Fix document of package PyRice

SouthGreenPlatform · Oct 22, 2019 · be09bb6 · be09bb6
1 parent 0f22a9b
commit be09bb6
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Showing 6 changed files with 148 additions and 94 deletions.
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
diff --git a/docs/source/pyrice_module.rst b/docs/source/pyrice_module.rst
@@ -1,15 +1,15 @@
 Pyrice module
 =============
 
-pyrice.build_dictionary module
+pyrice.build\_dictionary module
 -------------------------------
 
 .. automodule:: pyrice.build_dictionary
     :members:
     :undoc-members:
     :show-inheritance:
 
-pyrice.multi_query module
+pyrice.multi\_query module
 --------------------------
 
 .. automodule:: pyrice.multi_query

diff --git a/pyrice/__pycache__/multi_query.cpython-36.pyc b/pyrice/__pycache__/multi_query.cpython-36.pyc
diff --git a/pyrice/database_description.xml b/pyrice/database_description.xml
@@ -90,7 +90,7 @@
         <prettify replaceBy='\s'>\n>LOC_.*\n|\n|\r|\t</prettify>
     </database>
 
-    <database dbname="arabidpsis" type="text/html" method="GET">
+    <database dbname="arabidopsis" type="text/html" method="GET">
         <link stern="https://www.arabidopsis.org/servlets/TairObject?" aft="&amp;type=locus"/>
         <headers>
             <header type="">Representative Gene Model</header>

diff --git a/pyrice/main.py b/pyrice/main.py
@@ -18,14 +18,14 @@
 args = parser.parse_args()
 
 if __name__ == "__main__":
-    # # Search gene and query loc
+    # Search gene and query loc
     query = MultiQuery()
     result = query.search_on_chromosome(chro="chr01", start_pos="1",
                                end_pos="20000", number_process = 4, dbs="all", save_path="./result/")
     print("Output database:", result)
 
 
-    # # Query with chromosome
+    # Query with chromosome
     query = MultiQuery()
     result = query.query_by_chromosome(chro="chr01", start_pos="1",
                          end_pos="20000", number_process = 4, multi_processing=True, multi_threading=True,
@@ -43,13 +43,19 @@
     # query.save(result,save_path = "./result/",format=["csv","html","json","pkl"],hyper_link=False)
     # print("Output database:",result)
 
-    # # Query with new database
+    # Query with new database
     # query = MultiQuery()
     # result = query.query_new_database(atts=['TRAES3BF001000010CFD'], number_process= 4,
     #                     multi_processing=True,multi_threading=True,dbs=['urgi'])
     # query.save(result, save_path="./result/", format=["csv", "html", "json", "pkl"], hyper_link=False)
     # print("Output database:",result)
 
+    # query = MultiQuery()
+    # result = query.query_new_database(atts=['AT2G03340'], number_process=4,
+    #                                   multi_processing=False, multi_threading=False, dbs=['arabidopsis'])
+    # query.save(result, save_path="./result/", format=["csv", "html", "json", "pkl"], hyper_link=False)
+    # print("Output database:", result)
+
 
 # chro="chr01", start_pos="1", end_pos="43270923"
 # chro="chr02", start_pos="1", end_pos="35937250"

diff --git a/pyrice/multi_query.py b/pyrice/multi_query.py
@@ -12,7 +12,6 @@
 import os
 import copy
 import json2table
-from IPython.display import HTML
 
 class MultiQuery():
     """
@@ -254,7 +253,8 @@ def save(result, save_path, format=None, hyper_link=False):
                 elif form == "html":
                     my_db = data_folder + "db" + '.html'
                     df = pd.DataFrame.from_dict(html_dict, orient='index')
-                    HTML(df.to_html(my_db,escape=False))
+                    # HTML(df.to_html(my_db,escape=False))
+                    df.to_html(my_db, escape=False)
                 elif form =="json":
                     my_db = data_folder + "db" + '.json'
                     with open(my_db, 'w') as f:
@@ -781,7 +781,7 @@ def query_new_database(self, atts, number_process = cpu_count() -1, multi_proces
                 print("Query attribute: {} --- attribute {}/{}".format(key, i, number_query))
                 self.result.setdefault(key,dict())
                 for db in name_db:
-                    tmp = self.query(key, db, [key])
+                    tmp = self.query(key, db, [key],True)
                     if tmp != None:
                         self.result[tmp[0]].setdefault(tmp[1], tmp[2])
                 i+=1