| Name | uniprot-id-mapper JSON |
| Version |
1.1.4
JSON |
| download |
| home_page | None |
| Summary | A Python wrapper for the UniProt Mapping RESTful API. |
| upload_time | 2025-02-11 14:39:36 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.7 |
| license | MIT License
Copyright (c) 2023 David Araripe
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
|
| keywords |
uniprot
database
protein id
gene id
parser
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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[](https://pypi.org/project/uniprot-id-mapper/)
# UniProtMapper <img align="left" width="40" height="40" src="https://raw.githubusercontent.com/whitead/protein-emoji/main/src/protein-72-color.svg">
Easily retrieve UniProt data and map protein identifiers using this Python package for UniProt's Retrieve & ID Mapping RESTful APIs. [Read the full documentation](https://david-araripe.github.io/UniProtMapper/stable/index.html).
## 📚 Table of Contents
- [⛏️ Features](#️-features)
- [📦 Installation](#-installation)
- [🛠️ Usage](#️-usage)
- [Mapping IDs](#mapping-ids)
- [Retrieving Information](#retrieving-information)
- [Field-based Querying](#field-based-querying)
- [📖 Documentation](#-documentation)
- [💻 Command Line Interface (CLI)](#-command-line-interface-cli)
- [👏🏼 Credits](#-credits)
## ⛏️ Features
UniProtMapper is a tool for bioinformatics and proteomics research that supports:
1. Mapping any UniProt [cross-referenced IDs](https://github.com/David-Araripe/UniProtMapper/blob/master/src/UniProtMapper/resources/uniprot_mapping_dbs.json) to other identifiers & vice-versa;
2. Programmatically retrieving any of the supported [return](https://www.uniprot.org/help/return_fields) and [cross-reference fields](https://www.uniprot.org/help/return_fields_databases) from both UniProt-SwissProt and UniProt-TrEMBL (unreviewed) databases. For a full table containing all the supported resources, refer to the [supported fields](https://david-araripe.github.io/UniProtMapper/stable/field_reference.html#supported-fields) in the docs;
3. Querying UniProtKB entries using complex field-based queries with boolean operators `~` (NOT), `|` (OR), `&` (AND).
For the first two functionalities, check the examples [Mapping IDs](#mapping-ids) and [Retrieving Information](#retrieving-information) below. The third, see [Field-based Querying](#field-based-querying).
The ID mapping API can also be accessed through the CLI. For more information, check [CLI](#-command-line-interface-cli).
## 📦 Installation
### From PyPI (recommended):
```shell
python -m pip install uniprot-id-mapper
```
### Directly from GitHub:
```shell
python -m pip install git+https://github.com/David-Araripe/UniProtMapper.git
```
### From source:
```shell
git clone https://github.com/David-Araripe/UniProtMapper
cd UniProtMapper
python -m pip install .
```
# 🛠️ Usage
## Mapping IDs
Use UniProtMapper to easily map between different protein identifiers:
``` python
from UniProtMapper import ProtMapper
mapper = ProtMapper()
result, failed = mapper.get(
ids=["P30542", "Q16678", "Q02880"], from_db="UniProtKB_AC-ID", to_db="Ensembl"
)
```
The `result` is a pandas DataFrame containing the mapped IDs (see below), while `failed` is a list of identifiers that couldn't be mapped.
| | UniProtKB_AC-ID | Ensembl |
|---:|:------------------|:-------------------|
| 0 | P30542 | ENSG00000163485.17 |
| 1 | Q16678 | ENSG00000138061.12 |
| 2 | Q02880 | ENSG00000077097.17 |
## Retrieving Information
A DataFrame with the [supported return fields](https://david-araripe.github.io/UniProtMapper/stable/field_reference.html#supported-fields) is accessible through the attribute `ProtMapper.fields_table`:
```Python
from UniProtMapper import ProtMapper
mapper = ProtMapper()
df = mapper.fields_table
df.head()
```
| | label | returned_field | field_type | has_full_version | type |
|---:|:---------------------|:-----------------|:-----------------|:-------------------|:--------------|
| 0 | Entry | accession | Names & Taxonomy | - | uniprot_field |
| 1 | Entry Name | id | Names & Taxonomy | - | uniprot_field |
| 2 | Gene Names | gene_names | Names & Taxonomy | - | uniprot_field |
| 3 | Gene Names (primary) | gene_primary | Names & Taxonomy | - | uniprot_field |
| 4 | Gene Names (synonym) | gene_synonym | Names & Taxonomy | - | uniprot_field |
From the DataFrame, all `return_field` entries can be used to access UniProt data programmatically:
```Python
# To retrieve the default fields:
result, failed = mapper.get(["Q02880"])
>>> Fetched: 1 / 1
# Retrieve custom fields:
fields = ["accession", "organism_name", "structure_3d"]
result, failed = mapper.get(["Q02880"], fields=fields)
>>> Fetched: 1 / 1
```
Further, for the cross-referenced fields that have `has_full_version` set to `yes`, returning the same field with extra information is supported by passing `<field_name>_full`, such as `xref_pdb_full`.
