biocommons · reece · Dec 7, 2025 · Dec 7, 2025 · Dec 7, 2025
@@ -0,0 +1,138 @@
+#!/usr/bin/env python3
+"""
+Fetch and display key information from a RefSeq accession using Biopython.
+Usage:
+    python refseq_info.py NM_152783.5
+    efetch -db nucleotide -id NM_152783.5 -format gb | ./archive/eutils-fetch-biopython
+
+» efetch -db nucleotide -id NM_152783.5 -format gb | ./archive/eutils-fetch-biopython
+Reading XML from stdin...
+
+# Example usage:
+» efetch -db nucleotide -id NM_152783.5 -format gb | ./archive/eutils-fetch-biopython
+============================================================
+Accession.Version: NM_152783.5
+Length: 2566 bp
+Molecule Type: mRNA
+Species: Homo sapiens
+Locus: NM_152783
+Gene Name(s): D2HGDH
+
+----------------------CDS Information:----------------------
+CDS Start: 159
+CDS End: 1724
+
+------------------------Exon Table:-------------------------
+Exon       Start      End
+------------------------------
+Exon 1    1          66
+Exon 2    67         450
+Exon 3    451        508
+Exon 4    509        648
+Exon 5    649        842
+Exon 6    843        1011
+Exon 7    1012       1155
+Exon 8    1156       1298
+Exon 9    1299       1464
+Exon 10   1465       2566
+============================================================
+
+"""
+
+import sys
+
+from Bio import Entrez, SeqIO
+
+# Always provide your email to NCBI
+Entrez.email = "[email protected]"
+
+
+def get_refseq_info(accession):
+    """Fetch and parse RefSeq record information from NCBI."""
+
+    # Fetch the record from NCBI
+    print(f"Fetching {accession} from NCBI...")
+    handle = Entrez.efetch(db="nucleotide", id=accession, rettype="gb", retmode="text")
+    record = SeqIO.read(handle, "genbank")
+    handle.close()
+
+    return record
+
+
+def display_record_info(record):
+    """Display information from a SeqRecord."""
+
+    # Extract basic information
+    print(f"\n{'=' * 60}")
+    print(f"Accession.Version: {record.id}")
+    print(f"Length: {len(record.seq)} bp")
+    print(f"Molecule Type: {record.annotations.get('molecule_type', 'N/A')}")
+    print(f"Species: {record.annotations.get('organism', 'N/A')}")
+    print(f"Locus: {record.name}")
+
+    # Extract gene names
+    gene_names = set()
+    for feature in record.features:
+        if feature.type == "gene" and "gene" in feature.qualifiers:
+            gene_names.update(feature.qualifiers["gene"])
+
+    if gene_names:
+        print(f"Gene Name(s): {', '.join(sorted(gene_names))}")
+    else:
+        print("Gene Name(s): N/A")
+
+    # Find CDS coordinates
+    print(f"\n{'CDS Information:':-^60}")
+    cds_found = False
+    for feature in record.features:
+        if feature.type == "CDS":
+            cds_found = True
+            # Handle compound locations (spliced CDS)
+            start = int(feature.location.start) + 1  # Convert to 1-based
+            end = int(feature.location.end)
+            print(f"CDS Start: {start}")
+            print(f"CDS End: {end}")
+            break
+
+    if not cds_found:
+        print("CDS: Not found")
+
+    # Extract exon information
+    print(f"\n{'Exon Table:':-^60}")
+    print(f"{'Exon':<10} {'Start':<10} {'End':<10}")
+    print("-" * 30)
+
+    exon_count = 0
+    for feature in record.features:
+        if feature.type == "exon":
+            exon_count += 1
+            start = int(feature.location.start) + 1  # Convert to 1-based
+            end = int(feature.location.end)
+            print(f"Exon {exon_count:<4} {start:<10} {end:<10}")
+
+    if exon_count == 0:
+        print("No exon features found in record")
+
+    print(f"{'=' * 60}\n")
+
+
+if __name__ == "__main__":
+    try:
+        if len(sys.argv) == 2:  # noqa: PLR2004
+            # Accession provided as argument
+            accession = sys.argv[1]
+            record = get_refseq_info(accession)
+        elif len(sys.argv) == 1:
+            # No argument - read XML from stdin
+            print("Reading XML from stdin...")
+            record = SeqIO.read(sys.stdin, "genbank")
+        else:
+            print("Usage: python refseq_info.py <RefSeq_accession>", file=sys.stderr)
+            print("   or: cat record.xml | python refseq_info.py", file=sys.stderr)
+            sys.exit(1)
+
+        display_record_info(record)
+
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        sys.exit(1)
@@ -14,41 +14,49 @@ def __iter__(self):
         return (
             Rs(n)
             for n in self._xml_root.iterfind(
-                "docsum:Rs", namespaces={"docsum": self._xml_root.nsmap[None]}
+                "docsum:DocumentSummary", namespaces={"docsum": self._xml_root.nsmap[None]}
             )
         )
 
