Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/ostrokach/uniparc_xml_parser
UniParc dataset describing ~300 million protein sequences converted into relational tables accessible through Google BigQuery (and as Parquet files).
https://github.com/ostrokach/uniparc_xml_parser
bigquery bioinformatics csv-files parquet-files protein-domains protein-sequences
Last synced: 4 days ago
JSON representation
UniParc dataset describing ~300 million protein sequences converted into relational tables accessible through Google BigQuery (and as Parquet files).
- Host: GitHub
- URL: https://github.com/ostrokach/uniparc_xml_parser
- Owner: ostrokach
- License: apache-2.0
- Created: 2021-02-09T20:15:39.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2021-10-29T21:55:36.000Z (almost 3 years ago)
- Last Synced: 2024-04-27T11:07:25.773Z (5 months ago)
- Topics: bigquery, bioinformatics, csv-files, parquet-files, protein-domains, protein-sequences
- Language: Rust
- Homepage: https://gitlab.com/ostrokach/uniparc_xml_parser
- Size: 31.1 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# UniParc XML parser
[](https://gitlab.com/ostrokach/uniparc_xml_parser)
[](https://ostrokach.gitlab.io/uniparc_xml_parser/v0.2.1/)
[](https://crates.io/crates/uniparc_xml_parser/)
[](https://anaconda.org/ostrokach-forge/uniparc_xml_parser/)
[](https://gitlab.com/ostrokach/uniparc_xml_parser/commits/v0.2.1/)
- [Introduction](#introduction)
- [Usage](#usage)
- [Table schema](#table-schema)
- [Installation](#installation)
- [Binaries](#binaries)
- [Cargo](#cargo)
- [Conda](#conda)
- [Output files](#output-files)
- [Parquet](#parquet)
- [Google BigQuery](#google-bigquery)
- [Benchmarks](#benchmarks)
- [Example SQL queries](#example-sql-queries)
- [Find and extract all Gene3D domain sequences](#find-and-extract-all-gene3d-domain-sequences)
- [Find and extract all _unique_ Gene3D domain sequences](#find-and-extract-all-unique-gene3d-domain-sequences)
- [Map Ensembl identifiers to UniProt](#map-ensembl-identifiers-to-uniprot)
- [Find crystal structures of all GPCRs](#find-crystal-structures-of-all-gpcrs)
- [FAQ (Frequently Asked Questions)](#faq-frequently-asked-questions)
- [Roadmap](#roadmap)
## Introduction
`uniparc_xml_parser` is a small utility which can process the UniParc XML file (`uniparc_all.xml.gz`), available from the UniProt [website](http://www.uniprot.org/downloads), into a set of CSV files that can be loaded into a relational database.
We also provide Parquet files, which can be queried using tools such as AWS Athena and Apache Presto, and have uploaded the generated data to Google BigQuery (see: [Output files](#output-files)).
## Usage
Uncompressed XML data can be piped into `uniparc_xml_parser` in order to parse the data into a set of CSV files on the fly:
```bash
$ curl -sS ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/uniparc/uniparc_all.xml.gz \
| zcat \
| uniparc_xml_parser
```
The output is a set of CSV (or more specifically TSV) files:
```bash
$ ls
-rw-r--r-- 1 user group 174G Feb 9 13:52 xref.tsv
-rw-r--r-- 1 user group 149G Feb 9 13:52 domain.tsv
-rw-r--r-- 1 user group 138G Feb 9 13:52 uniparc.tsv
-rw-r--r-- 1 user group 107G Feb 9 13:52 protein_name.tsv
-rw-r--r-- 1 user group 99G Feb 9 13:52 ncbi_taxonomy_id.tsv
-rw-r--r-- 1 user group 74G Feb 9 20:13 uniparc.parquet
-rw-r--r-- 1 user group 64G Feb 9 13:52 gene_name.tsv
-rw-r--r-- 1 user group 39G Feb 9 13:52 component.tsv
-rw-r--r-- 1 user group 32G Feb 9 13:52 proteome_id.tsv
-rw-r--r-- 1 user group 15G Feb 9 13:52 ncbi_gi.tsv
-rw-r--r-- 1 user group 21M Feb 9 13:52 pdb_chain.tsv
-rw-r--r-- 1 user group 12M Feb 9 13:52 uniprot_kb_accession.tsv
-rw-r--r-- 1 user group 656K Feb 9 04:04 uniprot_kb_accession.parquet
```
## Table schema
The generated CSV files conform to the following schema:
## Installation
### Binaries
Linux binaries are available here: https://gitlab.com/ostrokach/uniparc_xml_parser/-/packages.
