Pfam interface for Python

This package provides a programming interface to retrive information from Pfam database.

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

Installation

This package is not in the pip repository yet. To install it you can use the following commands:

$ git clone https://github.com/AlbertoBoldrini/python-pfam
$ pip install ./python-pfam

Example

In these example we use the package beeprint to print to the termial data structured in a readable format.

import pfam
from beeprint import pp

# Retrive informations about the Piwi family from Pfam
piwi = pfam.family('Piwi')

# This data structure contains many fields
print('Description of Piwi family: ', piwi.comment)
print('Piwi family has %d different sequences.' % piwi.curation_details.num_seqs_full)

# We use pp() to print all data contained in the piwi structure
pp(piwi)

# Retrive the list of proteins in this family (big file...)
protein_list = piwi.proteins()

# Print a very very long list
# print(protein_list)

# Print the id of the first protein in this family
print('The ID of the first protein of the Piwi family is: ', protein_list[0].id)

# Retrive information about the first protein in this family
first_protein = protein_list[0].fetch()

# Print the sequence on this protein
print('The sequence of the first protein of the Piwi family is: ', first_protein.sequence)

# Retrive the clan (superfamily) of the Piwi family
clan = piwi.clan()

# What is the name of this clan?
print ("Piwi family belongs to %s clan." % clan.entry.id)

# Print the list of families in this clan
pp(clan.families)