# -*- coding: utf-8 -*-
# Copyright (C) 2009, Luís Pedro Coelho <lpc@cmu.edu>
# 
# Permission is hereby granted, free of charge, to any person obtaining a copy
#  of this software and associated documentation files (the "Software"), to deal
#  in the Software without restriction, including without limitation the rights
#  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
#  copies of the Software, and to permit persons to whom the Software is
#  furnished to do so, subject to the following conditions:
# 
# The above copyright notice and this permission notice shall be included in
#  all copies or substantial portions of the Software.
# 
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
#  THE SOFTWARE.

from __future__ import division
import numpy as np
import urllib
import re

__all__ = ['MUS_MUSCULUS','locate']

MUS_MUSCULUS = 'Mus Musculus'
def locate(name=None, ensembl=None, gene_name=None, organism=None):
    '''
    locations = locate(name=None, ensembl=None, gene_name=None, organism=None):

    Uniprot location for protein, identified by one of:
        * name: Gene or protein name (free-text search)
        * gene_name: Gene name
        * ensembl: Ensembl gene or peptide ID
        * organism: Organism (e.g., 'Mus Musculus' or 'Mouse')
    '''
    # This is based on a Matlab implementation of the same idea by Yanhua

    query = 'reviewed:yes'
    if name:
        query += ' ' + name
    if gene_name:
        query = ' gene:' + gene_name
    if organism:
        query += ' organism:"%s"' % organism
    if ensembl:
        query += ' "ensembl %s"' % ensembl
    if not query:
        raise ValueError, 'proteinlocate.locate: Empty query'
    accessions = []
    url = 'http://www.uniprot.org/uniprot/?' + urllib.urlencode({'query' : query, 'format':'tab', 'columns':'id'})
    for line in urllib.urlopen(url):
        accessions.append(line.strip())
    results = []
    for acc in accessions:
        for line in urllib.urlopen('http://www.uniprot.org/uniprot/%s.txt' % acc):
            match = re.search('GO; +GO:([0-9]+);\s*C:([^;]*);',line)
            if match:
                go_nr,go_name = match.groups()
                results.append((acc,go_nr,go_name))
    return results

    


# vim: set ts=4 sts=4 sw=4 expandtab smartindent:

@@ -1999,17 +1999,16 @@
 ry += ' 
-%22
 ensembl 
@@ -2009,17 +2009,16 @@
 sembl %25s
-%22
 ' %25 ense

Fix quoting bug.