gtfreader 0.1.0

Fast Cython-backed parsing for GTF attribute columns.

gtfreader

gtfreader is a small package for parsing and reading GTF files into pandas dataframes.

Install

python -m pip install -e .

Usage

from gtfreader import read_gtf, read_gtf_python

df = read_gtf("annotation.gtf")
df_python = read_gtf_python("annotation.gtf")

read_gtf(...) uses the compiled parser path when available. read_gtf_python(...) uses the high-level pure Python parser path used by the current pyrunges reader style.

If you want to use the compiled low-level parser directly, pass it raw attribute strings from column 9 of the GTF before they have been expanded:

import pandas as pd

from gtfreader import find_first_data_line_index, parse_chunk_columns

skiprows = find_first_data_line_index("annotation.gtf")
attribute_lines = pd.read_csv(
    "annotation.gtf",
    sep="\t",
    header=None,
    usecols=[8],
    names=["Attribute"],
    skiprows=skiprows,
)["Attribute"].tolist()

compiled_columns = parse_chunk_columns(attribute_lines)

Build

python -m build

Test

python -m pytest -q