Merge pull request #135 from hammerlab/fewer-default-ensembl-release-…

…objects

Fix Ensembl release 83

.travis.yml

@@ -36,13 +36,14 @@ install:
   - pip install .
   - pip install coveralls
 script:
-  # human releases
+  # older human releases
   - pyensembl install --release 54 --species human
   - pyensembl install --release 75 --species human
   - pyensembl install --release 77 --species human
-  - pyensembl install --release 81 --species human
-  # mouse releases
-  - pyensembl install --release 81 --species mouse
+  # latest human release
+  - pyensembl install --release 83 --species human
+  # latest mouse release
+  - pyensembl install --release 83 --species mouse
   # run tests
   - nosetests test --with-coverage --cover-package=pyensembl  && ./lint.sh
 after_success:

pyensembl/__init__.py

@@ -18,6 +18,7 @@
 from .download_cache import DownloadCache
 from .ensembl_release import EnsemblRelease
 from .ensembl_release_versions import check_release_number, MAX_ENSEMBL_RELEASE
+from .exon import Exon
 from .genome import Genome
 from .gene import Gene
 from .gtf import GTF
@@ -57,12 +58,31 @@ def genome_for_reference_name(reference_name):
 
 ensembl_grch36 = ensembl54 = cached_release(54)  # last release for GRCh36/hg18
 ensembl_grch37 = ensembl75 = cached_release(75)  # last release for GRCh37/hg19
+ensembl_grch38 = cached_release(MAX_ENSEMBL_RELEASE)  # most recent for GRCh38
 
-ensembl77 = cached_release(77)
-ensembl78 = cached_release(78)
-ensembl79 = cached_release(79)
-ensembl80 = cached_release(80)
-ensembl81 = cached_release(81)
-ensembl82 = cached_release(82)
-ensembl83 = cached_release(83)
-ensembl_grch38 = ensembl83  # most recent for GRCh38
+
+__all__ = [
+    "MemoryCache",
+    "DownloadCache",
+    "EnsemblRelease",
+    "MAX_ENSEMBL_RELEASE",
+    "cached_release",
+    "Gene",
+    "Transcript",
+    "Exon",
+    "SequenceData",
+    "find_nearest_locus",
+    "find_species_by_name",
+    "find_species_by_reference",
+    "which_reference",
+    "check_species_object",
+    "normalize_reference_name",
+    "normalize_species_name",
+    "Genome",
+    "GTF",
+    "Locus",
+    "Exon",
+    "ensembl_grch36",
+    "ensembl_grch37",
+    "ensembl_grch38",
+]

pyensembl/genome.py

@@ -148,10 +148,10 @@ def _get_cached_path(
 
     def _get_gtf_path(self, download_if_missing=False, overwrite=False):
         return self._get_cached_path(
-                field_name="gtf",
-                path_or_url=self._gtf_path_or_url,
-                download_if_missing=download_if_missing,
-                overwrite=overwrite)
+            field_name="gtf",
+            path_or_url=self._gtf_path_or_url,
+            download_if_missing=download_if_missing,
+            overwrite=overwrite)
 
     def _get_transcript_fasta_path(
             self,
@@ -465,12 +465,12 @@ def gene_ids_at_locus(self, contig, position, end=None, strand=None):
 
     def gene_names_at_locus(self, contig, position, end=None, strand=None):
         return self.db.distinct_column_values_at_locus(
-             column="gene_name",
-             feature="gene",
-             contig=contig,
-             position=position,
-             end=end,
-             strand=strand)
+            column="gene_name",
+            feature="gene",
+            contig=contig,
+            position=position,
+            end=end,
+            strand=strand)
 
     def exon_ids_at_locus(self, contig, position, end=None, strand=None):
         return self.db.distinct_column_values_at_locus(
@@ -1040,4 +1040,4 @@ def protein_ids(self, contig=None, strand=None):
             strand=strand,
             distinct=True)
         # drop None values
-        return [protein_id for protein_id in protein_ids if protein_id]
+        return [protein_id for protein_id in protein_ids if protein_id]

setup.py

@@ -40,7 +40,7 @@
 if __name__ == '__main__':
     setup(
         name='pyensembl',
-        version="0.8.6",
+        version="0.8.7",
         description="Python interface to ensembl reference genome metadata",
         author="Alex Rubinsteyn",
         author_email="alex {dot} rubinsteyn {at} mssm {dot} edu",

test/common.py

@@ -3,10 +3,10 @@
 import functools
 
 from pyensembl import (
-    ensembl_grch36,
     ensembl_grch37,
     ensembl_grch38,
-    cached_release
+    cached_release,
+    MAX_ENSEMBL_RELEASE,
 )
 from nose.tools import nottest
 
