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Posted by Bloguero_Connor on Fri 21 Mar 22:47
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  1. """This module contains code to access EZRetrieve.
  3. Functions:
  4. retrieve_single  Retrieve a single sequence from EZRetrieve.
  5. parse_single     Parse the results from EZRetrieve into a SeqRecord.
  7. """
  8.  
  9. def retrieve_single(id, from_, to, retrieve_by=None, organism=None,
  10.                     parse_results=1):
  11.     import urllib
  12.    
  13.     CGI = "http://siriusb.umdnj.edu:18080/EZRetrieve/single_r_run.jsp"
  14.     org2value = {"Hs" : "0", "Mm" : "1", "Rn" : 2}
  15.     organism = organism or "Hs"
  16.     assert organism in org2value
  17.  
  18.     acctype2value = {"genbank":0, "unigene":1, "locuslink":2, "image":3}
  19.     retrieve_by = retrieve_by or "GenBank"
  20.     retrieve_by = retrieve_by.lower()
  21.     assert retrieve_by in acctype2value
  22.  
  23.     params = {
  24.         "input" : str(id),
  25.         "from" : str(from_),
  26.         "to" : str(to),
  27.         "org" : org2value[organism],
  28.         "AccType" : acctype2value[retrieve_by],
  29.         }
  30.     options = urllib.urlencode(params)
  31.     handle = urllib.urlopen(CGI, options)
  32.     if parse_results:
  33.         results = parse_single(handle)
  34.     else:
  35.         results = handle.read()
  36.     return results
  37.  
  38. def parse_single(handle):
  39.     """Return a SeqRecord object for the sequence.  May raise an
  40.     AssertionError if there was a problem retrieving the sequence.
  42.     """
  43.     import re
  44.     from Bio.Seq import Seq
  45.     from Bio.SeqRecord import SeqRecord
  46.     results = handle.read()
  47.     lresults = results.lower()
  48.    
  49.     i = results.find("Error: ")
  50.     if i >= 0:
  51.         j = lresults.index("<br>", i)
  52.         errmsg = results[i:j].strip()
  53.         raise AssertionError, errmsg
  54.  
  55.     i = lresults.find("<b>>")
  56.     assert i >= 0, "Couldn't find sequence."
  57.     j = lresults.find("<br><br>", i)
  58.     seqdata = results[i:j]
  59.     reobj = re.compile(r"<[^>]*>", re.IGNORECASE|re.DOTALL)
  60.     seqdata = reobj.sub("", seqdata)
  61.     seqdata = re.sub(r"\s+", r"\n", seqdata)
  62.     seqdata = seqdata.strip() + "\n"
  63.     seqtitle = seqdata[1:seqdata.index('\n')]
  64.     seqdata = seqdata[seqdata.index('\n'):].replace('\n','')
  65.     seq=Seq(seqdata)
  66.     seq=SeqRecord(seq, id=seqtitle, description='')
  67.     return seq

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