"""
.. versionadded:: 0.2.3
This module defines routine to access Pfam information using a
network connection
"""
from . import url_open
PFAM_URL = "http://pfam.xfam.org/"
[docs]def get_pfam_families(key='id'):
"""
.. versionadded:: 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
Arguments:
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:
dict: 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 :ref:`hmmer2gff` script output uses ID as *gene_id*
value when using the HMM provided by Pfam
"""
families = {}
for line in url_open(PFAM_URL + "families?output=text", stream=True):
line = line.decode('utf8').strip()
if line.startswith('#') or (not line):
continue
acc, p_id, description = line.strip().split('\t')
if key != 'id':
p_id, acc = acc, p_id
families[p_id] = (acc, description)
return families