From 624f1c780c87d46486e6cb646f0dc03e04e4b0fe Mon Sep 17 00:00:00 2001 From: Trent Hauck Date: Mon, 5 Feb 2024 11:27:15 -0800 Subject: [PATCH] revert: revert genbank update --- python/biobear/genbank_reader.py | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/python/biobear/genbank_reader.py b/python/biobear/genbank_reader.py index 2167c6a..5ec46a2 100644 --- a/python/biobear/genbank_reader.py +++ b/python/biobear/genbank_reader.py @@ -1,9 +1,6 @@ """Genbank file reader.""" import os -import pyarrow as pa -import pyarrow.dataset as ds - from biobear.reader import Reader from biobear.compression import Compression @@ -30,26 +27,6 @@ def __init__( else: self._reader = _ExonReader(str(path), "GENBANK", None) - def to_polars(self): - """Read the GFF file and return a polars DataFrame.""" - try: - import polars as pl - except ImportError as import_error: - raise ImportError( - "The polars library is required to convert a GFF file " - "to a polars DataFrame." - ) from import_error - - return pl.from_arrow(self.to_arrow().read_all()) - - def to_arrow(self) -> pa.RecordBatchReader: - """Convert the GFF reader to an arrow batch reader.""" - return self._reader.to_pyarrow() - - def to_arrow_scanner(self) -> ds.Scanner: - """Convert the GFF reader to an arrow scanner.""" - return ds.Scanner.from_batches(self.to_arrow()) - @property def inner(self): """Return the inner reader."""