Merge branch 'main' into 82-migrate-to-new-biocommons-python-package-template

Author: reece

Makefile

@@ -37,7 +37,6 @@ publish: build ## publish package to PyPI
 	$(call INFO_MESSAGE, "Publishing package")
 	uv publish  # Requires UV_PUBLISH_TOKEN or Trusted Publishing setup
 
-
 ############################################################################
 #= FORMATTING, TESTING, AND CODE QUALITY
 
@@ -55,6 +54,10 @@ test: ## Test the code with pytest
 	@echo "🚀 Testing code: Running pytest"
 	uv run pytest --cov=. --cov-report=xml
 
+# to be incorporated
+# test-learn:
+#	VCR_RECORD_MODE=new_episodes pytest -x
+
 ############################################################################
 #= DOCUMENTATION
 

pyproject.toml

@@ -50,7 +50,7 @@ readme = "README.md"
 requires-python = ">=3.11"
 
 [project.urls]
-Documentation = "https://biocommons.github.io/python-package/"
+Documentation = "https://biocommons.github.io/bioutils/"
 Homepage = "https://github.com/biocommons/bioutils"
 Issues = "https://github.com/biocommons/bioutils/issues"
 Repository = "https://github.com/biocommons/bioutils"

src/bioutils/seqfetcher.py

@@ -15,9 +15,10 @@
 ncbi_tool = "bioutils"
 ncbi_email = "[email protected]"
 retry_limit = 3
+enst_default_seq_type = "cdna"
 
 
-def fetch_seq(ac, start_i=None, end_i=None):
+def fetch_seq(ac, start_i=None, end_i=None, **rest):
     """Fetches sequences and subsequences from NCBI eutils and Ensembl REST interfaces.
 
     Args:
@@ -82,13 +83,13 @@ def fetch_seq(ac, start_i=None, end_i=None):
         raise RuntimeError("No sequence fetcher for {ac}".format(ac=ac))
 
     if len(eligible_fetchers) >= 1:  # pragma: nocover (no way to test)
-        _logger.debug("Multiple sequence fetchers found for " "{ac}; using first".format(ac=ac))
+        _logger.debug("Multiple sequence fetchers found for {ac}; using first".format(ac=ac))
 
     fetcher = eligible_fetchers[0]
     _logger.debug("fetching {ac} with {f}".format(ac=ac, f=fetcher))
 
     try:
-        return fetcher(ac, start_i, end_i)
+        return fetcher(ac, start_i, end_i, **rest)
     except requests.RequestException as ex:
         raise RuntimeError("Failed to fetch {ac} ({ex})".format(ac=ac, ex=ex))
 
@@ -97,7 +98,7 @@ def fetch_seq(ac, start_i=None, end_i=None):
 # Internal functions
 
 
-def _fetch_seq_ensembl(ac, start_i=None, end_i=None):
+def _fetch_seq_ensembl(ac, start_i=None, end_i=None, seq_type=None):
     """Fetch sequence slice from Ensembl public REST interface.
 
     Args:
@@ -106,6 +107,7 @@ def _fetch_seq_ensembl(ac, start_i=None, end_i=None):
             Defaults to None.
         end_i (int, optional): The end index (interbase coordinates) of the subsequence to fetch.
             Defaults to None.
+        seq_type (str, optional): The type of Ensembl sequence to fetch
 
     Returns:
         str: The requested (sub)sequence
@@ -141,7 +143,16 @@ def _fetch_seq_ensembl(ac, start_i=None, end_i=None):
         ac, version = m.groups()
         version = int(version)
 