All available return fields are also accessible through the attribute `ProtMapper.supported_return_fields`:
```python
from UniProtMapper import ProtMapper
mapper = ProtMapper()
print(mapper.supported_return_fields)
>>> ['accession',
>>> 'id',
>>> 'gene_names',
>>> ...
>>> 'xref_smart_full',
>>> 'xref_supfam_full']
```
## Field-based Querying
UniProtMapper supports complex field-based protein queries using boolean operators (AND, OR, NOT) through the `uniprotkb_fields` module. This allows you to create sophisticated searches combining multiple criteria. For example:
```python
from UniProtMapper import ProtKB
from UniProtMapper.uniprotkb_fields import (
organism_name,
length,
reviewed,
date_modified
)
# Find reviewed human proteins with length between 100-200 amino acids
# that were modified after January 1st, 2024
query = (
organism_name("human") &
reviewed(True) &
length(100, 200) &
date_modified("2024-01-01", "*")
)
protkb = ProtKB()
result = protkb.get(query)
```
For a list of all fields and their descriptions, check the API reference for the [uniprotkb_fields](https://david-araripe.github.io/UniProtMapper/stable/api/UniProtMapper.html#module-UniProtMapper.uniprotkb_fields) module reference.
## 📖 Documentation
- [Stable Branch Documentation](https://david-araripe.github.io/UniProtMapper/stable/index.html) (master branch)
- [Development Documentation](https://david-araripe.github.io/UniProtMapper/dev/index.html) (dev branch)
# 💻 Command Line Interface (CLI)
UniProtMapper provides a CLI for the ID Mapping class, `ProtMapper`, for easy access to lookups and data retrieval. Here is a list of the available arguments, shown by `protmap -h`:
```text
usage: UniProtMapper [-h] -i [IDS ...] [-r [RETURN_FIELDS ...]] [--default-fields] [-o OUTPUT]
[-from FROM_DB] [-to TO_DB] [-over] [-pf]
Retrieve data from UniProt using UniProt's RESTful API. For a list of all available fields, see: https://www.uniprot.org/help/return_fields
Alternatively, use the --print-fields argument to print the available fields and exit the program.
optional arguments:
-h, --help show this help message and exit
-i [IDS ...], --ids [IDS ...]
List of UniProt IDs to retrieve information from. Values must be
separated by spaces.
-r [RETURN_FIELDS ...], --return-fields [RETURN_FIELDS ...]
If not defined, will pass `None`, returning all available fields.
Else, values should be fields to be returned separated by spaces. See
--print-fields for available options.
--default-fields, -def
This option will override the --return-fields option. Returns only the
default fields stored in: <pkg_path>/resources/cli_return_fields.txt
-o OUTPUT, --output OUTPUT
Path to the output file to write the returned fields. If not provided,
will write to stdout.
-from FROM_DB, --from-db FROM_DB
The database from which the IDs are. For the available cross
references, see: <pkg_path>/resources/uniprot_mapping_dbs.json
-to TO_DB, --to-db TO_DB
The database to which the IDs will be mapped. For the available cross
references, see: <pkg_path>/resources/uniprot_mapping_dbs.json
-over, --overwrite If desired to overwrite an existing file when using -o/--output
-pf, --print-fields Prints the available return fields and exits the program.
```
Usage example, retrieving default fields from `<pkg_path>/resources/cli_return_fields.txt`:
<p align="center">
<img src="https://github.com/David-Araripe/UniProtMapper/blob/master/figures/cli_example_fig.png?raw=true" alt="Image displaying the output of UniProtMapper's CLI, protmap"/>
</p>
## 👏🏼 Credits
- [UniProt](https://www.uniprot.org/) for providing the API and the amazing database;
- [Andrew White and the University of Rochester](https://github.com/whitead/protein-emoji) for the protein emoji;
---
For issues, feature requests, or questions, please open an issue on the GitHub repository.
