mgkit.net.pfam module

New in version 0.2.3.

This module defines routine to access Pfam information using a network connection

mgkit.net.pfam.get_pfam_families(key='id')[source]

New in version 0.2.3.

Gets a dictionary with the accession/id/description of Pfam families from Pfam. This list can be accessed using the URL: http://pfam.xfam.org/families?output=text

The output is a tab separated file where the fields are:

  • ACCESSION

  • ID

  • DESCRIPTION

Parameters

key (str) – if the value is id, the key of the dictionary is the ID, otherwise ID swaps position with ACCESSION (the new key)

Returns

by default the function returns a dictionary that uses the ID as key, while the value is a tuple (ACCESSION, DESCRIPTION). ID is the default because the hmmer2gff - Convert HMMER output to GFF script output uses ID as gene_id value when using the HMM provided by Pfam

Return type

dict