pfam2go 1.1.2

A package to match Pfam accession numbers to corresponding GO terms

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:

https://www.ebi.ac.uk/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)