Library for converting between various bioinformatic accession types for genes, transcripts and proteins.
Project description
Accessive
Accessive is a Python library designed to facilitate the conversion between various bioinformatic accession types, streamlining the process of working with biological data identifiers across different databases and formats. Features
- Convert between a wide array of accession types.
- Support for major bioinformatics databases and identifier formats.
- Flexible query options with support for filtering by taxon.
Supported Accession Types
Accessive supports the following accession types:
- Ensembl
- Gene (ENSG00000096717)
- mRNA (ENST00000361390)
- Proteoform (ENSP00000354689)
- Uniprot
- Swissprot (P00750)
- TrEMBL (A0A024R161)
- Isoform (P00750-1)
- RefSeq
- mRNA (NM_001278)
- ncRNA (NR_001278)
- Proteoform (NP_001265)
- Nextprot
- Gene (NX_P00750)
- Proteoform (NX_P00750-1)
- Alphafold id (AF-B0QZ35-F1)
- ArrayExpress (E-GEOD-3307)
- BioGRID index
- CCDS (CCDS81469)
- EMBL (AK074805)
- Entrez Gene id
- GeneCards index
- HGNC (HGNC:142929)
- MIM_GENE index (601739)
- PDB (4IG9)
- Pfam (PF02146)
- UCSC (uc057tpn.1)
- UniParc (UPI000015D95A)
- WikiGene index
Installation
To install Accessive, use pip:
pip install accessive
After installation, install the database via the included utiltiy:
python -m accessive.database_ops --download
Note that the Accessive database requires approximately 500MB of disk space.
Usage Example
>>> from accessive import Accessive
>>> acc = Accessive()
>>> acc.map(ids=['SIRT1', 'UCP1', 'VGF'], to_types=['uniprot_swissprot', 'uniprot_trembl', 'refseq_mrna'], taxon = 9606)
uniprot_swissprot uniprot_trembl refseq_mrna
gene_name
SIRT1 None B0QZ35 None
SIRT1 None E9PC49 NM_001142498
SIRT1 Q96EB6 A0A024QZQ1 NM_012238
SIRT1 None B0QZ35 NM_001314049
VGF O15240 None None
VGF O15240 None NM_003378
UCP1 P25874 None NM_021833
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
accessive-0.1.0.tar.gz
(14.0 kB
view hashes)
Built Distribution
accessive-0.1.0-py3-none-any.whl
(16.0 kB
view hashes)
Close
Hashes for accessive-0.1.0-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f6ff400d61bf128845047d7801477a8c51e78118a117881c9504c4a7539092fb |
|
MD5 | 1d8266e6c1a5368fd8334aa672898a14 |
|
BLAKE2b-256 | 95ceab4a8fb7c019c4b81b831ad5738b982a6c7984ea97c43a8aae94b9482b6d |