Merge pull request #44 from standage/fix/entrytype

Fix entry type inference by inheriting from object

CHANGELOG.md

@@ -6,6 +6,9 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Changed
 - CLI implemented using `entry_points` instead of a dedicated script.
 
+### Fixed
+- Entry type inference now correct by inheriting from `object`.
+
 ## [0.1.0] - 2016-12-16
 ### Added
 - Basic data structures

tag/__init__.py

@@ -13,7 +13,9 @@
 except:  # pragma: no cover
     import builtins
 from . import comment
+from . import directive
 from . import feature
+from . import sequence
 from . import range
 from . import reader
 from . import writer

tag/comment.py

@@ -8,7 +8,7 @@
 # ------------------------------------------------------------------------------
 
 
-class Comment():
+class Comment(object):
     """
     Represents a comment in an annotation (GFF3) file.
 
@@ -24,10 +24,6 @@ def __init__(self, data):
         assert data.startswith('#')
         self._rawdata = data
 
-    @property
-    def entry_type(self):
-        return 'tag.comment.Comment'
-
     def __repr__(self):
         return self._rawdata
 

tag/directive.py

@@ -15,7 +15,7 @@
             'attribute-ontology', 'source-ontology', 'genome-build']
 
 
-class Directive():
+class Directive(object):
     """
     Represents a directive from a GFF3 file.
 
@@ -86,10 +86,6 @@ def __init__(self, data):
 
         assert self.dirtype is not None
 
-    @property
-    def entry_type(self):
-        return 'tag.directive.Directive'
-
     @property
     def type(self):
         if self.dirtype in dirtypes:

tag/feature.py

@@ -76,10 +76,6 @@ def __init__(self, data):
             assert self.phase in [0, 1, 2], \
                 'invalid phase "{}"'.format(self.phase)
 
-    @property
-    def entry_type(self):
-        return 'tag.feature.Feature'
-
     def __str__(self):
         """String representation of the feature, sans children."""
         score = '.'

tag/reader.py

@@ -47,20 +47,19 @@ class GFF3Reader():
 
     >>> reader = GFF3Reader(infilename='tests/testdata/pbar-withseq.gff3')
     >>> for entry in reader:
-    ...     print(entry.entry_type)
-    tag.directive.Directive
-    tag.directive.Directive
-    tag.directive.Directive
-    tag.comment.Comment
-    tag.feature.Feature
-    tag.feature.Feature
-    tag.feature.Feature
-    tag.sequence.Sequence
-    tag.sequence.Sequence
+    ...     print(type(entry))
+    <class 'tag.directive.Directive'>
+    <class 'tag.directive.Directive'>
+    <class 'tag.directive.Directive'>
+    <class 'tag.comment.Comment'>
+    <class 'tag.feature.Feature'>
+    <class 'tag.feature.Feature'>
+    <class 'tag.feature.Feature'>
+    <class 'tag.sequence.Sequence'>
+    <class 'tag.sequence.Sequence'>
     >>> reader = GFF3Reader(infilename='tests/testdata/pbar-withseq.gff3')
     >>> for feature in tag.select.features(reader, type='gene'):
     ...     print(feature.slug)
-    ...
     gene@NW_011929623.1[4557, 5749]
     gene@NW_011929624.1[3725, 4229]
 

tag/sequence.py

@@ -11,7 +11,7 @@
 import re
 
 
-class Sequence():
+class Sequence(object):
     """
     Represents a sequence (almost always a nucleotide sequence).
 
@@ -39,10 +39,6 @@ def __init__(self, defline, seq):
         self.defline = defline
         self.seq = seq
 
-    @property
-    def entry_type(self):
-        return 'tag.sequence.Sequence'
-
     def __str__(self):
         return self.defline + '\n' + self.format_seq()