
+
         if translated and untranslated:
             msg = ("Some input VCFs [{}] were not translated by Jacquard. "
                    "Review input and/or use --included_all flag")
@@ -811,7 +813,7 @@ def add_subparser(subparser):
     parser.add_argument("--force", action='store_true', help="Overwrite contents of output directory")
     parser.add_argument("--log_file", help="Log file destination", metavar="")
     parser.add_argument("-v", "--verbose", action='store_true')
-    
+
 def _predict_output(args):
     desired_output_files = set([os.path.basename(args.output)])
 
@@ -844,7 +846,8 @@ def execute(args, execution_context):
 #and _build_contigs behave differently. It seems like we could make the
 #signatures of these methods more similar or even combine some methods to
 #reduce excess iterations over the coordinates/vcf_readers
-        merge_vcf_readers = _create_merge_vcf_readers(file_readers, format_tag_regex)
+        merge_vcf_readers = _create_merge_vcf_readers(file_readers,
+                                                      format_tag_regex)
         _validate_consistent_input(merge_vcf_readers, args.include_all)
         _validate_consistent_samples(merge_vcf_readers)
         merge_vcf_readers = _sort_readers(merge_vcf_readers,

jacquard/utils/summarize_rollup_transform.py

@@ -7,7 +7,6 @@
 
 from collections import defaultdict
 from decimal import Decimal
-import re
 
 import jacquard.utils.utils as utils
 import jacquard.variant_caller_transforms.common_tags as common_tags
@@ -109,8 +108,8 @@ def _add_caller_count_values(vcf_record, tag_type, tag_id):
     sample_tag = {}
     for sample, tags in vcf_record.sample_tag_values.items():
         sample_tag[sample] = 0
-        desired_tags = common_tags.AbstractJacquardTag.get_matching_tags(tags,
-                                                                         tag_type)
+        desired_tags = common_tags.AbstractJacquardTag\
+                       .get_matching_tags(tags, tag_type)
         for tag in desired_tags:
             if desired_tags[tag] != "0" and desired_tags[tag] != ".":
                 sample_tag[sample] += int(desired_tags[tag])
@@ -180,8 +179,8 @@ def __init__(self):
         super(self.__class__,
               self).__init__(SUMMARY_TAG,
                              CALLERS_PASSED_COUNT,
-                             ('Count of variant callers where FILTER = PASS for '
-                              'this variant in the Jacquard tagged VCF'))
+                             ('Count of variant callers where FILTER = PASS '
+                              'for this variant in the Jacquard tagged VCF'))
 
     def add_tag_values(self, vcf_record):
         _add_caller_count_values(vcf_record,

jacquard/utils/summarize_zscore_transform.py

@@ -169,7 +169,7 @@ def _get_dependent_value(tag_values, dependent_tag_id):
     def _init_population_stats(self, vcf_reader, dependent_tag_id):
         '''Derive mean and stdev.
 
-        Adapted from online variance algorithm from Knuth, The Art of Computer 
+        Adapted from online variance algorithm from Knuth, The Art of Computer
         Programming, volume 2
 
         Returns: mean and stdev when len(values) > 1, otherwise (None, None)

jacquard/variant_caller_transforms/common_tags.py

@@ -88,7 +88,7 @@ class ReportedTag(AbstractJacquardTag):
     it explicitly simplifies how summary tags are generated.
     """
     #pylint: disable=too-few-public-methods
-    
+
     def __init__(self, caller_abbreviation):
         super(self.__class__,
               self).__init__(caller_abbreviation,

test/merge_test.py

@@ -82,7 +82,7 @@ def test_gets_desired_format_tags_raisesErrorIfExcludeAll(self):
         mock_file_reader = MockFileReader("my_dir/my_file.txt", file_contents)
 
         self.assertRaisesRegexp(utils.UsageError,
-                                "The specified format tag regex \[.*\] would exclude all format tags. Review inputs/usage and try again",
+                                r"The specified format tag regex \[.*\] would exclude all format tags. Review inputs/usage and try again",
                                 merge.MergeVcfReader,
                                 mock_file_reader,
                                 "FOO.*")
@@ -819,15 +819,15 @@ def test_disambiguate_format_tags_considersDifferentCallers(self):
                           self.entab("chr2|1|.|A|C|.|.|INFO|DP|15|87")]
         mock_file_reader1 = MockFileReader("fileA.txt", file_contents1)
         merge_vcf_reader1 = merge.MergeVcfReader(mock_file_reader1, "DP")
- 
+
         file_contents2 = ["##metaheader1\n",
                           "##jacquard.translate.caller=VarScan",
                           '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">\n',
                           self.entab("#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|SampleNormal|SampleTumor\n"),
                           self.entab("chr2|1|.|A|C|.|.|INFO|DP|75|65")]
         mock_file_reader2 = MockFileReader("fileB.txt", file_contents2)
         merge_vcf_reader2 = merge.MergeVcfReader(mock_file_reader2, "DP")
- 
+
         format_tags = {"DP": ['##FORMAT=<ID=DP,Number=1,Type=Integer,Description="[MuTect]: Read Depth">',
                               '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="[VarScan]: Read Depth">']}