@@ -23,9 +23,12 @@ def test_ensembl_releases(*versions):
     Run a unit test which takes an EnsemblRelease as an argument
     for multiple releases (most recent for each reference genome)
     """
+
     if len(versions) == 0:
         ensembl_releases = major_releases
     else:
+        if any(version > MAX_ENSEMBL_RELEASE for version in versions):
+            raise ValueError("Invalid ensembl release numbers: %s" % (versions,))
         ensembl_releases = [cached_release(version) for version in versions]
 
     def decorator(test_fn):

test/test_ensembl_object_properties.py

@@ -6,11 +6,11 @@
 from __future__ import absolute_import
 
 from nose.tools import eq_
-from pyensembl import EnsemblRelease
+from pyensembl import EnsemblRelease, MAX_ENSEMBL_RELEASE
 
-def test_reference_name():
+def test_human_reference_name():
     eq_(EnsemblRelease(release=54).reference_name, "NCBI36")
     eq_(EnsemblRelease(release=74).reference_name, "GRCh37")
     eq_(EnsemblRelease(release=75).reference_name, "GRCh37")
-    eq_(EnsemblRelease(release=78).reference_name, "GRCh38")
-    eq_(EnsemblRelease(release=79).reference_name, "GRCh38")
+    for release in range(76, MAX_ENSEMBL_RELEASE):
+        eq_(EnsemblRelease(release=release).reference_name, "GRCh38")

test/test_exon_id.py

@@ -4,7 +4,9 @@
 """
 from __future__ import absolute_import
 
-from pyensembl import ensembl_grch38 as ensembl
+from pyensembl import cached_release
+
+ensembl = cached_release(77)
 
 # all exons associated with TP53 gene in Ensembl release 77
 TP53_EXON_IDS_RELEASE_77 = [
@@ -85,9 +87,8 @@ def test_exon_ids_of_transcript_name():
             len(TP53_TRANSCRIPT_26_EXON_IDS_RELEASE_77),
             len(exon_ids))
     assert all(
-            exon_id in TP53_TRANSCRIPT_26_EXON_IDS_RELEASE_77
-            for exon_id in exon_ids
-    )
+        exon_id in TP53_TRANSCRIPT_26_EXON_IDS_RELEASE_77
+        for exon_id in exon_ids)
 
 def exon_ids_of_transcript_id():
     """
@@ -101,5 +102,5 @@ def exon_ids_of_transcript_id():
             len(TP53_TRANSCRIPT_26_EXON_IDS_RELEASE_77),
             len(exon_ids))
     assert all(
-            exon_id in TP53_TRANSCRIPT_26_EXON_IDS_RELEASE_77
-            for exon_id in exon_ids)
+        exon_id in TP53_TRANSCRIPT_26_EXON_IDS_RELEASE_77
+        for exon_id in exon_ids)

test/test_exon_object.py

@@ -5,7 +5,9 @@
 """
 from __future__ import absolute_import
 
-from pyensembl import ensembl_grch38 as ensembl
+from pyensembl import cached_release
+
+ensembl = cached_release(77)
 
 def test_exon_object_by_id():
     """
@@ -25,8 +27,8 @@ def test_exon_object_by_id():
 
 def test_exon_object_by_id_on_negative_strand():
     """
-    test_exon_object_by_id : check properties of exon 1 from CXCR3 when looked
-    up by ID in Ensembl 77.
+    test_exon_object_by_id_on_negative_strand : check properties of exon 1
+    from CXCR3 when looked up by ID in Ensembl 77.
     """
     exon = ensembl.exon_by_id("ENSE00001817013")
     assert exon.gene_name == "CXCR3", \
@@ -69,3 +71,22 @@ def test_exon_object_at_locus_on_negative_strand():
         assert exon.on_negative_strand
         assert exon.start <= 71618517, "Unexpected exon start: %s" % exon.start
         assert exon.end >= 71618517, "Unexpected exon end: %s" % exon.end
+
+def test_exon_basic_properties_str():
+    exon = ensembl.exon_by_id("ENSE00001817013")
+    assert isinstance(str(exon), str)
+    assert isinstance(repr(exon), str)
+    # for now we're assuming that __repr__ and __str__ do the same thing,
+    # if we later change that assumption we should do so explicitly and
+    # change this test
+    assert str(exon) == repr(exon), "%s != %s" % (str(exon), repr(exon))
+
+def test_exon_basic_properties_hash():
+    exon = ensembl.exon_by_id("ENSE00001817013")
+    assert isinstance(hash(exon), int), \
+        "Hash function returns %s instead of int" % (
+            type(hash(exon),))
+    assert hash(exon) == hash(exon), "Hash function is non-deterministic!"
+    other_exon = ensembl.exon_by_id("ENSE00003464041")
+    assert exon != other_exon
+    assert hash(exon) != hash(other_exon)

