biofiles 0.0.13__py3-none-any.whl → 0.1.1__py3-none-any.whl

biofiles/dialects/detector.py

@@ -0,0 +1,74 @@
+import sys
+from itertools import islice
+from pathlib import Path
+
+from biofiles.dialects.gencode import GENCODE_DIALECT
+from biofiles.dialects.refseq import REFSEQ_DIALECT
+from biofiles.dialects.stringtie import STRINGTIE_DIALECT
+from biofiles.types.feature import Dialect
+from biofiles.utility.feature import RawFeatureReader
+
+
+class CantDetectDialect(Exception):
+    pass
+
+
+class DialectDetector:
+    def __init__(self, raw_reader: RawFeatureReader, num_samples: int = 1000) -> None:
+        self._raw_reader = raw_reader
+        self._num_samples = num_samples
+
+    def detect(self) -> Dialect:
+        gencode_rows = 0
+        refseq_rows = 0
+        stringtie_rows = 0
+        total_rows = 0
+        for fd in islice(self._raw_reader, self._num_samples):
+            total_rows += 1
+            source = fd.source.lower()
+            if source in ("havana", "ensembl"):
+                gencode_rows += 1
+            elif source in ("bestrefseq", "bestrefseq%2cgnomon", "gnomon", "refseq"):
+                refseq_rows += 1
+            elif source in ("stringtie",):
+                stringtie_rows += 1
+
+        if gencode_rows > 0 and gencode_rows >= 0.9 * total_rows:
+            return GENCODE_DIALECT
+        if refseq_rows > 0 and refseq_rows >= 0.9 * total_rows:
+            return REFSEQ_DIALECT
+        if stringtie_rows > 0 and stringtie_rows >= 0.9 * total_rows:
+            return STRINGTIE_DIALECT
+
+        raise CantDetectDialect(
+            f"of {total_rows} read rows {gencode_rows} look like GENCODE, "
+            f"{refseq_rows} look like RefSeq, {stringtie_rows} look like StringTie"
+        )
+
+
+def detect_dialect(path: Path) -> Dialect:
+    if path.suffix == ".gtf":
+        from biofiles.gtf import RawGTFReader
+
+        raw_reader = RawGTFReader(path)
+    elif path.suffix in (".gff", ".gff3"):
+        from biofiles.gff import RawGFFReader
+
+        raw_reader = RawGFFReader(path)
+    else:
+        raise CantDetectDialect(f"unknown file extension {path.suffix}")
+    detector = DialectDetector(raw_reader=raw_reader)
+    return detector.detect()
+
+
+if __name__ == "__main__":
+    exit_code = 0
+    for path_str in sys.argv[1:]:
+        path = Path(path_str)
+        try:
+            dialect = detect_dialect(path)
+            print(f"{path}\t{dialect.name}")
+        except CantDetectDialect as exc:
+            print(f"Failed to detect dialect for {path}: {exc}", file=sys.stderr)
+            exit_code = 1
+    sys.exit(exit_code)

