Merge pull request #3 from NHS-NGS/dev

v0.1.0

README.md

@@ -32,13 +32,23 @@ BRAF
 >> hgnc_queries.get_id("BRAF", verbose = False)
 HGNC:1097
 
->>hgnc_queries.get_symbol_from_id("1097", verbose = False)
+>> hgnc_queries.get_symbol_from_id("1097", verbose = False)
 BRAF
 
 # new function more for in-script use
 # get the hgnc symbol if gene symbol not recognized by the process you're using
->>print(queries.get_hgnc_symbol("RN5S49"))
+>> print(queries.get_hgnc_symbol("RN5S49"))
 RNA5SP49
->>print(queries.get_hgnc_symbol("BRAF1"))
+>> print(queries.get_hgnc_symbol("BRAF1"))
 BRAF
+
+>> hgnc_queries.get_refseq("BRCA1", False)
+['NM_007294']
+>> hgnc_queries.get_ensembl("BRCA1", False)
+"ENSG00000012048"
+
+>> hgnc_queries.convert_refseq2ensembl("NM_007294", False)
+"ENSG00000012048"
+>> hgnc_queries.convert_ensembl2refseq("ENSG00000012048", False)
+['NM_007294']
 ```

hgnc_queries/__init__.py

@@ -1,6 +1,10 @@
+from .api import get_api_response, URL
+from .conversion import (
+    convert_ensembl2refseq, convert_refseq2ensembl
+)
 from .queries import (
     get_new_symbol, get_gene_starting_with, get_alias,
     get_main_symbol, get_prev_symbol, get_id,
-    get_symbol_from_id, get_hgnc_symbol
-)
-from .api import get_api_response
+    get_symbol_from_id, get_hgnc_symbol,
+    get_ensembl, get_refseq
+)

hgnc_queries/api.py

@@ -1,6 +1,7 @@
-import requests
-import sys
 import json
+import sys
+
+import requests
 
 URL = "http://rest.genenames.org"
 

hgnc_queries/conversion.py

@@ -0,0 +1,78 @@
+from .api import get_api_response, URL
+
+
+def convert_refseq2ensembl(refseq: str, verbose: bool = True):
+    """ Convert refseq number to ensembl gene id
+
+    Args:
+        refseq (str): Refseq accession number
+        verbose (bool, optional): Print output. Defaults to True.
+
+    Returns:
+        None
+        ensembl_id (str)
+    """
+
+    refseq = refseq.strip().upper()
+
+    if not refseq.startswith("NM"):
+        print("Refseq given: {} doesn't start with \"NM\"".format(refseq))
+        return
+
+    ext = "fetch/refseq_accession/{}".format(refseq)
+    data = get_api_response("{}/{}".format(URL, ext))
+    res = data["response"]["docs"]
+
+    if not res:
+        if verbose:
+            print("Refseq \"{}\" not found".format(refseq))
+
+        return
+    else:
+        ensembl_id = res[0]["ensembl_gene_id"]
+
+        if verbose:
+            print("Refseq \"{}\" -> Ensembl \"{}\"".format(refseq, ensembl_id))
+
+        return ensembl_id
+
+
+def convert_ensembl2refseq(ensembl_id: str, verbose: bool = True):
+    """ Convert Ensembl id to refseq number
+
+    Args:
+        ensembl_id (str): Ensembl id
+        verbose (bool, optional): Prints the output. Defaults to True.
+
+    Returns:
+        None
+        refseq (str)
+    """
+
+    ensembl_id = ensembl_id.strip().upper()
+
+    if not ensembl_id.startswith("ENSG"):
+        print("Ensembl_id given: {} doesn't start with \"NM\"".format(
+            ensembl_id
+        ))
+        return
+
+    ext = "fetch/ensembl_gene_id/{}".format(ensembl_id)
+    data = get_api_response("{}/{}".format(URL, ext))
+    res = data["response"]["docs"]
+
+    if not res:
+        if verbose:
+            print("Ensembl_id \"{}\" not found".format(ensembl_id))
+
