rewrote faidx function to be more efficient in dicitonary access

phykit/services/alignment/faidx.py

@@ -1,3 +1,5 @@
+from typing import Dict
+
 from Bio import SeqIO
 
 from .base import Alignment
@@ -7,11 +9,13 @@ class Faidx(Alignment):
     def __init__(self, args) -> None:
         super().__init__(**self.process_args(args))
 
-    def run(self):
+    def run(self) -> None:
         record_dict = SeqIO.index(self.fasta, "fasta")
-        entry = self.entry.split(',')
-        for e in entry:
-            print(f">{record_dict[e].name}\n{record_dict[e].seq}")
 
-    def process_args(self, args):
+        # Split entries and iterate
+        for e in map(str.strip, self.entry.split(',')):
+            record = record_dict[e]
+            print(f">{record.name}\n{record.seq}")
+
+    def process_args(self, args) -> Dict[str, str]:
         return dict(fasta=args.fasta, entry=args.entry)

tests/integration/alignment/test_faidx.py

@@ -2,15 +2,14 @@
 import sys
 from mock import patch, call
 from pathlib import Path
-from textwrap import dedent
 
 from phykit.phykit import Phykit
 
 here = Path(__file__)
 
 
 @pytest.mark.integration
-class TestGCContent(object):
+class TestFaidx(object):
     @patch("builtins.print")
     def test_faidx(self, mocked_print):
         expected_result = ">1\nA-GTAT"