biofiles/dialects/gencode.py

@@ -0,0 +1,235 @@
+"""Feature dialect for GENCODE .gtf/.gff3 files."""
+
+from enum import StrEnum
+from types import NoneType
+
+from biofiles.dialects.genomic_base import (
+    Gene as BaseGene,
+    Transcript as BaseTranscript,
+    Exon as BaseExon,
+    CDS as BaseCDS,
+    UTR as BaseUTR,
+)
+from biofiles.types.feature import (
+    Feature,
+    id_field,
+    field,
+    relation,
+    no_id_field,
+    Dialect,
+)
+
+
+class GeneType(StrEnum):
+    ARTIFACT = "artifact"
+    IG_C_GENE = "IG_C_gene"
+    IG_C_PSEUDOGENE = "IG_C_pseudogene"
+    IG_D_GENE = "IG_D_gene"
+    IG_D_PSEUDOGENE = "IG_D_pseudogene"
+    IG_J_GENE = "IG_J_gene"
+    IG_J_PSEUDOGENE = "IG_J_pseudogene"
+    IG_PSEUDOGENE = "IG_pseudogene"
+    IG_V_GENE = "IG_V_gene"
+    IG_V_PSEUDOGENE = "IG_V_pseudogene"
+    LNCRNA = "lncRNA"
+    MIRNA = "miRNA"
+    MISC_RNA = "misc_RNA"
+    MT_RRNA = "Mt_rRNA"
+    MT_TRNA = "Mt_tRNA"
+    PROCESSED_PSEUDOGENE = "processed_pseudogene"
+    PROTEIN_CODING = "protein_coding"
+    RIBOZYME = "ribozyme"
+    RRNA = "rRNA"
+    RRNA_PSEUDOGENE = "rRNA_pseudogene"
+    SRNA = "sRNA"
+    SCRNA = "scRNA"
+    SCARNA = "scaRNA"
+    SNRNA = "snRNA"
+    SNORNA = "snoRNA"
+    TEC = "TEC"
+    TR_C_GENE = "TR_C_gene"
+    TR_C_PSEUDOGENE = "TR_C_pseudogene"
+    TR_D_GENE = "TR_D_gene"
+    TR_D_PSEUDOGENE = "TR_D_pseudogene"
+    TR_J_GENE = "TR_J_gene"
+    TR_J_PSEUDOGENE = "TR_J_pseudogene"
+    TR_V_GENE = "TR_V_gene"
+    TR_V_PSEUDOGENE = "TR_V_pseudogene"
+    TRANSCRIBED_PROCESSED_PSEUDOGENE = "transcribed_processed_pseudogene"
+    TRANSCRIBED_UNITARY_PSEUDOGENE = "transcribed_unitary_pseudogene"
+    TRANSCRIBED_UNPROCESSED_PSEUDOGENE = "transcribed_unprocessed_pseudogene"
+    TRANSLATED_PROCESSED_PSEUDOGENE = "translated_processed_pseudogene"
+    UNITARY_PSEUDOGENE = "unitary_pseudogene"
+    UNPROCESSED_PSEUDOGENE = "unprocessed_pseudogene"
+    VAULT_RNA = "vault_RNA"
+
+
+class TranscriptType(StrEnum):
+    ARTIFACT = "artifact"
+    IG_C_GENE = "IG_C_gene"
+    IG_C_PSEUDOGENE = "IG_C_pseudogene"
+    IG_D_GENE = "IG_D_gene"
+    IG_D_PSEUDOGENE = "IG_D_pseudogene"
+    IG_J_GENE = "IG_J_gene"
+    IG_J_PSEUDOGENE = "IG_J_pseudogene"
+    IG_PSEUDOGENE = "IG_pseudogene"
+    IG_V_GENE = "IG_V_gene"
+    IG_V_PSEUDOGENE = "IG_V_pseudogene"
+    LNCRNA = "lncRNA"
+    MIRNA = "miRNA"
+    MISC_RNA = "misc_RNA"
+    MT_RRNA = "Mt_rRNA"
+    MT_TRNA = "Mt_tRNA"
+    PROCESSED_PSEUDOGENE = "processed_pseudogene"
+    PROTEIN_CODING = "protein_coding"
+    RIBOZYME = "ribozyme"
+    RRNA = "rRNA"
+    RRNA_PSEUDOGENE = "rRNA_pseudogene"
+    SRNA = "sRNA"
+    SCRNA = "scRNA"
+    SCARNA = "scaRNA"
+    SNRNA = "snRNA"
+    SNORNA = "snoRNA"
+    TEC = "TEC"
+    TR_C_GENE = "TR_C_gene"
+    TR_C_PSEUDOGENE = "TR_C_pseudogene"
+    TR_D_GENE = "TR_D_gene"
+    TR_D_PSEUDOGENE = "TR_D_pseudogene"
+    TR_J_GENE = "TR_J_gene"
+    TR_J_PSEUDOGENE = "TR_J_pseudogene"
+    TR_V_GENE = "TR_V_gene"
+    TR_V_PSEUDOGENE = "TR_V_pseudogene"
+    TRANSCRIBED_PROCESSED_PSEUDOGENE = "transcribed_processed_pseudogene"
+    TRANSCRIBED_UNITARY_PSEUDOGENE = "transcribed_unitary_pseudogene"
+    TRANSCRIBED_UNPROCESSED_PSEUDOGENE = "transcribed_unprocessed_pseudogene"
+    TRANSLATED_PROCESSED_PSEUDOGENE = "translated_processed_pseudogene"
+    UNITARY_PSEUDOGENE = "unitary_pseudogene"
+    UNPROCESSED_PSEUDOGENE = "unprocessed_pseudogene"
+    VAULT_RNA = "vault_RNA"
+
+    # Transcript-specific:
+    NON_STOP_DECAY = "non_stop_decay"
+    NONSENSE_MEDIATED_DECAY = "nonsense_mediated_decay"
+    PROCESSED_TRANSCRIPT = "processed_transcript"
+    PROTEIN_CODING_CDS_NOT_DEFINED = "protein_coding_CDS_not_defined"
+    PROTEIN_CODING_LOF = "protein_coding_LoF"
+    RETAINED_INTRON = "retained_intron"
+
+
+transcript_gene, gene_transcripts = relation(source="gene_id")
+selenocysteine_gene, _ = relation(source="gene_id")
+selenocysteine_transcript, _ = relation(source="transcript_id")
