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