Raw data
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"description": "[](https://opensource.org/licenses/MIT)\n[](https://github.com/astral-sh/ruff)\n[](https://github.com/psf/black)\n[](https://pycqa.github.io/isort/)\n[](https://actions-badge.atrox.dev/David-Araripe/UniProtMapper/goto?ref=master)\n[](https://pypi.org/project/uniprot-id-mapper/)\n\n# UniProtMapper <img align=\"left\" width=\"40\" height=\"40\" src=\"https://raw.githubusercontent.com/whitead/protein-emoji/main/src/protein-72-color.svg\">\n\nEasily retrieve UniProt data and map protein identifiers using this Python package for UniProt's Retrieve & ID Mapping RESTful APIs. [Read the full documentation](https://david-araripe.github.io/UniProtMapper/stable/index.html).\n\n## \ud83d\udcda Table of Contents\n\n- [\u26cf\ufe0f Features](#\ufe0f-features)\n- [\ud83d\udce6 Installation](#-installation)\n- [\ud83d\udee0\ufe0f Usage](#\ufe0f-usage)\n - [Mapping IDs](#mapping-ids)\n - [Retrieving Information](#retrieving-information)\n - [Field-based Querying](#field-based-querying)\n- [\ud83d\udcd6 Documentation](#-documentation)\n- [\ud83d\udcbb Command Line Interface (CLI)](#-command-line-interface-cli)\n- [\ud83d\udc4f\ud83c\udffc Credits](#-credits)\n\n## \u26cf\ufe0f Features\nUniProtMapper is a tool for bioinformatics and proteomics research that supports:\n\n1. Mapping any UniProt [cross-referenced IDs](https://github.com/David-Araripe/UniProtMapper/blob/master/src/UniProtMapper/resources/uniprot_mapping_dbs.json) to other identifiers & vice-versa;\n2. Programmatically retrieving any of the supported [return](https://www.uniprot.org/help/return_fields) and [cross-reference fields](https://www.uniprot.org/help/return_fields_databases) from both UniProt-SwissProt and UniProt-TrEMBL (unreviewed) databases. For a full table containing all the supported resources, refer to the [supported fields](https://david-araripe.github.io/UniProtMapper/stable/field_reference.html#supported-fields) in the docs;\n3. Querying UniProtKB entries using complex field-based queries with boolean operators `~` (NOT), `|` (OR), `&` (AND).\n\nFor the first two functionalities, check the examples [Mapping IDs](#mapping-ids) and [Retrieving Information](#retrieving-information) below. The third, see [Field-based Querying](#field-based-querying). \n\nThe ID mapping API can also be accessed through the CLI. For more information, check [CLI](#-command-line-interface-cli).\n\n## \ud83d\udce6 Installation\n\n### From PyPI (recommended):\n```shell\npython -m pip install uniprot-id-mapper\n```\n\n### Directly from GitHub:\n```shell\npython -m pip install git+https://github.com/David-Araripe/UniProtMapper.git\n```\n\n### From source:\n```shell\ngit clone https://github.com/David-Araripe/UniProtMapper\ncd UniProtMapper\npython -m pip install .\n```\n\n# \ud83d\udee0\ufe0f Usage\n\n## Mapping IDs\nUse UniProtMapper to easily map between different protein identifiers:\n\n``` python\nfrom UniProtMapper import ProtMapper\n\nmapper = ProtMapper()\n\nresult, failed = mapper.get(\n ids=[\"P30542\", \"Q16678\", \"Q02880\"], from_db=\"UniProtKB_AC-ID\", to_db=\"Ensembl\"\n)\n```\nThe `result` is a pandas DataFrame containing the mapped IDs (see below), while `failed` is a list of identifiers that couldn't be mapped.\n\n| | UniProtKB_AC-ID | Ensembl |\n|---:|:------------------|:-------------------|\n| 0 | P30542 | ENSG00000163485.17 |\n| 1 | Q16678 | ENSG00000138061.12 |\n| 2 | Q02880 | ENSG00000077097.17 |\n\n## Retrieving Information\n\nA DataFrame with the [supported return fields](https://david-araripe.github.io/UniProtMapper/stable/field_reference.html#supported-fields) is accessible through the attribute `ProtMapper.fields_table`:\n\n```Python\nfrom UniProtMapper import ProtMapper\n\nmapper = ProtMapper()\ndf = mapper.fields_table\ndf.head()\n```\n| | label | returned_field | field_type | has_full_version | type |\n|---:|:---------------------|:-----------------|:-----------------|:-------------------|:--------------|\n| 0 | Entry | accession | Names & Taxonomy | - | uniprot_field |\n| 1 | Entry Name | id | Names & Taxonomy | - | uniprot_field |\n| 2 | Gene Names | gene_names | Names & Taxonomy | - | uniprot_field |\n| 3 | Gene Names (primary) | gene_primary | Names & Taxonomy | - | uniprot_field |\n| 4 | Gene Names (synonym) | gene_synonym | Names & Taxonomy | - | uniprot_field |\n\nFrom the DataFrame, all `return_field` entries can be used to access UniProt data programmatically:\n\n```Python\n# To retrieve the default fields:\nresult, failed = mapper.get([\"Q02880\"])\n>>> Fetched: 1 / 1\n\n# Retrieve custom fields:\nfields = [\"accession\", \"organism_name\", \"structure_3d\"]\nresult, failed = mapper.get([\"Q02880\"], fields=fields)\n>>> Fetched: 1 / 1\n```\n\nFurther, for the cross-referenced fields that have `has_full_version` set to `yes`, returning the same field with extra information is supported by passing `<field_name>_full`, such as `xref_pdb_full`.