### Cargo
Use [`cargo`](https://crates.io/) to compile and install `uniparc_xml_parser` for your target platform:
```bash
cargo install uniparc_xml_parser
```
### Conda
Use [`conda`](https://docs.conda.io/en/latest/miniconda.html) to install precompiled binaries:
```bash
conda install -c ostrokach-forge uniparc_xml_parser
```
## Output files
### Parquet
Parquet files containing the processed data are available at the following URL and are updated monthly: .
### Google BigQuery
The latest data can also be queried directly using Google BigQuery: .
## Benchmarks
Parsing 10,000 XML entires takes around 30 seconds (the process is mostly IO-bound):
```bash
$ time bash -c "zcat uniparc_top_10k.xml.gz | uniparc_xml_parser >/dev/null"
real 0m33.925s
user 0m36.800s
sys 0m1.892s
```
The actual `uniparc_all.xml.gz` file has around 373,914,570 elements.
## Example SQL queries
### Find and extract all Gene3D domain sequences
```sql
SELECT
uniparc_id,
database_id AS gene3d_id,
interpro_name,
interpro_id,
domain_start,
domain_end,
SUBSTR(sequence, domain_start, domain_end - domain_start + 1) AS domain_sequence
FROM `ostrokach-data.uniparc.uniparc` u
JOIN `ostrokach-data.uniparc.domain` d
USING (uniparc_id)
WHERE d.database = 'Gene3D';
```
BigQuery: .
### Find and extract all _unique_ Gene3D domain sequences
```sql
SELECT
ARRAY_AGG(uniparc_id ORDER BY uniparc_id, domain_start, domain_end) uniparc_id,
ARRAY_AGG(gene3d_id ORDER BY uniparc_id, domain_start, domain_end) gene3d_id,
ARRAY_AGG(interpro_name ORDER BY uniparc_id, domain_start, domain_end) interpro_name,
ARRAY_AGG(interpro_id ORDER BY uniparc_id, domain_start, domain_end) interpro_id,
ARRAY_AGG(domain_start ORDER BY uniparc_id, domain_start, domain_end) domain_start,
ARRAY_AGG(domain_end ORDER BY uniparc_id, domain_start, domain_end) domain_end,
domain_sequence
FROM (
SELECT
uniparc_id,
database_id AS gene3d_id,
interpro_name,
interpro_id,
domain_start,
domain_end,
SUBSTR(sequence, domain_start, domain_end - domain_start + 1) AS domain_sequence
FROM `ostrokach-data.uniparc.uniparc` u
JOIN `ostrokach-data.uniparc.domain` d
USING (uniparc_id)
WHERE d.database = 'Gene3D') t
GROUP BY
domain_sequence;
```
BigQuery: .
### Map Ensembl identifiers to UniProt
Find UniProt indentifiers for Ensembl transcript identifiers corresponding to the same sequence:
```sql
SELECT
ensembl.db_id ensembl_id,
uniprot.db_id uniprot_id
FROM (
SELECT uniparc_id, db_id
FROM `ostrokach-data.uniparc.xref`
WHERE db_type = 'Ensembl') ensembl
JOIN (
SELECT uniparc_id, db_id
FROM `ostrokach-data.uniparc.xref`
WHERE db_type = 'UniProtKB/Swiss-Prot') uniprot
USING (uniparc_id);
```
BigQuery: .
### Find crystal structures of all GPCRs
```sql
SELECT
uniparc_id,
SUBSTR(p.value, 1, 4) pdb_id,
SUBSTR(p.value, 5) pdb_chain,
d.database_id pfam_id,
d.domain_start,
d.domain_end,
u.sequence pdb_chain_sequence
FROM `ostrokach-data.uniparc.uniparc` u
JOIN `ostrokach-data.uniparc.domain` d USING (uniparc_id)
JOIN `ostrokach-data.uniparc.pdb_chain` p USING (uniparc_id)
WHERE d.database = 'Pfam'
AND d.database_id = 'PF00001';
```
BigQuery: .
## FAQ (Frequently Asked Questions)
**Why not split `uniparc_all.xml.gz` into multiple small files and process them in parallel?**
- Splitting the file requires reading the entire file. If we're reading the entire file anyway, why not parse it as we read it?
- Having a single process which parses `uniparc_all.xml.gz` makes it easier to create an incremental unique index column (e.g. `xref.xref_id`).
## Roadmap
- [ ] Add support for writing Apache Parquet files directly.
- [ ] Add support for writing output to object stores (such as S3 and GCS).
- [ ] Avoid decoding the input into strings (keep everything as bytes throughout).