openvax/gtfparse

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Parsing tools for GTF (gene transfer format) files

Stars: 129
Forks: 34
Open beginner issues: 0
Indexed issues: 23

Dominant language: Python
License: Apache-2.0
Last GitHub push: Jul 8, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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23 open issues indexed

Clean up stale docstrings, history comments, and leftover CI/test cache files Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

openvax/gtfparse#76 · Opened Sep 14, 2026
Triage: 11 open issues appear resolved on master Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

openvax/gtfparse#75 · Opened Sep 14, 2026
Evaluate migration from polars to pyarrow + pandas (with measurement plan) Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

openvax/gtfparse#69 · Opened May 13, 2026
Optional incompleteness flag for required features (start_codon / stop_codon / CDS pairs) Open

Difficulty 5/5 Over a week Newbie friendliness 45/100

openvax/gtfparse#66 · Opened May 13, 2026
create_missing_features: opt-in / configurable strictness for synthesized parent rows Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

openvax/gtfparse#65 · Opened May 13, 2026
Pin `numpy` to 1.X.X Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

openvax/gtfparse#55 · 1 reaction · Opened Mar 10, 2025
Tests fail when using the PYPI tarball because the 'data' module is missing Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

openvax/gtfparse#53 · Opened Dec 6, 2024
pandas is imported but isn't listed in https://github.com/openvax/gtfparse Open

Difficulty 1/5 Under an hour Newbie friendliness 48/100

openvax/gtfparse#52 · Opened Nov 12, 2024
DeprecationWarning: The argument `dtypes` for `read_csv` is deprecated. Open

Difficulty 1/5 Under an hour Newbie friendliness 48/100

openvax/gtfparse#50 · 1 comment · Opened Oct 28, 2024
Error in gtfparse when calling vcf-expression-annotator Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

openvax/gtfparse#49 · 1 comment · Opened Aug 26, 2024
Update gtfparse to support pyarrow >=0.15 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

openvax/gtfparse#47 · 3 comments · 1 reaction · Opened May 9, 2024
ImportError: cannot import name table_to_blockmanager Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

openvax/gtfparse#45 · 1 comment · 2 reactions · Opened Jan 25, 2024
Fix bug for records with ";" in the value Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

openvax/gtfparse#44 · Opened Jan 17, 2024
Bioconda wrong dependencies for version 2.1.0 Open

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

openvax/gtfparse#43 · Opened Dec 29, 2023
Please do not use logging basicConfig for library software Open

Difficulty 1/5 Under an hour Newbie friendliness 55/100

openvax/gtfparse#40 · 2 reactions · Opened Sep 13, 2023
BackTrace for exception when parsing gtf file Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

openvax/gtfparse#38 · 1 comment · Opened Aug 5, 2023
How to iter a huge gtf file line by line ? Open

Difficulty 2/5 1-3 hours Newbie friendliness 30/100

openvax/gtfparse#37 · Opened Jul 11, 2023
read_gtf has ERROR "scan_csv() got an unexpected keyword argument 'sep'" Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

openvax/gtfparse#36 · 9 comments · Opened Jun 11, 2023
Conversion to Pandas in read_gtf has missing dependency Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

openvax/gtfparse#32 · Opened Feb 7, 2023
Attribute parsing fix Open

Difficulty 1/5 Under an hour Newbie friendliness 55/100

openvax/gtfparse#23 · Opened Oct 14, 2021
gtfparse.parsing_error.ParsingError: Integer column has NA values in column 3 Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

openvax/gtfparse#19 · Opened Sep 7, 2020
The column names are not correct Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

openvax/gtfparse#16 · Opened Nov 14, 2018
Example of how to find a feature by gene_id or transcript_id Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

openvax/gtfparse#13 · Opened Jun 26, 2018

openvax/gtfparse

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