Add Msigdb API, now mouse symbol/entrze could be download easy #204

gseapy/msigdb.py

@@ -0,0 +1,76 @@
+import re
+
+import pandas as pd
+import requests
+
+class Msigdb:
+    def __init__(self, dbver : str ="2023.1.Hs"):
+        """
+        dbver: MSIGDB version number. default: 2023.1.Hs
+        """
+        self.url = "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/"
+        self._db_version = self._get_db_version()
+        self.categoires = self.list_category(dbver)
+        self._pattern = re.compile("(\w.+)\.(v\d.+)\.(entrez|symbols)\.gmt")
+
+
+    def _get_db_version(self):
+        resp = requests.get(self.url)
+        if resp.ok:
+            d = pd.read_html(resp.text)[0]
+            # remove item : parent dictory and NA columns
+            d = d.dropna(how="all").iloc[1:, 1:3].reset_index(drop=True)
+            d.iloc[:, 0] = d.iloc[:, 0].str.rstrip("/")
+            return d
+        return None
+
+    def get_gmt(
+        self, 
+        category: str = "h.all", 
+        dbver: str = "7.5.1", 
+        entrez: bool = False
+    ):
+        """
+        example: "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.1.Hs/c2.cp.kegg.v2023.1.Hs.entrez.gmt"
+        """
+        identifier = "symbols"
+        if entrez:
+            identifier = "entrez"
+        url = f"{self.url}/{dbver}/{category}.v{dbver}.{identifier}.gmt"
+        resp = requests.get(url)
+        if resp.ok:
+            d = {}
+            for line in resp.text.strip().split("\n"):
+                row = line.split("\t")
+                d[row[0]] = row[2:]
+            return d
+        return None
+
+    def list_dbver(self):
+        # self._db_version.columns = ["dbver", "date"]
+        return self._db_version
+
+    def list_category(self, dbver):
+        """
+        dbver: MSIGDB version number. default: 2023.1.Hs
+        """
+        d = self.list_gmt(dbver)
+        if d is not None:
+            categories = (
+                d.iloc[:, 0]
+                .apply(lambda s: self._pattern.match(s).groups()[0])
+                .drop_duplicates()
+            )
+            return categories.to_list()
+        return None
+
+    def list_gmt(self, db):
+        url = self.url + db
+        resp = requests.get(url)
+        if resp.ok:
+            d = pd.read_html(resp.text)[0]
+            # remove item : parent dictory and NA columns
+            d = d.dropna(how="all").iloc[1:, 1:4]
+            d = d[d.iloc[:, 0].str.match(self._pattern)]
+            return d.reset_index(drop=True)
+        return None