test/test_gene_ids.py

@@ -7,10 +7,11 @@
 from __future__ import absolute_import
 
 from nose.tools import assert_raises, ok_
-from pyensembl import ensembl_grch38, ensembl77
+from pyensembl import ensembl_grch38, cached_release
 
 from .common import test_ensembl_releases
 
+ensembl77 = cached_release(77, "human")
 
 def test_gene_ids_grch38_hla_a():
     # chr6:29,945,884  is a position for HLA-A

test/test_gene_names.py

@@ -7,19 +7,19 @@
 
 from .common import test_ensembl_releases
 
-# make sure that familia
 KNOWN_GENE_NAMES = [
     "TP53",
     "ERBB2",
     "SMAD4",
     "CTAG1A",
+    "HLA-A",
 ]
 
 @test_ensembl_releases()
 def test_all_gene_names(ensembl):
     """
     test_all_gene_names : Make sure some known gene names such as
-    SMAD4, HSP90AA1, TP53, ERBB2
+    SMAD4, TP53, ERBB2, &c
     """
     gene_names = ensembl.gene_names()
     print(type(gene_names))
@@ -46,3 +46,15 @@ def test_gene_names_on_contig(ensembl):
     assert "SMAD4" in gene_names_chr18, \
         "No SMAD4 in gene names on chr18 of %s, gene names: %s ... (%d)" % (
             ensembl, list(gene_names_chr18[:4]), len(gene_names_chr18))
+
+
+def test_gene_name_of_HLA_gene_id():
+    gene_ids = ensembl_grch38.gene_ids_of_gene_name("HLA-A")
+    gene_names = [
+        ensembl_grch38.gene_name_of_gene_id(gene_id)
+        for gene_id in gene_ids
+    ]
+    unique_gene_names = list(set(gene_names))
+    assert len(unique_gene_names) == 1, (len(unique_gene_names), unique_gene_names)
+    gene_name = unique_gene_names[0]
+    assert gene_name == "HLA-A", gene_name

test/test_gtf_path.py

@@ -35,4 +35,4 @@ def test_gtf_creates_csv_files_in_cache_dir():
         # GTF parsing and then saving the parsed results in a csv file
         gtf_object.dataframe()
         assert len(glob(search_pattern)) > 0, \
-            "Expected GTF to save files in cache_dir"
+            "Expected GTF to save files in cache_dir"

test/test_id_length.py

@@ -12,7 +12,7 @@ def check_id_length(method_name):
         idents = method(contig="Y")
         assert len(idents) > 0, "No values returned by %s" % method_name
         assert all(len(ident) == 15 for ident in idents), \
-           "Invalid IDs for %s: %s" % (
+            "Invalid IDs for %s: %s" % (
                 method_name,
                 [ident for ident in idents if len(ident) != 15])
 

test/test_release_versions.py

@@ -1,6 +1,6 @@
 from __future__ import absolute_import
 
-from pyensembl import EnsemblRelease
+from pyensembl import EnsemblRelease, MAX_ENSEMBL_RELEASE
 
 from nose.tools import raises
 
@@ -21,10 +21,17 @@ def test_version_is_not_numeric():
 def test_version_is_none():
     EnsemblRelease(None)
 
+def test_max_ensembl_release():
+    assert isinstance(MAX_ENSEMBL_RELEASE, int), \
+        "Unexpected type for MAX_ENSEMBL_RELEASE: %s" % (
+            type(MAX_ENSEMBL_RELEASE),)
+    assert 83 <= MAX_ENSEMBL_RELEASE < 1000, \
+        "Unexpected value for MAX_ENSEMBL_RELEASE: %d" % MAX_ENSEMBL_RELEASE
+
 def test_int_version():
-    for version in range(54, 81):
+    for version in range(54, MAX_ENSEMBL_RELEASE):
         EnsemblRelease(version)
 
 def test_str_version():
-    for version in range(54, 81):
+    for version in range(54, MAX_ENSEMBL_RELEASE):
         EnsemblRelease(str(version))