added gitignore, deleted some ignored files

Author: Zulko

python_codon_tables/.gitignore

@@ -0,0 +1,53 @@
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+*.tar.gz
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+__pycache__
+
+# Sublime
+.sublime-project
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Temp files
+
+*~
+
+# Pipy codes
+
+.pypirc
+
+examples/reports
+examples/features/downloaded_data
+
+.cache

python_codon_tables/README.rst

@@ -28,27 +28,6 @@ and here is the original paper to cite:
     status for the year 2000.
     Nakamura, Y., Gojobori, T. and Ikemura, T. (2000) Nucl. Acids Res. 28, 292.
 
-
-Contribute
-----------
-
-This project was started at the Edinburgh Genome Foundry by Zulko and is released on `Github <https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables>`_ under a Public Domain licence (and no warranty whatsoever, please cross-check the codon usage with other sources if you are not sure). Feel free to add other tables if you think of more commonly used species.
-
-Installation
-------------
-
-via pip:
-
-.. code:: bash
-
-    pip install python_codon_tables
-
-Manual:
-
-.. code:: bash
-
-    (sudo) python setup.py install
-
 Usage
 -----
 
@@ -62,18 +41,41 @@ Usage
     # 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['*']['TAA'])  # returns 0.61
 
     # LOAD ONE TABLE BY TAXID (it will get it from the internet if it is not
     # in the builtin tables)
     table = pct.get_codons_table(1423)
     print (table['T']['ACA'])  # returns 0.4
-    print (table['*']['UAA'])  # returns 0.61
+    print (table['*']['TAA'])  # returns 0.61
 
     # LOAD ALL BUIL-IN TABLES AT ONCE
     codons_tables = pct.get_all_available_codons_tables()
-    print (codons_tables['c_elegans_6239']['L']['CUA'])  # returns 0.09
+    print (codons_tables['c_elegans_6239']['L']['CTA'])  # returns 0.09
 
-In ``get_codons_table`` you can also provide a "shorthand" notation
+- Notice that by default the tables use nucleotide T instead of U. Using
+  ``get_codons_table('e_coli', replace_U_by_T=False)`` will leave Us as Us.
+
+- In ``get_codons_table`` you can also provide a "shorthand" notation
 ``b_subtilis``, which will be automatically extended to ``b_subtilis_1423`` as
 it appears so in the built-in table (use this feature at your own risks!)
+
+Contribute
+----------
+
+This project was started at the Edinburgh Genome Foundry by Zulko and is released on `Github <https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables>`_ under a Public Domain licence (and no warranty whatsoever, please cross-check the codon usage with other sources if you are not sure). Feel free to add other tables if you think of more commonly used species.
+
+Installation
+------------
+
+via pip:
+
+.. code:: bash
+
+    pip install python_codon_tables
+
+Manual:
+
+.. code:: bash
+
+    (sudo) python setup.py install

python_codon_tables/__pycache__/__init__.cpython-36.pyc

@@ -42,15 +42,18 @@ def table_with_U_replaced_by_T(table):
 @lru_cache(maxsize=128)
 def get_codons_table(table_name, replace_U_by_T=True):
     """Get data from one of this package's builtin codon usage tables.
-    
-    Returns a dict {"*": {'UAA': 0.64...}, 'K': {'AAA': 0.76...}, ...}
 
-    The table_name argument very flexible on purpose, it can be either an
+    The ``table_name`` argument very flexible on purpose, it can be either an
     integer representing a taxonomic ID (which will be downloaded from
     the kazusa database), or a string "12245" representing a TaxID, or a string
     "e_coli_316407" referring to a builtin table of python_codon_optimization,
     or a short form "e_coli" which will be automatically extended to
     "e_coli_316407" (at your own risks).
+
+    The ``replace_U_by_T`` argument will replace all codons names from UAA to
+    TAA etc.
+
+    Returns a dict {"*": {'TAA': 0.64...}, 'K': {'AAA': 0.76...}, ...}
     """
     if replace_U_by_T:
         table = get_codons_table(table_name, replace_U_by_T=False)
@@ -62,10 +65,10 @@ def get_codons_table(table_name, replace_U_by_T=True):
     with open(os.path.join(_tables_dir, table_name + '.csv'), 'r') as f:
         return csv_string_to_codons_dict(f.read())
 
-def get_all_available_codons_tables():
+def get_all_available_codons_tables(replace_U_by_T=True):
     """Get all data from all of this package's builtin codon usage tables."""
     return {
-        table_name: get_codons_table(table_name)
+        table_name: get_codons_table(table_name, replace_U_by_T=replace_U_by_T)
         for table_name in available_codon_tables_names
     }
 

python_codon_tables/codon_usage_tables.egg-info/PKG-INFO

@@ -8,11 +8,11 @@ def test_basics():
     # LOAD ONE TABLE BY NAME
     table = pct.get_codons_table("b_subtilis_1423")
     assert table['T']['ACA'] == 0.4
-    assert table['*']['UAA'] == 0.61
+    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']['CUA'] == 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)
@@ -23,24 +23,24 @@ def test_download_codon_table(tmpdir):
 def test_readme_example():
     table = pct.get_codons_table("b_subtilis_1423")
     assert table['T']['ACA'] == 0.4
-    assert table['*']['UAA'] == 0.61
+    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']['CUA'] == 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['*']['TGA'] == 0.29
 
 def test_readme_example():
     table = pct.get_codons_table("b_subtilis_1423")
     assert table['T']['ACA'] == 0.4
-    assert table['*']['UAA'] == 0.61
+    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']['CUA'] == 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)
@@ -50,4 +50,8 @@ 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['*']['UAA'] == 0.61
+        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