# 🧬🏦 `gb-io.py` [](https://github.com/althonos/gb-io.py/stargazers)
*A Python interface to [`gb-io`], a fast [GenBank] parser and serializer written in [Rust].*
[`gb-io`]: https://crates.io/crates/gb-io
[GenBank]: https://www.ncbi.nlm.nih.gov/genbank/
[Rust]: https://www.rust-lang.org/
[](https://github.com/althonos/gb-io.py/actions)
[](https://codecov.io/gh/althonos/gb-io.py/)
[](https://choosealicense.com/licenses/mit/)
[](https://pypi.org/project/gb-io)
[](https://anaconda.org/bioconda/gb-io)
[](https://aur.archlinux.org/packages/python-gb-io)
[](https://pypi.org/project/gb-io/#files)
[](https://pypi.org/project/gb-io/#files)
[](https://pypi.org/project/gb-io/#files)
[](https://github.com/althonos/gb-io.py/)
[](https://git.embl.de/larralde/gb-io.py/)
[](https://github.com/althonos/gb-io.py/issues)
[](https://github.com/althonos/gb-io.py/blob/master/CHANGELOG.md)
[](https://pepy.tech/project/gb-io)
[](https://gb-io.readthedocs.io)
## 🗺️ Overview
`gb-io.py` is a Python package that provides an interface to `gb-io`, a very
fast GenBank format parser implemented in Rust. It can reach much higher
speed than the [Biopython](http://biopython.org/) or
the [scikit-bio](http://scikit-bio.org/) 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](https://pypi.org/project/gb-io)
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](https://gb-io.readthedocs.io/en/stable/api.html)
can be found in the [online documentation](https://gb-io.readthedocs.io/),
or directly from the command line using
[`pydoc`](https://docs.python.org/3/library/pydoc.html):
```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.type == "CDS", record.features):
qualifiers = feature.qualifiers.to_dict()
dst.write(">{}\n".format(qualifiers["locus_tag"][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](https://github.com/althonos/gb-io.py/issues) 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`](https://github.com/althonos/gb-io.py/blob/main/CONTRIBUTING.md)
for more details.
## ⚖️ License
This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).
The `gb-io` Rust crate package was written by [David Leslie](https://github.com/dlesl)
and is licensed under the terms of the [MIT License](https://choosealicense.com/licenses/mit/).
This package vendors the source of several additional packages that are
licensed under the [Apache-2.0](https://choosealicense.com/licenses/apache-2.0/),
[MIT](https://choosealicense.com/licenses/mit/) or
[BSD-3-Clause](https://choosealicense.com/licenses/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](https://github.com/dlesl). It was developed
by [Martin Larralde](https://github.com/althonos/) during his PhD project
at the [European Molecular Biology Laboratory](https://www.embl.de/) in
the [Zeller team](https://github.com/zellerlab).*
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"description": "# \ud83e\uddec\ud83c\udfe6 `gb-io.py` [](https://github.com/althonos/gb-io.py/stargazers)\n\n*A Python interface to [`gb-io`], a fast [GenBank] parser and serializer written in [Rust].*\n\n[`gb-io`]: https://crates.io/crates/gb-io\n[GenBank]: https://www.ncbi.nlm.nih.gov/genbank/\n[Rust]: https://www.rust-lang.org/\n\n[](https://github.com/althonos/gb-io.py/actions)\n[](https://codecov.io/gh/althonos/gb-io.py/)\n[](https://choosealicense.com/licenses/mit/)\n[](https://pypi.org/project/gb-io)\n[](https://anaconda.org/bioconda/gb-io)\n[](https://aur.archlinux.org/packages/python-gb-io)\n[](https://pypi.org/project/gb-io/#files)\n[](https://pypi.org/project/gb-io/#files)\n[](https://pypi.org/project/gb-io/#files)\n[](https://github.com/althonos/gb-io.py/)\n[](https://git.embl.de/larralde/gb-io.py/)\n[](https://github.com/althonos/gb-io.py/issues)\n[](https://github.com/althonos/gb-io.py/blob/master/CHANGELOG.md)\n[](https://pepy.tech/project/gb-io)\n[](https://gb-io.readthedocs.io)\n\n## \ud83d\uddfa\ufe0f Overview\n\n`gb-io.py` is a Python package that provides an interface to `gb-io`, a very\nfast GenBank format parser implemented in Rust. It can reach much higher\nspeed than the [Biopython](http://biopython.org/) or\nthe [scikit-bio](http://scikit-bio.org/) parsers.\n\nThis library has no external dependency and is available for all modern Python\nversions (3.7+).\n\nTo improve performance, the library implements a *copy-on-access* pattern, \nso that data is only copied on the Python heap when it is actually being \naccessed, rather than on object creation. For instance, if the consumer\nof the parser only requires the GenBank features and not the record sequence,\nthe sequence will not be copied to a Python `bytes` object.