Retrieve only the experimentally characterized cazy (#43)

* upgrade poetry * simplify cli * add missing characterized option * update tests * update version
rvhonorato · Oct 12, 2023 · f267586 · f267586
1 parent cf3657e
commit f267586
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Showing 6 changed files with 85 additions and 127 deletions.
diff --git a/.trunk/trunk.yaml b/.trunk/trunk.yaml
@@ -1,23 +1,23 @@
 version: 0.1
 cli:
-  version: 1.6.1
+  version: 1.16.2
 plugins:
   sources:
     - id: trunk
-      ref: v0.0.13
+      ref: v1.2.1
       uri: https://github.com/trunk-io/plugins
 lint:
   enabled:
-    - actionlint@1.6.23
-    - black@23.1.0
+    - actionlint@1.6.26
+    - black@23.9.1
     - git-diff-check
-    - gitleaks@8.16.1
+    - gitleaks@8.18.0
     - isort@5.12.0
-    - markdownlint@0.33.0
-    - prettier@2.8.4
-    - ruff@0.0.256
-    - taplo@0.7.0
-    - yamllint@1.29.0
+    - markdownlint@0.37.0
+    - prettier@3.0.3
+    - ruff@0.0.292
+    - taplo@0.8.1
+    - yamllint@1.32.0
   ignore:
     - linters: [ALL]
       paths:

diff --git a/cazy_parser/cli.py b/cazy_parser/cli.py
@@ -16,75 +16,52 @@
 log.addHandler(ch)
 log.setLevel("DEBUG")
 
-# ===========================================================================================================
-# Define arguments
-ap = argparse.ArgumentParser()
 
-ap.add_argument(
-    "enzyme_class",
-    choices=["GH", "GT", "PL", "CA", "AA"],
-)
-
-ap.add_argument("-f", "--family", type=int)
-
-ap.add_argument("-s", "--subfamily")
-
-ap.add_argument("-c", "--characterized")
-
-ap.add_argument(
-    "-v",
-    "--version",
-    help="show version",
-    action="version",
-    version=f"Running {ap.prog} v{VERSION}",
-)
-
-
-def load_args(ap):
-    """
-    Load argument parser.
-
-    Parameters
-    ----------
-    ap : argparse.ArgumentParser
-        Argument parser.
+# ====================================================================================#
+# Main code
+def main():
+    """Main function."""
 
-    Returns
-    -------
-    cmd : argparse.Namespace
-        Parsed command-line arguments.
+    ap = argparse.ArgumentParser()
 
-    """
-    return ap.parse_args()
+    ap.add_argument(
+        "enzyme_class",
+        choices=["GH", "GT", "PL", "CA", "AA"],
+    )
 
+    ap.add_argument("-f", "--family", type=int, default=None)
 
-# ====================================================================================#
-# Define CLI
-def cli(ap, main):
-    """
-    Command-line interface entry point.
+    ap.add_argument("-s", "--subfamily", type=int, default=None)
 
-    Parameters
-    ----------
-    ap : argparse.ArgumentParser
-        Argument parser.
-    main : function
-        Main function.
+    ap.add_argument("-c", "--characterized", action="store_true", default=False)
 
-    """
-    cmd = load_args(ap)
-    main(**vars(cmd))
+    ap.add_argument(
+        "-v",
+        "--version",
+        help="show version",
+        action="version",
+        version=f"Running {ap.prog} v{VERSION}",
+    )
 
+    args = ap.parse_args()
 
-def maincli():
-    """Execute main client."""
-    cli(ap, main)
+    if args.enzyme_class not in ENZYME_LIST:
+        logging.error(f"Enzyme class {args.enzyme_class} not supported")
+        sys.exit()
+    else:
+        enzyme_name = ENZYME_LIST[args.enzyme_class]
 
+    id_list = retrieve_genbank_ids(
+        enzyme_name, args.family, args.subfamily, args.characterized
+    )
 
-# ====================================================================================#
-# Main code
-def main(enzyme_class, family, subfamily, characterized):
-    """Main function."""
+    output_fname = f"{args.enzyme_class}"
+    if args.family:
+        output_fname += f"{args.family}"
+    if args.subfamily:
+        output_fname += f"_{args.subfamily}"
+    if args.characterized:
+        output_fname += "_characterized"
 
     log.info("-" * 42)
     log.info("")
@@ -94,20 +71,6 @@ def main(enzyme_class, family, subfamily, characterized):
     log.info("")
     log.info("-" * 42)
 
-    if enzyme_class not in ENZYME_LIST:
-        logging.error(f"Enzyme class {enzyme_class} not supported")
-        sys.exit()
-    else:
-        enzyme_name = ENZYME_LIST[enzyme_class]
-
-    id_list = retrieve_genbank_ids(enzyme_name, family, subfamily, characterized)
-
-    output_fname = f"{enzyme_class}"
-    if family:
-        output_fname += f"{family}"
-    if subfamily:
-        output_fname += f"_{subfamily}"
-
     today = time.strftime("%d%m%Y")
     output_fname += f"_{today}.fasta"
     try:
@@ -128,4 +91,4 @@ def main(enzyme_class, family, subfamily, characterized):
 
 
 if __name__ == "__main__":
-    sys.exit(maincli())
+    sys.exit(main())
diff --git a/cazy_parser/modules/html.py b/cazy_parser/modules/html.py
@@ -5,6 +5,8 @@
 import string
 import sys
 import urllib
+import urllib.request
+from typing import Optional
 
 import requests
 from bs4 import BeautifulSoup
@@ -176,21 +178,13 @@ def get_data_from_txt(link):
     return data_list
 
