a44e3254174152b2d4b3f241d1935654cd139181
vsmalladi
  Tue May 8 10:11:21 2012 -0700
Renamed library from ucscgenomics to ucscGb. Redmine #7029.
diff --git python/lib/ucscGb/geo.py python/lib/ucscGb/geo.py
new file mode 100644
index 0000000..90d0e22
--- /dev/null
+++ python/lib/ucscGb/geo.py
@@ -0,0 +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 = 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 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')
+