Update 2022.11.29 little change

1. add utility.get_result_from_file()
2. fixed some bugs

patpat/querier.py

@@ -376,7 +376,7 @@ def get_properties(self):
 
         return self.digestion_params, self.source, self.filtered_peptides
 
-    def query(self):
+    def query(self, threshold=1):
         """Functions for external calls. 供外部调用的函数。
 
         Raises:
@@ -386,7 +386,7 @@ def query(self):
             raise ValueError('Please run func self.set_params() first. 请先运行self.set_params()函数')
 
         self.digestion()
-        self.search()
+        self.search(threshold=1)
 
 
 class UniProtPeptideQuerier(PeptideQuerier):

patpat/utility.py

@@ -4,6 +4,7 @@
 import os
 import re
 import time
+import json
 import gzip
 from urllib import parse
 from ftplib import FTP
@@ -162,7 +163,7 @@ def pagination_download_uniprot_proteome(identifier: str, reviewed: bool = True,
     total = int(response.headers['x-total-results'])
     fasta = [response.text]
 
-    for i in tqdm.tqdm(range(size, total, size)):
+    for _ in tqdm.tqdm(range(size, total, size)):
         try:
             response = session.get(response.links['next']['url'])
             fasta.extend([response.text])
@@ -266,3 +267,24 @@ def inner():
         return _instance[cls]
 
     return inner
+
+
+def get_result_from_file(task=None):
+    """Get Patpat search result from patpat_env/result/<task>/result.json
+
+    Args:
+        task: uuid
+
+    Returns:
+        dict, project metadata
+    """
+    if task:
+        with open(f'patpat_env/result/{task}/result.json') as f:
+            data_json = ''.join(f.readlines())
+            data_dict = json.loads(data_json)
+        f.close()
+
+        return data_dict
+
+    else:
+        print('Need to input task uuid.')