accessive 0.1.0

Library for converting between various bioinformatic accession types for genes, transcripts and proteins.

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