https://github.com/althonos/gb-io.py
A Python interface to gb-io, a fast GenBank parser written in Rust.
Science Score: 33.0%
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Low similarity (11.1%) to scientific vocabulary
Repository
A Python interface to gb-io, a fast GenBank parser written in Rust.
Basic Info
- Host: GitHub
- Owner: althonos
- License: mit
- Language: Python
- Default Branch: main
- Size: 2.68 MB
Statistics
- Stars: 19
- Watchers: 3
- Forks: 0
- Open Issues: 3
- Releases: 10
Metadata Files
README.md
🧬🏦 gb-io.py 
A Python interface to gb-io, a fast GenBank parser and serializer written in Rust.
🗺️ Overview
gb-io.py is a Python package that provides an interface to gb-io, a very
fast GenBank format parser implemented in Rust by David Leslie.
It can reach much higher speed than the Biopython or
the scikit-bio parsers.
This library has no external dependency and is available for all modern Python versions (3.7+).
To improve performance, the library implements a copy-on-access pattern,
so that data is only copied on the Python heap when it is actually being
accessed, rather than on object creation. For instance, if the consumer
of the parser only requires the GenBank features and not the record sequence,
the sequence will not be copied to a Python bytes object.
🔧 Installing
Install the gb-io package directly from PyPi
which hosts pre-compiled wheels that can be installed with pip:
console
$ pip install gb-io
Wheels are provided for common platforms, such as x86-64 Linux, Windows and MacOS, as well as Aarch64 Linux and MacOS. If no wheel is available, the source distribution will be downloaded, and a local copy of the Rust compiler will be downloaded to build the package, unless it is already installed on the host machine.
📖 Documentation
A complete API reference
can be found in the online documentation,
or directly from the command line using
pydoc:
console
$ pydoc gb_io
💡 Usage
Use the gb_io.load function to obtain a list of all GenBank records in a file:
python
records = gb_io.load("tests/data/AY048670.1.gb")
Reading from a file-like object is supported as well, both in text and
binary mode:
python
with open("tests/data/AY048670.1.gb") as file:
records = gb_io.load(file)
It is also possible to iterate over each record in the file without having
to load the entirety of the file contents to memory with the gb_io.iter
method, which returns an iterator instead of a list:
python
for record in gb_io.iter("tests/data/AY048670.1.gb"):
print(record.name, record.sequence[:10])
You can use the gb_io.dump method to write one or more records to a file
(either given as a path, or a file-like handle):
python
with open("tests/data/AY048670.1.gb", "wb") as file:
gb_io.dump(records, file)
📝 Example
The following small script will extract all the CDS features from a GenBank file, and write them in FASTA format to an output file: ```python import gb_io
with open("tests/data/AY048670.1.faa", "w") as dst: for record in gb_io.iter("tests/data/AY048670.1.gb"): for feature in filter(lambda feat: feat.kind == "CDS", record.features): qualifiers = {q.key:q.value for q in feature.qualifiers} dst.write(">{}\n".format(qualifiers["protein_id"][0])) dst.write("{}\n".format(qualifiers["translation"][0])) ```
Compared to similar implementations using Bio.SeqIO.parse, Bio.GenBank.parse
and Bio.GenBank.Scanner.GenBankScanner.parse_cds_features, the performance is
the following:
| | gb_io.iter | GenBankScanner | GenBank.parse | SeqIO.parse |
| ------------- | ------------- | ---------------- | --------------- | ------------- |
| Time (s) | 2.264 | 7.982 | 15.259 | 19.351 |
| Speed (MiB/s) | 136.5 | 37.1 | 20.5 | 16.2 |
| Speedup | x8.55 | x2.42 | x1.27 | - |
💭 Feedback
⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.
🏗️ Contributing
Contributions are more than welcome! See
CONTRIBUTING.md
for more details.
⚖️ License
This library is provided under the MIT License.
The gb-io Rust crate package was written by David Leslie
and is licensed under the terms of the MIT License.
This package vendors the source of several additional packages that are
licensed under the Apache-2.0,
MIT or
BSD-3-Clause licenses;
see the license file distributed with the source copy of each vendored
dependency for more information.
This project is in no way not affiliated, sponsored, or otherwise endorsed
by the original gb-io authors. It was developed
by Martin Larralde during his PhD project
at the European Molecular Biology Laboratory in
the Zeller team.
Owner
- Name: Martin Larralde
- Login: althonos
- Kind: user
- Location: Heidelberg, Germany
- Company: EMBL / LUMC, @zellerlab
- Twitter: althonos
- Repositories: 91
- Profile: https://github.com/althonos
PhD candidate in Bioinformatics, passionate about programming, SIMD-enthusiast, Pythonista, Rustacean. I write poems, and sometimes they are executable.
GitHub Events
Total
- Release event: 2
- Watch event: 6
- Delete event: 12
- Issue comment event: 14
- Push event: 23
- Pull request event: 23
- Create event: 10
Last Year
- Release event: 2
- Watch event: 6
- Delete event: 12
- Issue comment event: 14
- Push event: 23
- Pull request event: 23
- Create event: 10
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Martin Larralde | m****e@e****e | 128 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 5
- Total pull requests: 72
- Average time to close issues: 3 months
- Average time to close pull requests: 2 months
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 2.2
- Average comments per pull request: 1.33
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 72
Past Year
- Issues: 0
- Pull requests: 22
- Average time to close issues: N/A
- Average time to close pull requests: 14 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.73
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 22
Top Authors
Issue Authors
- xapple (2)
- nextgenusfs (2)
- camilogarciabotero (1)
Pull Request Authors
- dependabot[bot] (79)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 1,903 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 12
- Total maintainers: 1
pypi.org: gb-io
A Python interface to gb-io, a fast GenBank parser and serializer written in Rust.
- Homepage: https://github.com/althonos/gb-io.py/
- Documentation: https://gb-io.readthedocs.io/
- License: MIT
-
Latest release: 0.3.6
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
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