+exon_transcript, transcript_exons = relation(source="transcript_id")
+exon_gene, _ = relation(source="gene_id")
+cds_exon, exon_cds = relation(source=("transcript_id", "exon_number"), one_to_one=True)
+utr_transcript, transcript_utrs = relation(source="transcript_id")
+utr_gene, _ = relation(source="gene_id")
+five_prime_utr_transcript, transcript_five_prime_utr = relation(
+    source="transcript_id", one_to_one=True
+)
+five_prime_utr_gene, _ = relation(source="gene_id")
+three_prime_utr_transcript, transcript_three_prime_utr = relation(
+    source="transcript_id", one_to_one=True
+)
+three_prime_utr_gene, _ = relation(source="gene_id")
+start_codon_transcript, transcript_start_codon = relation(
+    source="transcript_id", one_to_one=True
+)
+start_codon_exon, _ = relation(source=("transcript_id", "exon_number"), one_to_one=True)
+stop_codon_transcript, transcript_stop_codon = relation(
+    source="transcript_id", one_to_one=True
+)
+stop_codon_exon, _ = relation(source=("transcript_id", "exon_number"), one_to_one=True)
+
+
+class Gene(BaseGene, type="gene"):
+    id: str = id_field(source="gene_id")
+    type: GeneType = field(source="gene_type")
+    name: str = field(source="gene_name")
+    transcripts: list["Transcript"] = gene_transcripts
+    tags: list[str] = field(source="tag", default_factory=list)
+
+
+class Transcript(BaseTranscript, type="transcript"):
+    id: str = id_field(source="transcript_id")
+    type: TranscriptType = field(source="transcript_type")
+    name: str = field(source="transcript_name")
+    gene: Gene = transcript_gene
+    exons: list["Exon"] = transcript_exons
+    utrs: list["UTR"] = transcript_utrs
+    start_codon: "StartCodon | None" = transcript_start_codon
+    stop_codon: "StopCodon | None" = transcript_stop_codon
+    tags: list[str] = field(source="tag", default_factory=list)
+
+
+class Selenocysteine(
+    Feature, type=("selenocysteine", "stop_codon_redefined_as_selenocysteine")
+):
+    id: str = no_id_field()
+    gene: Gene = selenocysteine_gene
+    transcript: Transcript = selenocysteine_transcript
+
+
+class Exon(BaseExon, type="exon"):
+    id: tuple[str, int] = id_field(source=("transcript_id", "exon_number"))
+    number: int = field(source="exon_number")
+    transcript: Transcript = exon_transcript
+    gene: Gene = exon_gene
+    cds: "CDS | None" = exon_cds
+    tags: list[str] = field(source="tag", default_factory=list)
+
+    @property
+    def cdss(self) -> list["CDS"]:
+        # In RefSeq, exon can have multiple CDS.
+        # This property is for compatibility with a more general case.
+        return [self.cds] if self.cds is not None else []
+
+
+class CDS(BaseCDS, type="cds"):
+    id: tuple[str, int] = id_field(source=("transcript_id", "exon_number"))
+    exon: Exon = cds_exon
+
+
+class UTR(BaseUTR, type="utr"):
+    id: NoneType = no_id_field()
+    transcript: Transcript = utr_transcript
+    gene: Gene = utr_gene
+
+
+class FivePrimeUTR(UTR, type="five_prime_utr"):
+    id: NoneType = no_id_field()
+    transcript: Transcript = five_prime_utr_transcript
+    gene: Gene = five_prime_utr_gene
+
+
+class ThreePrimeUTR(UTR, type="three_prime_utr"):
+    id: NoneType = no_id_field()
+    transcript: Transcript = three_prime_utr_transcript
+    gene: Gene = three_prime_utr_gene
+
+
+class StartCodon(Feature, type="start_codon"):
+    id: tuple[str, int] = id_field(source=("transcript_id", "exon_number"))
+    transcript: Transcript = start_codon_transcript
+    exon: Exon = start_codon_exon
+
+
+class StopCodon(Feature, type="stop_codon"):
+    id: tuple[str, int] = id_field(source=("transcript_id", "exon_number"))
+    transcript: Transcript = stop_codon_transcript
+    exon: Exon = stop_codon_exon
+
+
+GENCODE_FEATURE_TYPES = [
+    Gene,
+    Transcript,
+    Selenocysteine,
+    Exon,
+    CDS,
+    UTR,
+    FivePrimeUTR,
+    ThreePrimeUTR,
+    StartCodon,
+    StopCodon,
+]
+GENCODE_DIALECT = Dialect(name="GENCODE", feature_types=GENCODE_FEATURE_TYPES)

