Merge pull request #912 from cthoyt/patch-3

Add miRBase client

doc/modules/databases/index.rst

@@ -79,3 +79,7 @@ PubChem client (:py:mod:`indra.databases.pubchem_client`)
 .. automodule:: indra.databases.pubchem_client
     :members:
 
+miRBase client (:py:mod:`indra.databases.mirbase_client`)
+---------------------------------------------------------
+.. automodule:: indra.databases.mirbase_client
+    :members:

indra/databases/mirbase_client.py

@@ -0,0 +1,143 @@
+"""A client to miRBase."""
+
+import os
+
+__all__ = [
+    'get_mirbase_id_from_mirbase_name',
+    'get_mirbase_name_from_mirbase_id',
+    'get_hgnc_id_from_mirbase_id',
+    'get_mirbase_id_from_hgnc_id',
+    'get_mirbase_id_from_hgnc_symbol',
+]
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+MIRBASE_FILE = os.path.join(HERE, os.pardir, 'resources', 'mirbase.tsv')
+
+
+def get_mirbase_name_from_mirbase_id(mirbase_id):
+    """Return the miRBase name corresponding to the given miRBase ID.
+
+    Parameters
+    ----------
+    mirbase_id : str
+        The miRBase ID to be converted. Example: "MI0000060"
+
+    Returns
+    -------
+    mirbase_name : str
+        The miRBase name corresponding to the given miRBase ID.
+    """
+    return _mirbase_id_to_name.get(mirbase_id)
+
+
+def get_mirbase_id_from_mirbase_name(mirbase_name):
+    """Return the miRBase identifier corresponding to the given miRBase name.
+
+    Parameters
+    ----------
+    mirbase_name : str
+        The miRBase ID to be converted. Example: "hsa-mir-19b-2"
+
+    Returns
+    -------
+    mirbase_id : str
+        The miRBase ID corresponding to the given miRBase name.
+    """
+    return _mirbase_name_to_id.get(mirbase_name)
+
+
+def get_hgnc_id_from_mirbase_id(mirbase_id):
+    """Return the HGNC ID corresponding to the given miRBase ID.
+
+    Parameters
+    ----------
+    mirbase_id : str
+        The miRBase ID to be converted. Example: "MI0000060"
+
+    Returns
+    -------
+    hgnc_id : str
+        The HGNC ID corresponding to the given miRBase ID.
+    """
+    return _mirbase_id_to_hgnc_id.get(mirbase_id)
+
+
+def get_mirbase_id_from_hgnc_id(hgnc_id):
+    """Return the HGNC ID corresponding to the given miRBase ID.
+
+    Parameters
+    ----------
+    hgnc_id : str
+        An HGNC identifier to convert to miRBase, if it is indeed
+        an miRNA. Example: "31476"
+
+    Returns
+    -------
+    mirbase_id : str
+        The miRBase ID corresponding to the given HGNC ID.
+    """
+    return _hgnc_id_to_mirbase_id.get(hgnc_id)
+
+
+def get_mirbase_id_from_hgnc_symbol(hgnc_symbol):
+    """Return the HGNC gene symbol corresponding to the given miRBase ID.
+
+    Parameters
+    ----------
+    hgnc_symbol : str
+        An HGNC gene symbol to convert to miRBase, if it is indeed
+        an miRNA. Example: "MIR19B2"
+
+    Returns
+    -------
+    mirbase_id : str
+        The miRBase ID corresponding to the given HGNC gene symbol.
+    """
+    return _hgnc_symbol_to_mirbase_id.get(hgnc_symbol)
+
+
+def _read():
+    """Read the miRBase data into some lookup dictionaries."""
+    mirbase_id_to_name = {}
+    mirbase_name_to_id = {}
+    hgnc_id_to_mirbase_id = {}
+    mirbase_id_to_hgnc_id = {}
+    hgnc_symbol_to_mirbase_id = {}
+    mirbase_id_to_hgnc_symbol = {}
+
+    with open(MIRBASE_FILE) as file:
+        next(file)
+        for line in file:
+            try:
+                mirbase_id, mirbase_name, db, identifier, name = \
+                                                line.strip().split('\t')
+            except ValueError:  # fails on WORMBASE since no names
+                continue
+
+            mirbase_id_to_name[mirbase_id] = mirbase_name
+            mirbase_name_to_id[mirbase_name] = mirbase_id
+
+            if db == 'HGNC':
+                hgnc_id_to_mirbase_id[identifier] = mirbase_id
+                mirbase_id_to_hgnc_id[mirbase_id] = identifier
+                hgnc_symbol_to_mirbase_id[name] = mirbase_id
+                mirbase_id_to_hgnc_symbol[mirbase_id] = name
+
+    return (
+        mirbase_id_to_name,
+        mirbase_name_to_id,
+        hgnc_id_to_mirbase_id,
+        mirbase_id_to_hgnc_id,
+        hgnc_symbol_to_mirbase_id,
+        mirbase_id_to_hgnc_symbol,
+    )
+
+
+(
+    _mirbase_id_to_name,
+    _mirbase_name_to_id,
+    _hgnc_id_to_mirbase_id,
+    _mirbase_id_to_hgnc_id,
+    _hgnc_symbol_to_mirbase_id,
+    _mirbase_id_to_hgnc_symbol,
+) = _read()