pfam2go
The pfam2go package provides a short and simple interface to match the Pfam accesion numbres to Gene Ontology annotation data.
The Pfam - Go term mapping was taken from:
http://current.geneontology.org/ontology/external2go/pfam2go
Mitchell et al. (2015) Nucl. Acids Res. 43 :D213-D221
The Go term information is taken from QuickGO:
Installation
pfam2go can be installed via pip:
pip install pfam2go
Usage
pfam2go(pfam_seqs: Union[Iterable[str], str]) -> pd.DataFrame
Input:
pfam_seqs: string or an Iterable object containing strings (e.g., list or pd.Series).
Returns:
pd.Dataframe containing GO terms for all corresponding Pfam numbers. Dataframe contains 5 string fields:
- Pfam accession number
- GO accession number
- GO name
- GO definition
- GO functional aspect
One Pfam number can correspond to several GO terms.
In case the information about a specific GO term has not been found in QuickGO the last 3 columns will be assigned to NaN.
Example
from pfam2go import pfam2go
pfam_list = ['PF00032', 'PF00049', 'PF08463']
data = pfam2go(pfam_list)
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Metadata
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Release files for pfam2go 1.1.2
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| File | Size | Uploaded | Provenance | Actions |
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| pfam2go-1.1.2-py2.py3-none-any.whl | Python 3, Python 2 | none | any | Details for pfam2go-1.1.2-py2.py3-none-any.whl |
Total release size: 8.5 kB
Release files / pfam2go-1.1.2.tar.gz
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