biofiles/dialects/genomic_base.py

@@ -0,0 +1,25 @@
+from biofiles.types.feature import Feature
+
+
+class Gene(Feature):
+    type: str
+    transcripts: list["Transcript"]
+
+
+class Transcript(Feature):
+    type: str
+    gene: Gene
+    exons: list["Exon"]
+
+
+class Exon(Feature):
+    transcript: Transcript
+    cdss: list["CDS"]
+
+
+class CDS(Feature):
+    exon: Exon
+
+
+class UTR(Feature):
+    transcript: Transcript

biofiles/dialects/refseq.py

@@ -0,0 +1,142 @@
+"""Feature dialect for RefSeq .gtf/.gff3 files."""
+
+from enum import StrEnum
+
+from biofiles.dialects.genomic_base import (
+    Gene as BaseGene,
+    Transcript as BaseTranscript,
+    Exon as BaseExon,
+    CDS as BaseCDS,
+)
+from biofiles.types.feature import (
+    Feature,
+    id_field,
+    field,
+    relation,
+    no_id_field,
+    Dialect,
+)
+
+
+class GeneType(StrEnum):
+    ANTISENSE_RNA = "antisense_RNA"
+    C_REGION = "C_region"
+    C_REGION_PSEUDOGENE = "C_region_pseudogene"
+    D_SEGMENT = "D_segment"
+    D_SEGMENT_PSEUDOGENE = "D_segment_pseudogene"
+    J_SEGMENT = "J_segment"
+    J_SEGMENT_PSEUDOGENE = "J_segment_pseudogene"
+    LNCRNA = "lncRNA"
+    MIRNA = "miRNA"
+    MISC_RNA = "misc_RNA"
+    NCRNA = "ncRNA"
+    NCRNA_PSEUDOGENE = "ncRNA_pseudogene"
+    OTHER = "other"
+    PROTEIN_CODING = "protein_coding"
+    PSEUDOGENE = "pseudogene"
+    RNASE_MRP_RNA = "RNase_MRP_RNA"
+    RNASE_P_RNA = "RNase_P_RNA"
+    RRNA = "rRNA"
+    SCARNA = "scaRNA"
+    SCRNA = "scRNA"
+    SNORNA = "snoRNA"
+    SNRNA = "snRNA"
+    TELOMERASE_RNA = "telomerase_RNA"
+    TRANSCRIBED_PSEUDOGENE = "transcribed_pseudogene"
+    TRNA = "tRNA"
+    VAULT_RNA = "vault_RNA"
+    V_SEGMENT = "V_segment"
+    V_SEGMENT_PSEUDOGENE = "V_segment_pseudogene"
+    Y_RNA = "Y_RNA"
+
+
+class TranscriptType(StrEnum):
+    ANTISENSE_RNA = "antisense_RNA"
+    C_GENE_SEGMENT = "C_gene_segment"
+    D_GENE_SEGMENT = "D_gene_segment"
+    J_GENE_SEGMENT = "J_gene_segment"
+    LNC_RNA = "lnc_RNA"
+    MIRNA = "miRNA"
+    MRNA = "mRNA"
+    PRIMARY_TRANSCRIPT = "primary_transcript"
+    RNASE_MRP_RNA = "RNase_MRP_RNA"
+    RNASE_P_RNA = "RNase_P_RNA"
+    RRNA = "rRNA"
+    SCARNA = "scaRNA"
+    SCRNA = "scRNA"
+    SNORNA = "snoRNA"
+    SNRNA = "snRNA"
+    TELOMERASE_RNA = "telomerase_RNA"
+    TRANSCRIPT = "transcript"
+    TRNA = "tRNA"
+    VAULT_RNA = "vault_RNA"
+    V_GENE_SEGMENT = "V_gene_segment"
+    Y_RNA = "Y_RNA"
+
+
+transcript_gene, gene_transcripts = relation(source="gene_id")
+exon_transcript, transcript_exons = relation(source="transcript_id")
+exon_gene, _ = relation(source="gene_id")
+cds_exon, exon_cds = relation(source=("transcript_id", "exon_number"))
+start_codon_transcript, transcript_start_codon = relation(
+    source="transcript_id", one_to_one=True
+)
+start_codon_exon, _ = relation(source=("transcript_id", "exon_number"), one_to_one=True)
+stop_codon_transcript, transcript_stop_codon = relation(
+    source="transcript_id", one_to_one=True
+)
+stop_codon_exon, _ = relation(source=("transcript_id", "exon_number"), one_to_one=True)
+
+
+class Gene(BaseGene, type="gene"):
+    id: str = id_field(source="gene_id")
+    type: GeneType = field(source="gene_biotype")
+    name: str = field(source="gene")
+    synonyms: list[str] = field(source="gene_synonym", default_factory=list)
+    transcripts: list["Transcript"] = gene_transcripts
+
+
+class Transcript(BaseTranscript, type="transcript"):
+    id: str = id_field(source="transcript_id")
+    type: TranscriptType = field(source="transcript_biotype")
+    product: str | None = field(source="product", default=None)
+    gene: Gene = transcript_gene
+    exons: list["Exon"] = transcript_exons
+    start_codon: "StartCodon | None" = transcript_start_codon
+    stop_codon: "StopCodon | None" = transcript_stop_codon
+
+
+class Exon(BaseExon, type="exon"):
+    id: tuple[str, int] = id_field(source=("transcript_id", "exon_number"))
+    number: int = field(source="exon_number")
+    transcript: Transcript = exon_transcript
+    gene: Gene = exon_gene
+    cdss: list["CDS"] = exon_cds
+
+
+class CDS(BaseCDS, type="cds"):
+    id: tuple[str, int] = no_id_field()
+    exon: Exon = cds_exon
+
+
+class StartCodon(Feature, type="start_codon"):
+    id: tuple[str, int] = id_field(source=("transcript_id", "exon_number"))
+    transcript: Transcript = start_codon_transcript
+    exon: Exon = start_codon_exon
+
+
+class StopCodon(Feature, type="stop_codon"):
+    id: tuple[str, int] = id_field(source=("transcript_id", "exon_number"))
+    transcript: Transcript = stop_codon_transcript
+    exon: Exon = stop_codon_exon
+
+
+REFSEQ_FEATURE_TYPES = [
+    Gene,
+    Transcript,
+    Exon,
+    CDS,
+    StartCodon,
+    StopCodon,
+]
+REFSEQ_DIALECT = Dialect(name="RefSeq", feature_types=REFSEQ_FEATURE_TYPES)

