biodata-parsers
| Crates.io | biodata-parsers |
| lib.rs | biodata-parsers |
| version | 0.1.0 |
| created_at | 2017-01-15 01:56:35.198014+00 |
| updated_at | 2017-01-15 01:56:35.198014+00 |
| description | Scripts for parsing UniParc XML files downloaded from the Uniprot website into CSV files. |
| homepage | https://ostrokach.github.io/uniparc_xml_parser |
| repository | https://github.com/ostrokach/uniparc_xml_parser |
| max_upload_size | |
| id | 8074 |
| size | 45,016 |
Alexey Strokach (ostrokach)
documentation
https://ostrokach.github.io/uniparc_xml_parser
README
UniParc XML parser
Process the UniParc XML file (uniparc_all.xml.gz) downloaded from the UniProt website into CSV files that can be loaded into a relational database.
Example
Parsing 1 million lines takes about 5.5 seconds:
$ mkdir uniparc
$ time bash -c "zcat tests/uniparc_1mil.xml.gz | uniparc_xml_parser >/dev/null"
real 0m5.564s
user 0m5.528s
sys 0m0.132s
The actual uniparc_all.xml.gz file is about 5 billion rows.