old_contents: # -*- 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:
  
new_contents: # -*- 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:
  
subject: Fix quoting bug.