Fix Parent attribute handling for features with multiple parents (#85)

* Fix Parent attribute handling for features with multiple parents * Update change log * No longer explicitly support python 3.5
standage · Oct 21, 2020 · 9447ba8 · 9447ba8
1 parent a107d27
commit 9447ba8
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diff --git a/.travis.yml b/.travis.yml
@@ -7,7 +7,6 @@ branches:
     - master
 language: python
 python:
-    - 3.5
     - 3.6
     - 3.7
     - 3.8

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,11 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.5.1] - 2020-10-21
+### Fixed
+- A bug with handling of the "Parent" attribute for features with multiple parents (see #85).
+
+
 ## [0.5] - 2020-06-03
 ### Added
 - New `NamedIndex` class for storing and retrieving features by ID (see #82).

diff --git a/setup.py b/setup.py
@@ -30,7 +30,6 @@
           'Development Status :: 4 - Beta',
           'Environment :: Console',
           'License :: OSI Approved :: BSD License',
-          'Programming Language :: Python :: 3.5',
           'Programming Language :: Python :: 3.6',
           'Programming Language :: Python :: 3.7',
           'Programming Language :: Python :: 3.8',

diff --git a/tag/feature.py b/tag/feature.py
@@ -441,7 +441,7 @@ def add_attribute(self, attrkey, attrvalue, append=False, oldvalue=None):
                 oldid = self.get_attribute('ID')
                 for child in self.children:
                     child.add_attribute('Parent', attrvalue,
-                                        oldvalue=oldid)
+                                        oldvalue=oldid, append=True)
             self._attrs[attrkey] = attrvalue
             if self.is_multi:
                 self.multi_rep._attrs[attrkey] = attrvalue
@@ -451,8 +451,7 @@ def add_attribute(self, attrkey, attrvalue, append=False, oldvalue=None):
 
         # Handle all other attribute types
         if oldvalue is not None:
-            if attrkey in self._attrs:
-                assert oldvalue in self._attrs[attrkey]
+            if attrkey in self._attrs and oldvalue in self._attrs[attrkey]:
                 del self._attrs[attrkey][oldvalue]
         if attrkey not in self._attrs or append is False:
             self._attrs[attrkey] = dict()

diff --git a/tag/tests/data/eden-mod.gff3 b/tag/tests/data/eden-mod.gff3
@@ -12,12 +12,12 @@ ctg123	.	CDS	5000	5500	.	+	0	ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
 ctg123	.	CDS	7000	7600	.	+	0	ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
 ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=g1;Name=EDEN.3
 ctg123	.	exon	1300	1500	.	+	.	ID=exon00001;Parent=mRNA3
-ctg123	.	exon	3000	3902	.	+	.	ID=exon00003;Parent=mRNA3
+ctg123	.	exon	3000	3902	.	+	.	ID=exon00003;Parent=mRNA00001,mRNA3
 ctg123	.	CDS	3301	3902	.	+	0	ID=cds00003;Parent=mRNA3;Name=edenprotein.3
 ctg123	.	CDS	3391	3902	.	+	0	ID=cds00004;Parent=mRNA3;Name=edenprotein.4
-ctg123	.	exon	5000	5500	.	+	.	ID=exon00004;Parent=mRNA3
+ctg123	.	exon	5000	5500	.	+	.	ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA3
 ctg123	.	CDS	5000	5500	.	+	1	ID=cds00003;Parent=mRNA3;Name=edenprotein.3
 ctg123	.	CDS	5000	5500	.	+	1	ID=cds00004;Parent=mRNA3;Name=edenprotein.4
 ctg123	.	CDS	7000	7600	.	+	1	ID=cds00003;Parent=mRNA3;Name=edenprotein.3
 ctg123	.	CDS	7000	7600	.	+	1	ID=cds00004;Parent=mRNA3;Name=edenprotein.4
-ctg123	.	exon	7000	9000	.	+	.	ID=exon00005;Parent=mRNA3
+ctg123	.	exon	7000	9000	.	+	.	ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA3