Add rat, dog, cat, chicken species & increase MAX_ENSEMBL_RELEASE to 87 (#183)

* added chicken, dog, cat to species

* bump max ensembl release to 87

* added rat to species

* install ensembl 87 instead of 85

* increase version for new species & bump to max ensembl version

* more assertions in custom dir test

* fixed download cache test

Author: iskandr

.travis.yml

@@ -47,13 +47,12 @@ script:
   - pyensembl install --release 54 --species human
   - pyensembl install --release 75 --species human
   - pyensembl install --release 77 --species human
-  # latest human release
   - pyensembl install --release 83 --species human
-  - pyensembl install --release 85 --species human
+  - pyensembl install --release 87 --species human
   # older mouse release (last one for NCBIM37)
   # - pyensembl install --release 67 --species mouse
   # latest mouse release
-  - pyensembl install --release 85 --species mouse
+  - pyensembl install --release 87 --species mouse
   # run tests
   - nosetests test --verbose --with-coverage --cover-package=pyensembl
 after_success:

pyensembl/__init__.py

@@ -35,7 +35,7 @@
 )
 from .transcript import Transcript
 
-__version__ = '1.0.3'
+__version__ = '1.1.0'
 
 def cached_release(release, species="human"):
     """

pyensembl/ensembl_release_versions.py

@@ -15,7 +15,7 @@
 from __future__ import print_function, division, absolute_import
 
 MIN_ENSEMBL_RELEASE = 54
-MAX_ENSEMBL_RELEASE = 85
+MAX_ENSEMBL_RELEASE = 87
 
 def check_release_number(release):
     """

pyensembl/species.py

@@ -183,3 +183,29 @@ def check_species_object(species_name_or_object):
         "GRCm38": (68, MAX_ENSEMBL_RELEASE),
 
     })
+
+dog = Species.register(
+    latin_name="canis_familiaris",
+    synonyms=["dog"],
+    reference_assemblies={"CanFam3.1": (75, MAX_ENSEMBL_RELEASE)})
+
+cat = Species.register(
+    latin_name="felis_catus",
+    synonyms=["cat"],
+    reference_assemblies={"Felis_catus_6.2": (75, MAX_ENSEMBL_RELEASE)})
+
+chicken = Species.register(
+    latin_name="gallus_gallus",
+    synonyms=["chicken"],
+    reference_assemblies={
+        "Galgal4": (75, 85),
+        "Gallus_gallus-5.0": (86, MAX_ENSEMBL_RELEASE)})
+
+# Does the black rat (Rattus Rattus) get used for research too?
+brown_rat = Species.register(
+    latin_name="rattus_norvegicus",
+    synonyms=["brown rat", "lab rat", "rat"],
+    reference_assemblies={
+        "Rnor_5.0": (75, 79),
+        "Rnor_6.0": (80, MAX_ENSEMBL_RELEASE),
+    })

test/test_download_cache.py

@@ -33,18 +33,34 @@ def test_download_cache_missing_remote_file():
 
 def test_download_cache_custom_location():
     test_file = "refseq.ucsc.small.gtf"
-    tmp_dir = os.path.join(tempfile.gettempdir(), "pyensembl")
+    tmp_dir = tempfile.gettempdir()
+
+    print("DIR: %s" % tmp_dir)
+    assert tmp_dir is not None
+
     os.environ['PYENSEMBL_CACHE_DIR'] = tmp_dir
+
     # We need another instance of DownloadCache
     # that copies files over to cache folder
     download_cache = DownloadCache(
-        reference_name="test",
-        annotation_name="test",
+        reference_name="test_reference",
+        annotation_name="test_annotation",
         copy_local_files_to_cache=True)
+
     # clean up
     download_cache.delete_cache_directory()
     download_cache.download_or_copy_if_necessary(
         download_if_missing=True,
         path_or_url=data_path(test_file))
-    ok_(os.path.exists(os.path.join(tmp_dir, test_file)))
+
+    full_path = os.path.join(
+        tmp_dir,
+        "pyensembl",
+        "test_reference",
+        "test_annotation",
+        test_file)
+    print("FULL PATH: %s" % full_path)
+    assert len(full_path) > 0
+
+    ok_(os.path.exists(full_path))
     del os.environ['PYENSEMBL_CACHE_DIR']