+    if ac.startswith("ENST") and seq_type is None:
+        try:
+            seq_type = os.environ["ENST_DEFAULT_SEQ_TYPE"]
+        except KeyError:
+            seq_type = enst_default_seq_type
+            _logger.warning(f"{ac}: Transcript type not specified or set in ENST_DEFAULT_SEQ_TYPE; assuming {seq_type}")
+
     url = f"http://rest.ensembl.org/sequence/id/{ac}"
+    if seq_type:
+        url += f"?type={seq_type}"
     r = requests.get(url, headers={"Content-Type": "application/json"})
     r.raise_for_status()
     data = r.json()
@@ -204,7 +215,7 @@ def _fetch_seq_ncbi(ac, start_i=None, end_i=None):
     """
 
     db = "protein" if ac[1] == "P" else "nucleotide"
-    url_fmt = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?" "db={db}&id={ac}&rettype=fasta"
+    url_fmt = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db={db}&id={ac}&rettype=fasta"
 
     if start_i is None or end_i is None:
         url = url_fmt.format(db=db, ac=ac)

tests/data/cassettes/test_fetch_ENST00000617537_env

@@ -96,8 +96,6 @@ interactions:
         Oct 2025 01:38:10 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -164,8 +162,6 @@ interactions:
         Oct 2025 01:38:10 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -276,8 +272,6 @@ interactions:
         Oct 2025 01:38:11 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -345,8 +339,6 @@ interactions:
         Oct 2025 01:38:12 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -414,8 +406,6 @@ interactions:
         Oct 2025 01:38:12 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -483,8 +473,6 @@ interactions:
         Oct 2025 01:38:13 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -552,8 +540,6 @@ interactions:
         Oct 2025 01:38:13 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -620,8 +606,6 @@ interactions:
         Oct 2025 01:38:14 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -688,8 +672,6 @@ interactions:
         Oct 2025 01:38:14 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -757,8 +739,6 @@ interactions:
         Oct 2025 01:38:15 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -826,8 +806,6 @@ interactions:
         Oct 2025 01:38:15 GMT
       Strict-Transport-Security:
       - max-age=31536000; includeSubDomains; preload
-      Transfer-Encoding:
-      - chunked
       X-RateLimit-Limit:
       - '3'
       X-RateLimit-Remaining:
@@ -923,4 +901,45 @@ interactions:
     status:
       code: 200
       message: OK
+- request:
+    body: null
+    headers:
+      Accept:
+      - '*/*'
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      Content-Type:
+      - application/json
+      User-Agent:
+      - python-requests/2.32.3
+    method: GET
+    uri: http://rest.ensembl.org/sequence/id/ENST00000288602?type=cdna
+  response:
+    body:
+      string: '{"query":"ENST00000288602","molecule":"dna","desc":null,"seq":"CCGCTCGGGCCCCGGCTCTCGGTTATAAGATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAACGGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGACCCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACATATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAGGCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTGGAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTTACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAATCCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTCCTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGTCTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATTCAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAAGAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAAACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGCTGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGTGTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATACCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCACCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATTCCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGAGACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGATGACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGCCCCTTTGAACCAGCTGATGCGCTGTCTTCGGAAATACCAATCCCGGACTCCCAGTCCCCTCCTACATTCTGTCCCCAGTGAAATAGTGTTTGATTTTGAGCCTGGCCCAGTGTTCAGAGGATCAACCACAGGTTTGTCTGCTACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCAGGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACACTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGACAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTGGCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAATGAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCCACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCATCTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACTGCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAATAATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTGAAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATGGCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATATGCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAACAACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAGGTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAAAGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCATTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACAGAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATATGGTGCGTTTCCTGTCCACTGAAACAAATGAGTGAGAGAGTTCAGGAGAGTAGCAACAAAAGGAAAATAAATGAACATATGTTTGCTTATATGTTAAATTGAATAAAATACTCTCTTTTTTTTTAAGGTGAAC","id":"ENST00000288602","version":11}'
+    headers:
+      Content-Length:
+      - '2662'
+      Content-Type:
+      - application/json
+      Date:
+      - Wed, 05 Mar 2025 04:21:08 GMT
+      Vary:
+      - Content-Type
+      - Origin
+      X-RateLimit-Limit:
+      - '55000'
+      X-RateLimit-Period:
+      - '3600'
+      X-RateLimit-Remaining:
+      - '54999'
+      X-RateLimit-Reset:
+      - '2332'
+      X-Runtime:
+      - '0.206213'
+    status:
+      code: 200
+      message: OK
 version: 1

