コード例 #1
0
ファイル: importer.py プロジェクト: linkai1208/precon
def importGene(filename):
    filename = filename or r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-symbols.txt'
    cnt = 0
    set = {}
    col = mongo.db()['entity']
    with open(filename) as f:
        content = f.read()
        for line in content.split('\n'):
            line = line.strip()
            sym = line.lower()
            if (sym in set): continue
            set[sym] = 1

            doc = ObjDict()
            doc._id = 'enti_sym_%s' % sym
            doc.symbol = sym
            doc.group = 'protein'
            doc.name = line
            doc.label = line

            if (col.find({'symbol': sym}).count() > 0): continue

            col.save(doc, safe=True)
            cnt += 1
            print "Added # %d:  %s" % (cnt, sym)
    print "Inserted %d gene" % cnt
コード例 #2
0
ファイル: importer.py プロジェクト: tjworks/precon
def importGene(filename):
    filename = filename or r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-symbols.txt'
    cnt = 0
    set = {}
    col = mongo.db()['entity']
    with open(filename) as f:
        content = f.read()        
        for line in content.split('\n'):
            line = line.strip()
            sym = line.lower()
            if(sym in set): continue
            set[sym] = 1
            
            doc=ObjDict()
            doc._id = 'enti_sym_%s' %sym 
            doc.symbol = sym
            doc.group='protein'
            doc.name = line
            doc.label = line
            
            if(col.find({'symbol':sym}).count()>0): continue
                
            col.save( doc,safe=True)
            cnt += 1
            print "Added # %d:  %s" %(cnt, sym)
    print "Inserted %d gene" %cnt        
コード例 #3
0
ファイル: load.py プロジェクト: linkai1208/precon
def mongo_scripts():
    mydb = db()
    for f in filesInDir("etc/mongo"):
        if f.find(".js") < 0: continue
        funcname = f.replace(".js", "")
        handle = open("etc/mongo/%s" % f, 'r')
        funcbody = handle.read()
        handle.close()
        print "Load function: %s" % funcname
        mydb.system.js.save({'_id': funcname, 'value': funcbody}, safe=True)
    print "Done"
コード例 #4
0
ファイル: load.py プロジェクト: tjworks/precon
def mongo_scripts():
    mydb= db()
    for f in filesInDir("etc/mongo"):
        if f.find(".js")<0: continue
        funcname = f.replace(".js", "")
        handle = open("etc/mongo/%s" %f,'r')
        funcbody = handle.read()
        handle.close()
        print "Load function: %s" %funcname
        mydb.system.js.save({'_id':funcname, 'value':funcbody}, safe=True)            
    print "Done"
コード例 #5
0
ファイル: importer.py プロジェクト: linkai1208/precon
def importEdges(filename=None):
    """
    import edges, one pair per line 
    Edge property: - no direction, -> left to right, <- right to left
    """
    filename = filename or r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-Massaged.csv'

    # add a network
    n = Network.findOne({'name': "GBM Predicted Tumor Network"}) or Network()
    n.name = "GBM Predicted Tumor Network"
    n.group = "predicted"
    n.owner = 'precon'
    n.save()

    col = mongo.db()['entity']
    count = 0
    now = time.time()
    ec = mongo.getCollection('edge')
    with open(filename) as f:
        content = f.read()
        for line in content.split('\n'):
            doc = {}
            line = line.strip()
            pos = line.find("///")
            if pos > 0:
                line = line[0:pos].strip()
                doc['comment'] = line[pos:]

            items = line.split("->")
            if (len(items) == 1): items = line.split("<-")
            if (len(items) == 1): items = line.split(" - ")
            if (len(items) == 1):
                error("Ignore invalid line: [%s]" % line)
                continue
            count += 1
            if (count < 8378): continue

            tmp = []
            tmp.append(items[0].lower().strip())
            tmp.append(items[1].lower().strip())
            entities = ['', '']
            print "!!! %d " % (col.find({'symbol': {'$in': tmp}}).count())
            for r in col.find({'symbol': {'$in': tmp}}):
                if (r['symbol'] == tmp[0]):
                    entities[0] = Entity(r)
                if (r['symbol'] == tmp[1]):
                    entities[1] = Entity(r)

            if (len(entities) != 2):
                raise "Invalid nodes %s, continue" % entities

            node1 = Node.findOne({'network': n._id, 'entity': entities[0]._id})
            if not node1:
                node1 = Node({'network': n._id}, entities[0])
                node1.save()
            node2 = Node.findOne({'network': n._id, 'entity': entities[1]._id})
            if not node2:
                node2 = Node({'network': n._id}, entities[1])
                node2.save()

            con = Connection()
            con._id = "conn_%s_%s" % (tmp[0], tmp[1])
            con.nodes = [node1._id, node2._id]
            con.entities = [entities[0]._id, entities[1]._id]
            con.type = 'predicted'
            con.network = n._id
            con.label = ""
            con.save()

            print "Saving connection %d %s" % (count, con._id)

    finish = time.time()
    print "Imported %d edges, time elpased %d seconds" % (count, finish - now)
コード例 #6
0
ファイル: importer.py プロジェクト: tjworks/precon
def importEdges(filename=None):
    """
    import edges, one pair per line 
    Edge property: - no direction, -> left to right, <- right to left
    """
    filename = filename or  r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-Massaged.csv'    
    
    # add a network
    n = Network.findOne({'name': "GBM Predicted Tumor Network"}) or Network()
    n.name = "GBM Predicted Tumor Network"
    n.group = "predicted"
    n.owner = 'precon'
    n.save()
     
    
    col = mongo.db()['entity']
    count = 0
    now = time.time()
    ec = mongo.getCollection('edge')
    with open(filename) as f:
        content = f.read()        
        for line in content.split('\n'):
            doc  = {}
            line = line.strip()
            pos = line.find("///")            
            if pos>0: 
                line = line[0:pos].strip()
                doc['comment'] = line[pos:]
                             
            
            items = line.split("->")
            if (len(items) == 1): items = line.split("<-")
            if (len(items) == 1): items = line.split(" - ")
            if (len(items) == 1): 
                error("Ignore invalid line: [%s]" %line)
                continue
            count+=1
            if(count<8378): continue
            
            tmp =[]
            tmp.append( items[0].lower().strip())
            tmp.append( items[1].lower().strip())
            entities = ['','']
            print "!!! %d " %( col.find({'symbol': {'$in': tmp  } }).count() )
            for r in  col.find({'symbol': {'$in': tmp  } }):
                if(r['symbol'] == tmp[0]):
                    entities[0] = Entity(r)
                if(r['symbol'] == tmp[1]):
                    entities[1] = Entity(r)
            
            if(len(entities)!=2 ):
                raise "Invalid nodes %s, continue" % entities
            
            
            node1 = Node.findOne({'network': n._id, 'entity': entities[0]._id}) 
            if not node1:
                node1 = Node({'network':n._id}, entities[0])
                node1.save()
            node2 = Node.findOne({'network': n._id, 'entity': entities[1]._id}) 
            if not node2:
                node2 = Node({'network':n._id}, entities[1])
                node2.save()
            
         
            
            con = Connection()
            con._id  = "conn_%s_%s" %(tmp[0], tmp[1])
            con.nodes = [node1._id, node2._id]
            con.entities = [ entities[0]._id, entities[1]._id ] 
            con.type = 'predicted'
            con.network = n._id
            con.label = ""
            con.save()
                        
            
            print "Saving connection %d %s" % (count, con._id) 
            
    finish = time.time()
    print "Imported %d edges, time elpased %d seconds" %(count, finish - now)