     def __len__(self):
         return len(
-            self._xml_root.findall("docsum:Rs", namespaces={"docsum": self._xml_root.nsmap[None]})
+            self._xml_root.findall(
+                "docsum:DocumentSummary", namespaces={"docsum": self._xml_root.nsmap[None]}
+            )
         )
 
 
 class Rs:
-    _root_tag = "Rs"
+    _root_tag = "DocumentSummary"
 
     def __init__(self, rs_node):
-        assert rs_node.tag == "{https://www.ncbi.nlm.nih.gov/SNP/docsum}Rs"  # noqa: S101
+        assert rs_node.tag == "{https://www.ncbi.nlm.nih.gov/SNP/docsum}DocumentSummary"  # noqa: S101
         self._n = rs_node
 
     # def __str__(self):
     #    return "Rs({self.id})".format(self=self)
 
     @property
     def rs_id(self):
-        return "rs" + self._n.get("rsId")
+        ns = {"docsum": self._n.nsmap[None]}
+        snp_id = self._n.findtext("docsum:SNP_ID", namespaces=ns)
+        return "rs" + snp_id
 
     @property
     def withdrawn(self):
-        return "notwithdrawn" not in self._n.get("snpType")
+        # snpType is no longer available in DocumentSummary format
+        # This would need to be determined from other fields if available
+        return False
 
     @property
     def orient(self):
-        return self._n.get("orient")
+        # orient attribute is no longer available in DocumentSummary format
+        return None
 
     @property
     def strand(self):
-        return self._n.get("strand")
+        # strand attribute is no longer available in DocumentSummary format
+        return None
 
     @property
     def hgvs_tags(self):

@@ -36,7 +36,11 @@ def definition(self):
 
     @property
     def exons(self):
-        return [(f.start_i, f.end_i) for f in self.features.exons]
+        """This function is temporarily disabled because the XML schema changed
+        and this method no longer works."""
+        msg = "The exons property is no longer supported"
+        raise NotImplementedError(msg)
+        # return [(f.start_i, f.end_i) for f in self.features.exons]
 
     @property
     def features(self):

@@ -0,0 +1,152 @@
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+      - 0C36C7C25205FB1A_A2F6SID
+      Referrer-Policy:
+      - origin-when-cross-origin
+      Server:
+      - Finatra
+      Set-Cookie:
+      - ncbi_sid=0C36C7C25205FB1A_A2F6SID; domain=.nih.gov; path=/; expires=Mon, 07
+        Dec 2026 06:11:45 GMT
+      Strict-Transport-Security:
+      - max-age=31536000; includeSubDomains; preload
+      Transfer-Encoding:
+      - chunked
+      X-RateLimit-Limit:
+      - '10'
+      X-RateLimit-Remaining:
+      - '9'
+      X-UA-Compatible:
+      - IE=Edge
+      X-XSS-Protection:
+      - 1; mode=block
+      content-encoding:
+      - gzip
+    status:
+      code: 200
+      message: OK
+version: 1
@@ -3,7 +3,7 @@
 
 @vcr.use_cassette
 def test_esearchresult(client):
-    r = next(iter(client.efetch(db="nuccore", id="NM_152783.3")))
+    r = next(iter(client.efetch(db="nuccore", id="NM_152783.5")))
 
     # in #150 fails with AttributeError: 'GBSeq' object has no attribute 'seqids'
     assert r.gi == 119964727
@@ -28,10 +28,7 @@ def test_esearchresult(client):
     )
     assert prot == r.features.cds.translation
 
-    # this returns the ranges
-    exons = r.exons
-    assert len(exons) == 10
-
-    # this returns GBFeatureExon objects
-    exon = next(iter(r.features.exons))
-    assert exon.inference == "alignment:Splign:1.39.8"
+    # exons (and perhaps other methods) are currently broken
+    # See eutils/_internal/xmlfacades/gbseq.py#L38
+    # exons = r.exons
+    # assert len(exons) == 10