Merge pull request #5 from Edinburgh-Genome-Foundry/dev

Implements PR #4

Author: veghp

codon_usage_data/version.txt

@@ -1 +1 @@
-0.1.9
+0.1.10

python_codon_tables/examples/basic_example.py

@@ -1,14 +1,14 @@
 import python_codon_tables as pct
 
 # PRINT THE LIST OF NAMES OF ALL AVAILABLE TABLES
-print ('Available tables:', pct.available_codon_tables_names)
+print("Available tables:", pct.available_codon_tables_names)
 
 # LOAD ONE TABLE BY NAME
 table = pct.get_codons_table("b_subtilis_1423")
-print (table['T']['ACA'])  # returns 0.4
-print (table['*']['UAA'])  # returns 0.61
+print(table["T"]["ACA"])  # returns 0.4
+print(table["*"]["TAA"])  # returns 0.61
 
 
 # LOAD ALL TABLES AT ONCE
 codon_tables = pct.get_all_available_codons_tables()
-print (codon_tables['c_elegans_6239']['L']['CUA'])  # returns 0.09
+print(codon_tables["c_elegans_6239"]["L"]["CTA"])  # returns 0.09

python_codon_tables/python_codon_tables.py

@@ -15,9 +15,7 @@
 _this_dir = os.path.dirname(os.path.realpath(__file__))
 _tables_dir = os.path.join(_this_dir, "..", "codon_usage_data", "tables")
 
-available_codon_tables_names = [
-    filename[:-4] for filename in os.listdir(_tables_dir)
-]
+available_codon_tables_names = [filename[:-4] for filename in os.listdir(_tables_dir)]
 
 available_codon_tables_shortnames = {
     "_".join(table_name.split("_")[:-1]): table_name
@@ -68,9 +66,7 @@ def get_codons_table(table_name, replace_U_by_T=True, web_timeout=5):
     
     """
     if replace_U_by_T:
-        table = get_codons_table(
-            table_name, replace_U_by_T=False, web_timeout=5
-        )
+        table = get_codons_table(table_name, replace_U_by_T=False, web_timeout=5)
         return table_with_U_replaced_by_T(table)
     if isinstance(table_name, int) or str.isdigit(table_name):
         return download_codons_table(taxid=table_name, timeout=web_timeout)
@@ -92,8 +88,7 @@ def get_all_available_codons_tables(replace_U_by_T=True):
 def download_codons_table(taxid=316407, target_file=None, timeout=5):
     """Get all data from all of this package's builtin codon usage tables."""
     _kazusa_url = (
-        "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi"
-        "?aa=1&style=N&species=%s"
+        "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi" "?aa=1&style=N&species=%s"
     )
     _codon_regexpr = r"([ATGCU]{3}) ([A-Z]|\*) (\d.\d+)"
     url = _kazusa_url % taxid
@@ -112,14 +107,16 @@ def download_codons_table(taxid=316407, target_file=None, timeout=5):
             raise err
 
     html_content = web_handle.read().decode().replace("\n", " ")
+    if "<title>not found</title>" in html_content.lower():
+        raise RuntimeError(
+            "Codon usage table for taxonomy ID '%s' not found:" " %s" % (taxid, url)
+        )
     csv_data = "\n".join(
         ["amino_acid,codon,relative_frequency"]
         + sorted(
             [
                 "%s,%s,%s" % (aa, codon, usage)
-                for codon, aa, usage in re.findall(
-                    _codon_regexpr, html_content
-                )
+                for codon, aa, usage in re.findall(_codon_regexpr, html_content)
             ]
         )
     )

python_codon_tables/tests/test_basics.py

@@ -3,55 +3,65 @@
 import os
 import python_codon_tables as pct
 
+
 def test_basics():
 
     # LOAD ONE TABLE BY NAME
     table = pct.get_codons_table("b_subtilis_1423")
-    assert table['T']['ACA'] == 0.4
-    assert table['*']['TAA'] == 0.61
+    assert table["T"]["ACA"] == 0.4
+    assert table["*"]["TAA"] == 0.61
 
     # LOAD ALL TABLES AT ONCE
     codon_tables = pct.get_all_available_codons_tables()
-    assert codon_tables['c_elegans_6239']['L']['CTA'] == 0.09
+    assert codon_tables["c_elegans_6239"]["L"]["CTA"] == 0.09
+
 
 def test_download_codon_table(tmpdir):
     table = pct.download_codons_table(taxid=316407)
-    assert table['*']['UAG'] == 0.07
-    target = os.path.join(str(tmpdir), 'test.csv')
+    assert table["*"]["UAG"] == 0.07
+    target = os.path.join(str(tmpdir), "test.csv")
     table = pct.download_codons_table(taxid=316407, target_file=target)
 