biofiles/dialects/stringtie.py

@@ -0,0 +1,24 @@
+"""Feature dialect for StringTie .gtf/.gff output."""
+
+from biofiles.types.feature import Feature, relation, id_field, field, Dialect
+
+exon_transcript, transcript_exons = relation(source="transcript_id")
+
+
+class Transcript(Feature, type="transcript"):
+    id: str = id_field(source="transcript_id")
+    gene_id: str = field(source="gene_id")
+    exons: list["Exon"] = transcript_exons
+    coverage: float = field(source="cov")
+    fpkm: float = field(source="FPKM")
+    tpm: float = field(source="TPM")
+
+
+class Exon(Feature, type="exon"):
+    id: tuple[str, int] = id_field(source=("transcript_id", "exon_number"))
+    transcript: Transcript = exon_transcript
+    coverage: float = field(source="cov")
+
+
+STRINGTIE_FEATURE_TYPES = [Transcript, Exon]
+STRINGTIE_DIALECT = Dialect(name="StringTie", feature_types=STRINGTIE_FEATURE_TYPES)

biofiles/gff.py

@@ -3,15 +3,20 @@ from pathlib import Path
 from typing import Iterator, cast, TextIO
 
 from biofiles.common import Strand, Writer
+from biofiles.dialects.detector import detect_dialect
+from biofiles.dialects.genomic_base import Feature, Gene, Exon, UTR
 from biofiles.utility.cli import parse_pipeline_args
-from biofiles.utility.feature import FeatureReader, FeatureDraft, FeatureDrafts
-from biofiles.types.feature import Feature, Gene, Exon, UTR
+from biofiles.utility.feature import (
+    FeatureReader,
+    FeatureDraft,
+    RawFeatureReader,
+)
 
-__all__ = ["GFFReader", "GFF3Writer"]
+__all__ = ["RawGFFReader", "GFFReader", "GFF3Writer"]
 