\n\n## \ud83d\udd27 Installing\n\nInstall the `gb-io` package directly from [PyPi](https://pypi.org/project/gb-io)\nwhich hosts pre-compiled wheels that can be installed with `pip`:\n```console\n$ pip install gb-io\n```\n\nWheels are provided for common platforms, such as x86-64 Linux, Windows and \nMacOS, as well as Aarch64 Linux and MacOS. If no wheel is available, the source \ndistribution will be downloaded, and a local copy of the Rust compiler will be \ndownloaded to build the package, unless it is already installed on the host machine.\n\n## \ud83d\udcd6 Documentation\n\nA complete [API reference](https://gb-io.readthedocs.io/en/stable/api.html)\ncan be found in the [online documentation](https://gb-io.readthedocs.io/),\nor directly from the command line using\n[`pydoc`](https://docs.python.org/3/library/pydoc.html):\n```console\n$ pydoc gb_io\n```\n\n## \ud83d\udca1 Usage\n\nUse the `gb_io.load` function to obtain a list of all GenBank records in a file:\n```python\nrecords = gb_io.load(\"tests/data/AY048670.1.gb\")\n```\n\nReading from a file-like object is supported as well, both in text and\nbinary mode:\n```python\nwith open(\"tests/data/AY048670.1.gb\") as file:\n records = gb_io.load(file)\n```\n\nIt is also possible to iterate over each record in the file without having\nto load the entirety of the file contents to memory with the `gb_io.iter`\nmethod, which returns an iterator instead of a list:\n```python\nfor record in gb_io.iter(\"tests/data/AY048670.1.gb\"):\n print(record.name, record.sequence[:10])\n```\n\nYou can use the `gb_io.dump` method to write one or more records to a file\n(either given as a path, or a file-like handle):\n```python\nwith open(\"tests/data/AY048670.1.gb\", \"wb\") as file:\n gb_io.dump(records, file)\n```\n\n## \ud83d\udcdd Example\n\nThe following small script will extract all the CDS features from a GenBank\nfile, and write them in FASTA format to an output file:\n```python\nimport gb_io\n\nwith open(\"tests/data/AY048670.1.faa\", \"w\") as dst:\n for record in gb_io.iter(\"tests/data/AY048670.1.gb\"):\n for feature in filter(lambda feat: feat.type == \"CDS\", record.features):\n qualifiers = feature.qualifiers.to_dict()\n dst.write(\">{}\\n\".format(qualifiers[\"locus_tag\"][0]))\n dst.write(\"{}\\n\".format(qualifiers[\"translation\"][0]))\n```\n\nCompared to similar implementations using `Bio.SeqIO.parse`, `Bio.GenBank.parse`\nand `Bio.GenBank.Scanner.GenBankScanner.parse_cds_features`, the performance is\nthe following:\n\n| | `gb_io.iter` | `GenBankScanner` | `GenBank.parse` | `SeqIO.parse` |\n| ------------- | ------------- | ---------------- | --------------- | ------------- |\n| Time (s) | **2.264** | 7.982 | 15.259 | 19.351 |\n| Speed (MiB/s) | **136.5** | 37.1 | 20.5 | 16.2 |\n| Speedup | **x8.55** | x2.42 | x1.27 | - |\n\n\n\n## \ud83d\udcad Feedback\n\n### \u26a0\ufe0f Issue Tracker\n\nFound a bug ? Have an enhancement request ? Head over to the [GitHub issue\ntracker](https://github.com/althonos/gb-io.py/issues) if you need to report\nor ask something. If you are filing in on a bug, please include as much\ninformation as you can about the issue, and try to recreate the same bug\nin a simple, easily reproducible situation.\n\n### \ud83c\udfd7\ufe0f Contributing\n\nContributions are more than welcome! See\n[`CONTRIBUTING.md`](https://github.com/althonos/gb-io.py/blob/main/CONTRIBUTING.md)\nfor more details.\n\n## \u2696\ufe0f License\n\nThis library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).\nThe `gb-io` Rust crate package was written by [David Leslie](https://github.com/dlesl)\nand is licensed under the terms of the [MIT License](https://choosealicense.com/licenses/mit/).\nThis package vendors the source of several additional packages that are\nlicensed under the [Apache-2.0](https://choosealicense.com/licenses/apache-2.0/),\n[MIT](https://choosealicense.com/licenses/mit/) or\n[BSD-3-Clause](https://choosealicense.com/licenses/bsd-3-clause/) licenses;\nsee the license file distributed with the source copy of each vendored\ndependency for more information.\n\n*This project is in no way not affiliated, sponsored, or otherwise endorsed\nby the [original `gb-io` authors](https://github.com/dlesl). It was developed\nby [Martin Larralde](https://github.com/althonos/) during his PhD project\nat the [European Molecular Biology Laboratory](https://www.embl.de/) in\nthe [Zeller team](https://github.com/zellerlab).*\n",
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