+
 def test_readme_example():
     table = pct.get_codons_table("b_subtilis_1423")
-    assert table['T']['ACA'] == 0.4
-    assert table['*']['TAA'] == 0.61
+    assert table["T"]["ACA"] == 0.4
+    assert table["*"]["TAA"] == 0.61
 
     # LOAD ALL TABLES AT ONCE
     codons_tables = pct.get_all_available_codons_tables()
-    assert codons_tables['c_elegans_6239']['L']['CTA'] == 0.09
+    assert codons_tables["c_elegans_6239"]["L"]["CTA"] == 0.09
 
     # GET A TABLE DIRECTLY FROM THE INTERNET
     table = pct.download_codons_table(taxid=316407)
-    assert table['*']['TGA'] == 0.29
+    assert table["*"]["TGA"] == 0.29
+
+    with pytest.raises(RuntimeError):
+        table = pct.download_codons_table(taxid=000000000)  # does not exist
+
 
 def test_readme_example():
     table = pct.get_codons_table("b_subtilis_1423")
-    assert table['T']['ACA'] == 0.4
-    assert table['*']['TAA'] == 0.61
+    assert table["T"]["ACA"] == 0.4
+    assert table["*"]["TAA"] == 0.61
 
     # LOAD ALL TABLES AT ONCE
     codons_tables = pct.get_all_available_codons_tables()
-    assert codons_tables['c_elegans_6239']['L']['CTA'] == 0.09
+    assert codons_tables["c_elegans_6239"]["L"]["CTA"] == 0.09
 
     # GET A TABLE DIRECTLY FROM THE INTERNET
     table = pct.download_codons_table(taxid=316407)
-    assert table['*']['UGA'] == 0.29
+    assert table["*"]["UGA"] == 0.29
+
 
 def test_get_codons_table():
     for table_name in (1423, "1423", "b_subtilis", "b_subtilis_1423"):
         table = pct.get_codons_table(table_name)
-        assert table['T']['ACA'] == 0.4
-        assert table['*']['TAA'] == 0.61
+        assert table["T"]["ACA"] == 0.4
+        assert table["*"]["TAA"] == 0.61
+
 
 def test_replace_U_by_T():
     table = pct.get_codons_table("b_subtilis_1423", replace_U_by_T=False)
-    assert table['*']['UAA'] == 0.61
+    assert table["*"]["UAA"] == 0.61
+

setup.py

@@ -1,35 +1,40 @@
 import os
+
 try:
     from setuptools import setup
 except ImportError:
     try:
         from .python.ez_setup import use_setuptools
+
         use_setuptools()
     except ImportError:
-        raise ImportError("python_codon_tables could not be installed, "
-                          "probably because neither setuptools nor ez_setup "
-                          "are installed on this computer. \nInstall ez_setup "
-                          "([sudo] pip install ez_setup) and try again.")
+        raise ImportError(
+            "python_codon_tables could not be installed, "
+            "probably because neither setuptools nor ez_setup "
+            "are installed on this computer. \nInstall ez_setup "
+            "([sudo] pip install ez_setup) and try again."
+        )
 
 from setuptools import setup, find_packages
 
-with open(os.path.join('codon_usage_data', 'version.txt'), 'r') as f:
+with open(os.path.join("codon_usage_data", "version.txt"), "r") as f:
     __version__ = f.read()
 
-with open(os.path.join('python_codon_tables', 'README.rst'), 'r') as f:
+with open(os.path.join("python_codon_tables", "README.rst"), "r") as f:
     long_description = f.read()
 
-setup(name='python_codon_tables',
-      version=__version__,
-      author='Zulko',
-      description='Codon Usage Tables for Python, from kazusa.or.jp',
-      url='https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables',
-      long_description=long_description,
-      license='MIT',
-      keywords="DNA codon usage",
-      packages=find_packages(exclude='docs'),
-      include_package_data=True,
-      package_data={
-          'python_codon_tables': ['../codon_usage_data/*',
-                                  '../codon_usage_data/**/*']
-      })
+setup(
+    name="python_codon_tables",
+    version=__version__,
+    author="Zulko",
+    description="Codon Usage Tables for Python, from kazusa.or.jp",
+    url="https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables",
+    long_description=long_description,
+    license="Public Domain",
+    keywords="DNA codon usage",
+    packages=find_packages(exclude="docs"),
+    include_package_data=True,
+    package_data={
+        "python_codon_tables": ["../codon_usage_data/*", "../codon_usage_data/**/*"]
+    },
+)