1.0.7.0

- Now GenMine parses clone information
Changwanseo · Nov 18, 2022 · 95830f5 · 95830f5
1 parent 055ccfc
commit 95830f5
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Showing 4 changed files with 89 additions and 9 deletions.
diff --git a/GenMine/GenMine.py b/GenMine/GenMine.py
@@ -281,7 +281,9 @@ def filter_acc(acc_list, email) -> list:
     if len(return_acc_list) > 0:
         handle = Entrez.esearch(
             db="Nucleotide",
-            term=" OR ".join([f"{acc}[Nucleotide Accession]" for acc in return_acc_list]),
+            term=" OR ".join(
+                [f"{acc}[Nucleotide Accession]" for acc in return_acc_list]
+            ),
             retmax=len(return_acc_list),
             idtype="acc",
         )
@@ -619,7 +621,7 @@ def Get_note(record):
 
         return format_list(input_list=obj_list, filter_list=[], add=" = ", default="")
 
-    # Get note from given record json
+    # Get isolate from given record json
     def Get_isolate(record):
 
         obj_list = retrieve_parallel(
@@ -631,6 +633,18 @@ def Get_isolate(record):
 
         return format_list(input_list=obj_list, filter_list=[], add=" = ", default="")
 
+    # Get clone from given record json
+    def Get_clone(record):
+
+        obj_list = retrieve_parallel(
+            input_dict=record,
+            label="GBQualifier_name",
+            label_value="clone",
+            obj="GBQualifier_value",
+        )
+
+        return format_list(input_list=obj_list, filter_list=[], add=" = ", default="")
+
     def Get_author(record):
 
         author_list = []
@@ -763,6 +777,7 @@ def Get_author(record):
     # Transform to output format
     for record in json_data:
 
+        """
         dict_temp = {
             "acc": "",
             "length": "",
@@ -780,6 +795,8 @@ def Get_author(record):
             "upload_date": "",
             "seq": "",
         }
+        """
+        dict_temp = {}
 
         if (
             "GBSeq_sequence" in record or "GBSeq_feature-table" in record
@@ -799,6 +816,7 @@ def Get_author(record):
             dict_temp["culture_collection"] = Get_culture_collection(record)
             dict_temp["note"] = Get_note(record)
             dict_temp["isolate"] = Get_isolate(record)
+            dict_temp["clone"] = Get_clone(record)
 
             dict_temp["primer"] = classification(record["GBSeq_definition"])
             json_temp.append(dict_temp)
@@ -1107,6 +1125,7 @@ def classifier(json_in, out):
 
     return new_keys
 
+
 # get list of acc in transformed json
 def get_acc(json_file):
 

diff --git a/build_manual.md b/build_manual.md
@@ -1,8 +1,10 @@
 # test build
+```
+pip uninstall GenMine
+python setup.py clean --all
 python setup.py install
-
+```
 # pypi build
-
 In new conda environment
 ```
 conda install pip
@@ -12,11 +14,10 @@ python setup.py sdist
 twine upload dist/GenMine-{YOUR_VERSION}* 	// use current build number
 ```
 # conda build
-
 In new conda environment
 ```
 conda install -c conda-forge grayskull
-conda install -c packaging
+conda install -c conda-forge packaging
 conda install conda-build
 conda install conda-verify
 conda install anaconda-client

diff --git a/conda/GenMine/meta.yaml b/conda/GenMine/meta.yaml
@@ -0,0 +1,51 @@
+{% set name = "GenMine" %}
+{% set version = "1.0.7.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/GenMine-{{ version }}.tar.gz
+  sha256: ae4c5a04bd3465bcc1ab4a98d9f725bf391f6e3dad5f2dec4d9390f7eadc74f3
+
+build:
+  entry_points:
+    - GenMine = GenMine.main:main
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv
+  number: 0
+
+requirements:
+  host:
+    - python >=3.8
+    - pip
+  run:
+    - python >=3.8
+    - biopython
+    - pandas
+    - openpyxl
+    - xlrd
+    - numpy
+    - xmltodict
+    - pytz
+    - python-dateutil
+
+test:
+  imports:
+    - GenMine
+  commands:
+    - pip check
+    - GenMine --help
+  requires:
+    - pip
+
+about:
+  home: https://github.com/Changwanseo/GenMine
+  summary: GenBank data miner for fungal taxonomists
+  license: GPL-3.0
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - Changwanseo
diff --git a/setup.py b/setup.py
@@ -1,16 +1,25 @@
-# hey-insutance/setup.py
+# GenMine/setup.py
 from setuptools import setup, find_packages
 
 setup(
     name="GenMine",
-    version="1.0.6.3",
+    version="1.0.7.0",
     description="GenBank data miner for fungal taxonomists",
     author="Changwan Seo",
     author_email="wan101010@snu.ac.kr",
     url="https://github.com/Changwanseo/GenMine",
     python_requires=">= 3.8",
     packages=find_packages(include=["GenMine"]),
-    install_requires=["biopython", "pandas", "openpyxl", "xlrd", "numpy", "xmltodict", "pytz", "python-dateutil"],
+    install_requires=[
+        "biopython",
+        "pandas",
+        "openpyxl",
+        "xlrd",
+        "numpy",
+        "xmltodict",
+        "pytz",
+        "python-dateutil",
+    ],
     zip_safe=False,
     # important part
     entry_points={"console_scripts": ["GenMine = GenMine.main:main"]},