\n\nAll available return fields are also accessible through the attribute `ProtMapper.supported_return_fields`:\n\n```python\nfrom UniProtMapper import ProtMapper\nmapper = ProtMapper()\nprint(mapper.supported_return_fields)\n\n>>> ['accession',\n>>> 'id',\n>>> 'gene_names',\n>>> ...\n>>> 'xref_smart_full',\n>>> 'xref_supfam_full']\n```\n\n## Field-based Querying\n\nUniProtMapper supports complex field-based protein queries using boolean operators (AND, OR, NOT) through the `uniprotkb_fields` module. This allows you to create sophisticated searches combining multiple criteria. For example:\n\n```python\nfrom UniProtMapper import ProtKB\nfrom UniProtMapper.uniprotkb_fields import (\n organism_name, \n length, \n reviewed, \n date_modified\n)\n\n# Find reviewed human proteins with length between 100-200 amino acids\n# that were modified after January 1st, 2024\nquery = (\n organism_name(\"human\") & \n reviewed(True) & \n length(100, 200) & \n date_modified(\"2024-01-01\", \"*\")\n)\n\nprotkb = ProtKB()\nresult = protkb.get(query)\n```\nFor a list of all fields and their descriptions, check the API reference for the [uniprotkb_fields](https://david-araripe.github.io/UniProtMapper/stable/api/UniProtMapper.html#module-UniProtMapper.uniprotkb_fields) module reference.\n\n## \ud83d\udcd6 Documentation\n\n- [Stable Branch Documentation](https://david-araripe.github.io/UniProtMapper/stable/index.html) (master branch)\n- [Development Documentation](https://david-araripe.github.io/UniProtMapper/dev/index.html) (dev branch)\n\n# \ud83d\udcbb Command Line Interface (CLI)\n\nUniProtMapper provides a CLI for the ID Mapping class, `ProtMapper`, for easy access to lookups and data retrieval. Here is a list of the available arguments, shown by `protmap -h`:\n\n```text\nusage: UniProtMapper [-h] -i [IDS ...] [-r [RETURN_FIELDS ...]] [--default-fields] [-o OUTPUT]\n [-from FROM_DB] [-to TO_DB] [-over] [-pf]\n\nRetrieve data from UniProt using UniProt's RESTful API. For a list of all available fields, see: https://www.uniprot.org/help/return_fields \n\nAlternatively, use the --print-fields argument to print the available fields and exit the program.\n\noptional arguments:\n -h, --help show this help message and exit\n -i [IDS ...], --ids [IDS ...]\n List of UniProt IDs to retrieve information from. Values must be\n separated by spaces.\n -r [RETURN_FIELDS ...], --return-fields [RETURN_FIELDS ...]\n If not defined, will pass `None`, returning all available fields.\n Else, values should be fields to be returned separated by spaces. See\n --print-fields for available options.\n --default-fields, -def\n This option will override the --return-fields option. Returns only the\n default fields stored in: <pkg_path>/resources/cli_return_fields.txt\n -o OUTPUT, --output OUTPUT\n Path to the output file to write the returned fields. If not provided,\n will write to stdout.\n -from FROM_DB, --from-db FROM_DB\n The database from which the IDs are. For the available cross\n references, see: <pkg_path>/resources/uniprot_mapping_dbs.json\n -to TO_DB, --to-db TO_DB\n The database to which the IDs will be mapped. For the available cross\n references, see: <pkg_path>/resources/uniprot_mapping_dbs.json\n -over, --overwrite If desired to overwrite an existing file when using -o/--output\n -pf, --print-fields Prints the available return fields and exits the program.\n```\n\nUsage example, retrieving default fields from `<pkg_path>/resources/cli_return_fields.txt`:\n<p align=\"center\">\n <img src=\"https://github.com/David-Araripe/UniProtMapper/blob/master/figures/cli_example_fig.png?raw=true\" alt=\"Image displaying the output of UniProtMapper's CLI, protmap\"/>\n</p>\n\n## \ud83d\udc4f\ud83c\udffc Credits\n\n- [UniProt](https://www.uniprot.org/) for providing the API and the amazing database;\n- [Andrew White and the University of Rochester](https://github.com/whitead/protein-emoji) for the protein emoji;\n\n---\n\nFor issues, feature requests, or questions, please open an issue on the GitHub repository.\n",
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