tests/data/cassettes/test_fetch_ENST00000617537_noenv

@@ -4,11 +4,7 @@
 import pytest
 import vcr
 
-from bioutils.seqfetcher import (
-    _add_eutils_api_key,
-    _fetch_seq_ncbi,
-    fetch_seq,
-)
+from bioutils.seqfetcher import _add_eutils_api_key, _fetch_seq_ncbi, fetch_seq, enst_default_seq_type
 
 
 @pytest.fixture(autouse=True)
@@ -40,6 +36,40 @@ def test_fetch_seq():
     assert "MAALSGGGGGGAEPGQALFNGDMEP" == fetch_seq("ENSP00000288602", 0, 25)
 
 
+ENST00000617537_470_480 = {
+    # In [16]: s_gen[470:480], s_cdna[470:480], s_cds[470:480]
+    # Out[16]: ("TAGGTATGCA", "TAGGGTGTGT", "TGACATTTGT")
+    "genomic": "TAGGTATGCA",
+    "cdna": "TAGGGTGTGT",
+    "cds": "TGACATTTGT",
+}
+
+
+@vcr.use_cassette
+def test_fetch_ENST00000617537_noenv(caplog, monkeypatch):
+    """ensure expected lengths for ENST00000617537 with ENST_DEFAULT_SEQ_TYPE unset"""
+    monkeypatch.delenv("ENST_DEFAULT_SEQ_TYPE", raising=False)
+    ac = "ENST00000617537"
+    assert ENST00000617537_470_480[enst_default_seq_type] == fetch_seq(ac, start_i=470, end_i=480)
+    assert "Transcript type not specified or set in ENST_DEFAULT_SEQ_TYPE" in caplog.text
+    assert ENST00000617537_470_480["genomic"] == fetch_seq(ac, start_i=470, end_i=480, seq_type="genomic")
+    assert ENST00000617537_470_480["cdna"] == fetch_seq(ac, start_i=470, end_i=480, seq_type="cdna")
+    assert ENST00000617537_470_480["cds"] == fetch_seq(ac, start_i=470, end_i=480, seq_type="cds")
+
+
+@vcr.use_cassette
+def test_fetch_ENST00000617537_env(caplog, monkeypatch):
+    """ensure expected lengths for ENST00000617537 with ENST_DEFAULT_SEQ_TYPE set"""
+    user_enst_default_type = "cds"  # intentionally != enst_default_seq_type to ensure use
+    monkeypatch.setenv("ENST_DEFAULT_SEQ_TYPE", user_enst_default_type)
+    ac = "ENST00000617537"
+    assert ENST00000617537_470_480[user_enst_default_type] == fetch_seq(ac, start_i=470, end_i=480)
+    assert "Transcript type not specified or set in ENST_DEFAULT_SEQ_TYPE" not in caplog.text
+    assert ENST00000617537_470_480["genomic"] == fetch_seq(ac, start_i=470, end_i=480, seq_type="genomic")
+    assert ENST00000617537_470_480["cdna"] == fetch_seq(ac, start_i=470, end_i=480, seq_type="cdna")
+    assert ENST00000617537_470_480["cds"] == fetch_seq(ac, start_i=470, end_i=480, seq_type="cds")
+
+
 @vcr.use_cassette
 def test_fetch_seq_ncbi_invalid_positions():
     with pytest.raises(RuntimeError) as excinfo:
@@ -88,3 +118,5 @@ def test_rate_limit():
     num_requests = num_threads = 5
     p = multiprocessing.Pool(num_threads)
     p.map(_check1, range(num_requests))
+    p.close()
+    p.join()