35c0685ff195fd0332ba86828c6230a34eaaaacb
mmaddren
  Thu Apr 19 16:44:47 2012 -0700
added track viewing tools for GEO so that venkat can use it
diff --git python/lib/ucscgenomics/geo.py python/lib/ucscgenomics/geo.py
index 490bec8..90d0e22 100644
--- python/lib/ucscgenomics/geo.py
+++ python/lib/ucscgenomics/geo.py
@@ -1,81 +1,96 @@
 import urllib2, re, datetime
 
 # if the molecule is RNA, we need to map our data into !Sample_molecule, which only takes certain fields
 # first we check rnaExtractMapping. If its not there, we use the localization. This is because (at current)
 # polyA is the most important trait, otherwise its going to be nonPolyA which GEO doesn't accept. 
 rnaExtractMapping = {
     'shortPolyA': 'polyA RNA', 
     'longPolyA': 'polyA RNA', 
     'polyA': 'polyA RNA'
 }
 
 localizationMapping = {
     'cytosol': 'cytoplasmic RNA', 
     'polysome': 'cytoplasmic RNA',
     'membraneFraction': 'cytoplasmic RNA',
     'mitochondria': 'cytoplasmic RNA',
     'nucleus': 'nuclear RNA', 
     'nucleolus': 'nuclear RNA', 
     'nucleoplasm': 'nuclear RNA', 
     'nuclearMatrix': 'nuclear RNA', 
     'chromatin': 'nuclear RNA',
     'cell': 'total RNA'
 }
 
 # map our instrument names to GEO's names
 instrumentModels = {
     'Illumina_GA2x': 'Illumina Genome Analyzer II',
     'Illumina_GA2': 'Illumina Genome Analyzer II',
     'Illumina_HiSeq_2000': 'Illumina HiSeq 2000',
     'Illumina_GA1': 'Illumina Genome Analyzer',
     'Illumina_GA1_or_GA2': 'Illumina Genome Analyzer, Illumina Genome Analyzer II',
     'SOLiD_Unknown': 'SOLiD',
+    'AB_SOLiD_3.5': 'AB SOLiD 3.5',
     'Unknown': 'Illumina Genome Analyzer'
 }
 
 class Submission(object):
     
     @property
     def accessions(self):
         return self._accessions
         
     @property
     def dateSubmitted(self):
         return self._submitted
     
     @property
     def dateUpdated(self):
         return self._updated
     
     def __init__(self, geoId):
         html = getHtml(geoId)
-        self._accessions = getAccessions(html)
+        self._accessions = getGSE(html)
         self._submitted = getDateSubmitted(html)
         self._updated = getDateUpdated(html)
 
+    def getSample(self, geoId):
+        html = getHtml(geoId)
+        return getGSM(html)
+
 def getHtml(geoId):
     try:
         response = urllib2.urlopen('http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=%s' % geoId)
     except:
         return None
     return response.read()
     
-def getAccessions(html):
+def getGSE(html):
     gsms = re.findall('(GSM[0-9]+)</a></td>\n<td valign="top">([^<]+)</td>', html)
     d = dict()
     for gsm in gsms:
         d[gsm[1]] = gsm[0]
     return d
     
+def getGSM(html):
+    suppfiles = re.findall('<tr valign="top"><td bgcolor="#[0-9A-F]+">([^<]+)</td>', html)
+    d = dict()
+    for f in suppfiles:
+        print f
+        fname = f.rsplit('_', 1)[1]
+        d[fname] = fname
+    return d
+        
+    
 def getDateSubmitted(html):
     datestr = re.search('<td>Submission date</td>\n<td>([^<]+)</td>', html)
     if datestr == None:
         return None
     return datetime.datetime.strptime(datestr.group(1), '%b %d, %Y')
     
 def getDateUpdated(html):
     datestr = re.search('<td>Last update date</td>\n<td>([^<]+)</td>', html)
     if datestr == None:
         return None
     return datetime.datetime.strptime(datestr.group(1), '%b %d, %Y')