Add old symbols and implement client

indra/databases/rgd_client.py

@@ -0,0 +1,142 @@
+"""A client for accessing RGD rat gene data."""
+
+from collections import defaultdict
+from typing import List, Union
+
+from indra.util import read_unicode_csv
+from indra.resources import get_resource_path
+
+
+def get_id_from_name(name: str) -> Union[str, None]:
+    """Return an RGD ID from an RGD gene symbol.
+
+    Parameters
+    ----------
+    name :
+        The RGD gene symbol whose ID will be returned.
+
+    Returns
+    -------
+    :
+        The RGD ID (without prefix) or None if not available.
+    """
+    return rgd_name_to_id.get(name)
+
+
+def get_name_from_id(rgd_id: str) -> Union[str, None]:
+    """Return the RGD gene symbol for a given RGD ID.
+
+    Parameters
+    ----------
+    rgd_id :
+        The RGD ID (without prefix) whose symbol will be returned.
+
+    Returns
+    -------
+    :
+        The RGD symbol for the given ID or None if not available.
+    """
+    if rgd_id and rgd_id.startswith('RGD:'):
+        rgd_id = rgd_id[4:]
+    return rgd_id_to_name.get(rgd_id)
+
+
+def get_synonyms(rgd_id: str) -> List[str]:
+    """Return the synonyms for an RGD ID.
+
+    Parameters
+    ----------
+    rgd_id :
+        An RGD ID, without prefix.
+
+    Returns
+    -------
+    :
+        The list of synonyms corresponding to the RGD ID, or an empty list
+        if not available.
+    """
+    if rgd_id and rgd_id.startswith('RGD:'):
+        rgd_id = rgd_id[4:]
+    return rgd_synonyms.get(rgd_id, [])
+
+
+def get_id_from_name_synonym(name_synonym: str) -> Union[None, str, List[str]]:
+    """Return an RGD ID from an RGD gene symbol or synonym.
+
+    If the given name or synonym is the official symbol of a gene, its
+    ID is returned. If the input is a synonym, it can correspond to
+    one or more genes. If there is a single gene whose synonym matches
+    the input, the ID is returned as a string. If multiple genes share
+    the given synonym, their IDs are returned in a list. If the input
+    doesn't match any names or synonyms, None is returned.
+
+    Parameters
+    ----------
+    name_synonym :
+        The RGD gene symbol or synonym whose ID will be returned.
+
+    Returns
+    -------
+    :
+        The RGD ID (without prefix) of a single gene, a list of RGD IDs,
+        or None.
+    """
+    rgd_id = rgd_name_to_id.get(name_synonym)
+    if rgd_id:
+        return rgd_id
+    rgd_ids = rgd_synonyms_reverse.get(name_synonym)
+    if rgd_ids:
+        if len(rgd_ids) == 1:
+            return rgd_ids[0]
+        else:
+            return rgd_ids
+    return None
+
+
+def get_ensembl_id(rgd_id: str) -> Union[str, None]:
+    """Return the Ensembl ID for an RGD ID.
+
+    Parameters
+    ----------
+    rgd_id :
+        An RGD ID, without prefix.
+
+    Returns
+    -------
+    :
+        A list of Ensembl IDs corresponding to the RGD ID,
+        or None if not available.
+    """
+    return rgd_id_to_ensembl.get(rgd_id)
+
+
+def _read_rgd():
+    fname = get_resource_path('rgd_entries.tsv')
+    rgd_id_to_name = {}
+    rgd_name_to_id = {}
+    rgd_synonyms = {}
+    rgd_synonyms_reverse = defaultdict(list)
+    rgd_id_to_ensembl = {}
+    ensemble_id_to_rgd = {}
+    for rgd_id, name, synonyms_str, ensembl_id in \
+            read_unicode_csv(fname, '\t'):
+        if name:
+            rgd_id_to_name[rgd_id] = name
+            rgd_name_to_id[name] = rgd_id
+        if synonyms_str:
+            synonyms = synonyms_str.split(';')
+            rgd_synonyms[rgd_id] = synonyms
+            for synonym in synonyms:
+                rgd_synonyms_reverse[synonym].append(rgd_id)
+        if ensembl_id:
+            ensemble_ids = ensembl_id.split(';')
+            rgd_id_to_ensembl[rgd_id] = ensemble_ids
+            for ensemble_id in ensemble_ids:
+                ensemble_id_to_rgd[ensemble_id] = rgd_id
+
+    return rgd_id_to_name, rgd_name_to_id, rgd_synonyms, \
+        dict(rgd_synonyms_reverse), rgd_id_to_ensembl, ensemble_id_to_rgd
+
+
+rgd_id_to_name, rgd_name_to_id, rgd_synonyms, rgd_synonyms_reverse, \
+   rgd_id_to_ensembl, ensemble_id_to_rgd = _read_rgd()

indra/resources/update_resources.py

@@ -985,6 +985,20 @@ def update_ec_code():
     PyOboClient.update_by_prefix("ec-code", indra_prefix='eccode')
 
 
+def update_rgd():
+    url = "https://download.rgd.mcw.edu/data_release/GENES_RAT.txt"
+    df = pandas.read_csv(url, sep='\t', comment='#', dtype=str)
+    df = df[['GENE_RGD_ID', 'SYMBOL', 'OLD_SYMBOL', 'ENSEMBL_ID']]
+    df.rename(columns={'GENE_RGD_ID': 'ID',
+                       'SYMBOL': 'symbol',
+                       'OLD_SYMBOL': 'synonyms',
+                       'ENSEMBL_ID': 'ensembl'},
+              inplace=True)
+    df['ID'] = df['ID'].astype(str)
+    fname = os.path.join(path, 'rgd_entries.tsv')
+    df.to_csv(fname, index=None, sep='\t')
+
+
 def update_mgi():
     # This provides basic ID and naming resources
     url = "http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt"