Update sql conversion to text

Author: RJMW

beams/auxiliary.py

@@ -2,6 +2,9 @@
 # -*- coding: utf-8 -*-
 
 from collections import OrderedDict
+import gzip
+import sqlite3
+import pandas as pd
 from pyteomics import mass as pyteomics_mass
 from beams.db_parsers import parse_nist_database
 
@@ -141,16 +144,20 @@ def add_record(r, nm):
     return OrderedDict((k, lib[k]) for k in es)
 
 
-def convert_sql_to_text(path_sql, table_name, path_out, sep):
-    
-    with open(path_sql, "rb") as db_dump:
-        conn = sqlite3.connect(":memory:")
-        cursor = conn.cursor()
-        cursor.executescript(db_dump.read().decode('utf-8'))
-        conn.commit()
-        
-        df = pd.read_sql_query("select * from " + table_name, conn)
-        df.to_csv(path_out, sep="\t")
-        
-        conn.close()
-    return
+def convert_sql_to_text(path_sql, table_name, path_out, separator="\t"):
+
+    if path_sql.endswith(".gz"):
+        db_dump = gzip.GzipFile(path_sql, mode='rb')
+    else:
+        db_dump = open(path_sql, mode='rb')
+
+    conn = sqlite3.connect(":memory:")
+    cursor = conn.cursor()
+    cursor.executescript(db_dump.read().decode('utf-8'))
+    conn.commit()
+
+    df = pd.read_sql_query("select * from " + table_name, conn)
+    df.to_csv(path_out, sep=separator)
+
+    conn.close()
+    db_dump.close()