 
-class GFFReader(FeatureReader):
-    def __iter__(self) -> Iterator[Feature]:
+class RawGFFReader(RawFeatureReader):
+    def __iter__(self) -> Iterator[FeatureDraft]:
         for line in self._input:
             line = line.rstrip("\n")
             if line.startswith(_VERSION_PREFIX):
@@ -24,60 +29,51 @@ class GFFReader(FeatureReader):
                 continue
             raise ValueError(f"unexpected line {line!r}, expected version")
 
-    def _read_gff3(self) -> Iterator[Feature]:
-        drafts = FeatureDrafts()
+    def _read_gff3(self) -> Iterator[FeatureDraft]:
         idx = 0
-        for line in self._input:
+        for i, line in enumerate(self._input):
             if line.startswith("#"):
                 continue
-            line = line.rstrip("\n")
-            parts = line.split("\t", maxsplit=8)
-            if len(parts) != 9:
-                raise ValueError(f"unexpected line {line!r}, expected 9 columns")
-            (
-                sequence_id,
-                source,
-                type_,
-                start_str,
-                end_str,
-                score_str,
-                strand_str,
-                phase_str,
-                attributes_str,
-            ) = parts
-            score = self._parse_score(line, score_str)
-            strand = self._parse_strand(line, strand_str)
-            phase = self._parse_phase(line, phase_str)
-            attributes = self._parse_attributes(line, attributes_str)
+            try:
+                line = line.rstrip("\n")
+                parts = line.split("\t", maxsplit=8)
+                if len(parts) != 9:
+                    raise ValueError(f"unexpected line {line!r}, expected 9 columns")
+                (
+                    sequence_id,
+                    source,
+                    type_,
+                    start_str,
+                    end_str,
+                    score_str,
+                    strand_str,
+                    phase_str,
+                    attributes_str,
+                ) = parts
+                score = self._parse_score(line, score_str)
+                strand = self._parse_strand(line, strand_str)
+                phase = self._parse_phase(line, phase_str)
+                attributes = self._parse_attributes(line, attributes_str)
+            except Exception as exc:
+                raise ValueError(f"failed to parse line {i}: {exc}") from exc
 
             parent_id = attributes.get("Parent", None)
-            # if parent_id is None:
-            #     yield from self._finalize_drafts(drafts)
-            #     drafts = _FeatureDrafts()
-            if parent_id is not None and parent_id not in drafts.by_id:
-                raise ValueError(
-                    f"unexpected line {line!r}, parent ID not among recent feature IDs"
-                )
-
-            draft = FeatureDraft(
+            yield FeatureDraft(
                 idx=idx,
                 sequence_id=sequence_id,
                 source=source,
                 type_=type_,
                 start_original=int(start_str),
                 end_original=int(end_str),
+                start_c=int(start_str) - 1,
+                end_c=int(end_str),
                 score=score,
                 strand=strand,
                 phase=phase,
                 attributes=attributes,
             )
-            drafts.add(draft)
             idx += 1
 
-            # yield from self._finalize_drafts(drafts, self._streaming_window)
-
-        yield from self._finalize_drafts(drafts, None)
-
     def _parse_score(self, line: str, score_str: str) -> float | None:
         if score_str == ".":
             return None
@@ -105,14 +101,22 @@ class GFFReader(FeatureReader):
                 f"unexpected line {line!r}, phase should be an integer or '.'"
             ) from exc
 
-    def _parse_attributes(self, line: str, attributes_str: str) -> dict[str, str]:
+    def _parse_attributes(
+        self, line: str, attributes_str: str
+    ) -> dict[str, str | list[str]]:
         return {
-            k: v
+            k: v.split(",") if "," in v else v
             for part in attributes_str.strip(";").split(";")
             for k, v in (part.split("=", 1),)
         }
 
 
+class GFFReader(FeatureReader):
+
+    def _make_raw_feature_reader(self) -> RawFeatureReader:
+        return RawGFFReader(self._input)
+
+
 class GFF3Writer(Writer):
     def __init__(self, output: TextIO | Path | str) -> None:
         super().__init__(output)
@@ -147,7 +151,8 @@ if __name__ == "__main__":
         pipeline.mapper = lambda f: print(old_mapper(f))
 
     for path in pipeline.inputs:
-        with GFFReader(path) as r:
+        dialect = detect_dialect(path)
+        with GFFReader(path, dialect=dialect) as r:
             total_features = 0
             annotated_genes = 0
             annotated_exons = 0