Support InterProScan 5.74 output and non-spec GFF attributes

src/predectorutils/data/__init__.py

@@ -4,12 +4,21 @@
 for each database release. The latest version will always we the default one.
 """
 
-from pkg_resources import resource_filename
+from importlib.resources import files
 
 import json
 import xgboost as xgb
 
 
+def resource_filename(package: str, resource: str) -> str:
+    """Return the filesystem path to a data file bundled in the package.
+
+    Drop-in replacement for the deprecated
+    ``pkg_resources.resource_filename``.
+    """
+    return str(files(package).joinpath(resource))
+
+
 def get_interesting_pfam_ids(version: str = "latest") -> list[str]:
     fname = resource_filename(__name__, "hmms_of_interest.json")
     with open(fname, "r") as handle:

src/predectorutils/gff.py

@@ -478,11 +478,19 @@ def parse(
         if string.strip() in (".", ""):
             return cls()
 
-        fields = (
-            f.split("=", maxsplit=1)
-            for f
-            in string.strip(" ;").split(";")
-        )
+        # Split on ';', then on '='. Some tools (e.g. funannotate) emit values
+        # containing unescaped ';' characters, which is invalid GFF3 (';' in a
+        # value should be percent-encoded as %3B) but common in practice --
+        # e.g. gene names like "SULTR3;4". A piece without '=' is treated as a
+        # continuation of the previous value with the split ';' restored,
+        # rather than crashing.
+        fields: list[list[str]] = []
+        for piece in string.strip(" ;").split(";"):
+            if "=" in piece:
+                fields.append(piece.split("=", maxsplit=1))
+            elif len(fields) > 0:
+                fields[-1][1] = f"{fields[-1][1]};{piece}"
+            # A leading piece with no '=' has nothing to attach to; skip it.
 
         if strip_quote:
             kvpairs: dict[str, str] = {

src/predectorutils/subcommands/ipr_to_gff.py

@@ -44,8 +44,12 @@ def cli(parser: argparse.ArgumentParser) -> None:
     parser.add_argument(
         "--namespace",
         type=str,
-        default=NAMESPACE,
-        help="The XML dom namespace. This is mostly included for developers."
+        default=None,
+        help=(
+            "The XML dom namespace. By default this is auto-detected from "
+            "the root element of the XML file. This is mostly included for "
+            "developers."
+        )
     )
     return
 
@@ -63,10 +67,17 @@ def get_source(
 
 def get_tag(
     element: ET.Element,
-    namespace: str
+    namespace: Optional[str] = None
 ) -> str:
-    assert element.tag.startswith(namespace), element
-    return element.tag[len(namespace):]
+    # Strip any leading "{namespace-uri}" prefix to get the local tag name.
+    # We intentionally ignore the specific namespace URI so that the parser
+    # keeps working when InterProScan changes it between versions (e.g.
+    # http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5 ->
+    # https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas).
+    tag = element.tag
+    if tag.startswith("{"):
+        return tag[tag.index("}") + 1:]
+    return tag
 
 
 class Signature(NamedTuple):
@@ -333,7 +344,9 @@ def process_hmmer3(
     itree: Iterator[tuple[str, ET.Element]],
     ips_version: Optional[str],
     query_id: Optional[str],
-    namespace: str = NAMESPACE
+    namespace: str = NAMESPACE,
+    match_tag: str = "hmmer3-match",
+    location_tag: str = "hmmer3-location",
 ) -> Iterator[GFFRecord]:
     assert ips_version is not None
     assert query_id is not None
@@ -348,7 +361,7 @@ def process_hmmer3(
         event, element = next(itree)
         tag = get_tag(element, namespace)
 
-        if (event == "end") and (tag == "hmmer3-match"):
+        if (event == "end") and (tag == match_tag):
             break
         if (event == "start") and (tag == "signature"):
             signature = process_signature(element, itree)
@@ -361,7 +374,7 @@ def process_hmmer3(
             goterms = signature.goterms
             kind = signature.kind
 
-        elif (event == "start") and (tag == "hmmer3-location"):
+        elif (event == "start") and (tag == location_tag):
             start = element.attrib["start"]
             end = element.attrib["end"]
             env_start = element.attrib["env-start"]
@@ -1357,7 +1370,7 @@ def inner(records: Iterable[GFFRecord]):
 def inner(  # noqa: C901
     infile: TextIO,
     outfile: TextIO,
-    namespace: str,
+    namespace: Optional[str] = None,
 ):
     itree = ET.iterparse(
         infile,
@@ -1399,6 +1412,16 @@ def inner(  # noqa: C901
         elif (event == "start") and (tag == "hmmer3-match"):
             hmm = process_hmmer3(element, itree, ips_version, query_id)
             printer(hmm)
+        elif (event == "start") and (tag == "funfamhmmer3-match"):
+            hmm = process_hmmer3(
+                element,
+                itree,
+                ips_version,
+                query_id,
+                match_tag="funfamhmmer3-match",
+                location_tag="funfamhmmer3-location",
+            )
+            printer(hmm)
         elif (event == "start") and (tag == "panther-match"):
             hmm = process_panther(element, itree, ips_version, query_id)
             printer(hmm)