+        return
+    else:
+        refseq = res[0]["refseq_accession"]
+
+        if verbose:
+            print("Ensembl_id \"{}\" -> Refseq \"{}\"".format(
+                ensembl_id,
+                refseq
+            ))
+
+        return refseq

hgnc_queries/queries.py

@@ -1,9 +1,3 @@
-""" hgnc_queries.py
-
-Fetch data from HGNC api
-"""
-
-import argparse
 from .api import get_api_response, URL
 
 
@@ -19,7 +13,7 @@ def get_new_symbol(gene_symbol: str, verbose: bool = True):
     - None
     """
 
-    gene_symbol = gene_symbol.upper()
+    gene_symbol = gene_symbol.strip().upper()
 
     ext = "search/prev_symbol/{}".format(gene_symbol)
     data = get_api_response("{}/{}".format(URL, ext))
@@ -61,7 +55,7 @@ def get_gene_starting_with(gene_symbol: str, verbose: bool = True):
     - None
     """
 
-    gene_symbol = gene_symbol.upper()
+    gene_symbol = gene_symbol.strip().upper()
 
     ext = "search/symbol/{}*".format(gene_symbol)
     data = get_api_response("{}/{}".format(URL, ext))
@@ -97,7 +91,7 @@ def get_alias(gene_symbol: str, verbose: bool = True):
     - None
     """
 
-    gene_symbol = gene_symbol.upper()
+    gene_symbol = gene_symbol.strip().upper()
 
     ext = "fetch/symbol/{}".format(gene_symbol)
     data = get_api_response("{}/{}".format(URL, ext))
@@ -146,7 +140,7 @@ def get_main_symbol(gene_symbol: str, verbose: bool = True):
     - None
     """
 
-    gene_symbol = gene_symbol.upper()
+    gene_symbol = gene_symbol.strip().upper()
 
     ext = "search/alias_symbol/{}".format(gene_symbol)
     data = get_api_response("{}/{}".format(URL, ext))
@@ -184,7 +178,7 @@ def get_prev_symbol(gene_symbol: str, verbose: bool = True):
     - None
     """
 
-    gene_symbol = gene_symbol.upper()
+    gene_symbol = gene_symbol.strip().upper()
 
     ext = "fetch/symbol/{}".format(gene_symbol)
     data = get_api_response("{}/{}".format(URL, ext))
@@ -225,7 +219,7 @@ def get_id(gene_symbol: str, verbose: bool = True):
     - None
     """
 
-    gene_symbol = gene_symbol.upper()
+    gene_symbol = gene_symbol.strip().upper()
 
     ext = "fetch/symbol/{}".format(gene_symbol)
     data = get_api_response("{}/{}".format(URL, ext))
@@ -267,6 +261,8 @@ def get_symbol_from_id(gene_id: str, verbose: bool = True):
 
         return
 
+    gene_id = gene_id.strip()
+
     ext = "search/hgnc_id/{}".format(gene_id)
     data = get_api_response("{}/{}".format(URL, ext))
     res = data["response"]["docs"]
@@ -298,6 +294,8 @@ def get_hgnc_symbol(gene_symbol: str):
     - None
     """
 
+    gene_symbol = gene_symbol.strip()
+
     new_symbol = get_new_symbol(gene_symbol, False)
 
     if new_symbol:
@@ -311,68 +309,65 @@ def get_hgnc_symbol(gene_symbol: str):
             return
 
 
-def main():
-    pass
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description="Script to interface with the HGNC api"
-    )
-    subparsers = parser.add_subparsers(help="Commands")
-
-    new_symbol = subparsers.add_parser("new_symbol", help="Get the new symbol")
-    new_symbol.add_argument("gene_symbol", help="Gene symbol")
-    new_symbol.set_defaults(func=get_new_symbol)
-
-    alias = subparsers.add_parser(
-        "alias",
-        help="Get the aliases of given symbol"
-    )
-    alias.add_argument("gene_symbol", help="Gene symbol")