 
-def fetch_links(enzyme_class, family, subfamily):
-    """
-    Fetch link structure for an enzyme class.
-
-    Parameters
-    ----------
-    enzyme_class : str
-        Enzyme class to fetch links for.
-
-    Returns
-    -------
-    page_list : list
-        List of links to the pages.
-
-    """
+def fetch_links(
+    enzyme_class: str,
+    family: Optional[int] = None,
+    subfamily: Optional[int] = None,
+    characterized: Optional[bool] = None,
+) -> list[str]:
+    """Fetch link structure for an enzyme class."""
 
     main_class_link = f"http://www.cazy.org/{enzyme_class}.html"
     log.info(f"Fetching links for {enzyme_class}, url: {main_class_link}")
@@ -205,6 +199,9 @@ def fetch_links(enzyme_class, family, subfamily):
             log.info(f"Only using links of family {family}")
             family_list = [e for e in family_list if int(e[2:]) == family]
 
+    if characterized:
+        log.info("Only using characterized links")
+
     if not family_list:
         log.error("No links were found.")
         sys.exit()
@@ -259,6 +256,9 @@ def fetch_links(enzyme_class, family, subfamily):
             else:
                 page_list.append(page_zero)
 
+    if characterized:
+        page_list = [e for e in page_list if "characterized" in e]
+
     return page_list
 
 
@@ -341,28 +341,11 @@ def fetch_species():
     return species_dic
 
 
-def retrieve_genbank_ids(enzyme_name, family=None, subfamily=None, characterized=None):
-    """
-    Retrieve genbank IDs for a given enzyme.
-
-    Parameters
-    ----------
-    enzyme_name : str
-        Enzyme name to retrieve genbank IDs for.
-    family : int
-        Family number to retrieve genbank IDs for.
-    subfamily : int
-        Subfamily number to retrieve genbank IDs for.
-    characterized : bool
-        Whether to retrieve genbank IDs for characterized enzymes.
-
-    Returns
-    -------
-    genbank_id_list : list
-        List of genbank IDs.
-
-    """
-    page_list = fetch_links(enzyme_name, family, subfamily)
+def retrieve_genbank_ids(
+    enzyme_name: str, family: int, subfamily: int, characterized: bool
+) -> list[str]:
+    """Retrieve genbank IDs for a given enzyme."""
+    page_list = fetch_links(enzyme_name, family, subfamily, characterized)
     data = fetch_data(page_list)
     genbank_id_list = []
     for element in data:

diff --git a/cazy_parser/version.py b/cazy_parser/version.py
@@ -1 +1 @@
-VERSION = "2.0.2"
+VERSION = "2.0.3"
diff --git a/pyproject.toml b/pyproject.toml
@@ -3,9 +3,9 @@ pythonpath = ["src"]
 
 [tool.poetry]
 name = "cazy-parser"
-version = "2.0.2"
+version = "2.0.3"
 description = "A way to extract specific information from CAZy"
-authors = ["Rodrigo V. Honorato <r.vargashonorato@uu.nl>"]
+authors = ["Rodrigo V. Honorato <rvhonorato@protonmail.com>"]
 readme = "README.md"
 packages = [{ include = "cazy_parser" }]
 classifiers = [
@@ -34,7 +34,7 @@ coverage = "^7.2.5"
 hypothesis = "^6.75.1"
 
 [tool.poetry.scripts]
-cazy-parser = 'cazy_parser.cli:maincli'
+cazy-parser = 'cazy_parser.cli:main'
 
 [build-system]
 requires = ["poetry-core"]

diff --git a/tests/test_html.py b/tests/test_html.py
@@ -1,4 +1,4 @@
-import urllib
+import urllib.request
 
 import pytest
 from bs4 import BeautifulSoup
@@ -78,7 +78,12 @@ def test_get_data_from_txt():
 
 
 def test_fetch_links():
-    observed_links = fetch_links("Carbohydrate-Esterases", family=None, subfamily=None)
+    observed_links = fetch_links("Carbohydrate-Esterases", characterized=True)
+
+    assert "http://www.cazy.org/CE20_characterized.html" in observed_links
+    assert "http://www.cazy.org/IMG/cazy_data/CE20.txt" not in observed_links
+
+    observed_links = fetch_links("Carbohydrate-Esterases", characterized=False)
 
     assert "http://www.cazy.org/CE20_characterized.html" in observed_links
     assert "http://www.cazy.org/IMG/cazy_data/CE20.txt" in observed_links
@@ -99,8 +104,15 @@ def test_fetch_species():
 
 def test_retrieve_genbank_ids():
     observed_id_list = retrieve_genbank_ids(
-        enzyme_name="Glycoside-Hydrolases", family=5, subfamily=1
+        enzyme_name="Glycoside-Hydrolases", family=5, subfamily=1, characterized=False
     )
 
     assert observed_id_list
     assert len(observed_id_list) >= 1223
+
+    observed_id_list = retrieve_genbank_ids(
+        enzyme_name="Glycoside-Hydrolases", family=5, subfamily=1, characterized=True
+    )
+
+    assert observed_id_list
+    assert 36 <= len(observed_id_list) <= 1000