-    alias.set_defaults(func=get_alias)
-
-    main_symbol = subparsers.add_parser(
-        "main_symbol",
-        help="Get the main symbol from alias"
-    )
-    main_symbol.add_argument("gene_symbol", help="Gene symbol")
-    main_symbol.set_defaults(func=get_main_symbol)
-
-    prev_symbol = subparsers.add_parser(
-        "prev_symbol",
-        help="Get the previous symbol"
-    )
-    prev_symbol.add_argument("gene_symbol", help="Gene symbol")
-    prev_symbol.set_defaults(func=get_prev_symbol)
-
-    gene_symbol = subparsers.add_parser(
-        "gene",
-        help="Get the gene symbols starting with"
-    )
-    gene_symbol.add_argument("gene_symbol", help="Gene symbol")
-    gene_symbol.set_defaults(func=get_gene_starting_with)
-
-    gene_id = subparsers.add_parser(
-        "id",
-        help="Get the ID from a gene symbol"
-    )
-    gene_id.add_argument("gene_symbol", help="Gene symbol")
-    gene_id.set_defaults(func=get_id)
-
-    id2symbol = subparsers.add_parser(
-        "id2symbol",
-        help="Get the gene symbol from the id"
-    )
-    id2symbol.add_argument("gene_id", help="Gene ID")
-    id2symbol.set_defaults(func=get_symbol_from_id)
-
-    args = parser.parse_args()
-
-    if hasattr(args, "gene_symbol"):
-        gene_symbol = args.gene_symbol.upper()
-        args.func(gene_symbol)
-
-    elif hasattr(args, "gene_id"):
-        gene_id = args.gene_id
-        args.func(gene_id)
+def get_refseq(gene_symbol: str, verbose: bool = True):
+    """ Get refseq given a gene symbol
+
+    Args:
+        gene_symbol (str): Gene symbol
+        verbose (bool, optional): Prints the output. Defaults to True.
+
+    Returns:
+        None
+        refseq (str)
+    """
+
+    gene_symbol = gene_symbol.strip().upper()
+
+    ext = "fetch/symbol/{}".format(gene_symbol)
+    data = get_api_response("{}/{}".format(URL, ext))
+    res = data["response"]["docs"]
+
+    if not res:
+        if verbose:
+            print("Gene \"{}\" not found".format(gene_symbol))
+
+        return
+    else:
+        refseq = res[0]["refseq_accession"]
+
+        if verbose:
+            print("Refseq for \"{}\": {}".format(gene_symbol, refseq))
+
+        return refseq
+
+
+def get_ensembl(gene_symbol: str, verbose: bool = True):
+    """ Get the ensembl id for given gene symbol
+
+    Args:
+        gene_symbol (str): Gene symbol
+        verbose (bool, optional): Prints the output. Defaults to True.
+
+    Returns:
+        None
+        ensembl_id (str)
+    """
+
+    gene_symbol = gene_symbol.strip().upper()
+
+    ext = "fetch/symbol/{}".format(gene_symbol)
+    data = get_api_response("{}/{}".format(URL, ext))
+    res = data["response"]["docs"]
+
+    if not res:
+        if verbose:
+            print("Gene \"{}\" not found".format(gene_symbol))
+
+        return
+    else:
+        ensembl_id = res[0]["ensembl_gene_id"]
+
+        if verbose:
+            print("Ensembl_id for \"{}\": {}".format(gene_symbol, ensembl_id))
+
+        return ensembl_id

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="hgnc_queries",
-    version="0.0.3",
+    version="0.1.0",
     author="Yujin Kim",
     author_email="[email protected]",
     description="Make HGNC queries for gene symbols",