diff seg2matrix/CGData/BaseTable.py @ 31:ab20c0d04f4a

add seg2matrix tool

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seg2matrix/CGData/BaseTable.py	Fri Jul 24 13:10:11 2015 -0700
@@ -0,0 +1,233 @@
+
+from CGData import CGObjectBase
+
+import csv
+import types
+
+class TableRow(object):
+    def __init__(self):
+        pass
+        
+    def __str__(self):
+        return "<" + ",".join( "%s=%s" % (col, getattr(self,col)) for col in self.__format__['columnOrder']) + ">"
+
+class InvalidFormat(Exception):
+    def __init__(self, txt):
+        Exception.__init__(self, txt)
+
+class BaseTable(CGObjectBase):
+    def __init__(self):
+        super(BaseTable,self).__init__()        
+        self.__row_class__ = type( "TableRow_" + self['cgformat']['name'], (TableRow,), dict(__format__=self.__format__) )        
+        self.free()
+    
+    def free(self):
+        self.firstKey = None
+        self.secondKey = None
+        self.groupKey = None
+        self.loaded = False
+        if 'primaryKey' in self['cgformat']:
+            self.firstKey = self['cgformat']['primaryKey']
+            setattr(self, self['cgformat']['primaryKey'] + "_map", {} )
+            self.groupKey = False
+        
+        #setup the map for groupKeys
+        if 'groupKey' in self['cgformat']:
+            self.firstKey = self['cgformat']['groupKey']
+            setattr(self, self['cgformat']['groupKey'] + "_map", {} )
+            self.groupKey = True
+        
+        if 'secondaryKey' in self['cgformat']:
+            self.secondKey = self['cgformat']['secondaryKey']
+    
+    def read(self, handle):
+        cols = self['cgformat']['columnOrder']
+        colType = {}
+        for col in cols:
+            if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'type' in self['cgformat']['columnDef'][col]:
+                if self['cgformat']['columnDef'][col]['type'] == 'float':
+                    colType[col] = float
+                elif self['cgformat']['columnDef'][col]['type'] == 'int':
+                    colType[col] = int
+                else:
+                    colType[col] = str
+            else:
+                colType[col] = str
+                
+        read = csv.reader(handle, delimiter="\t")
+
+        storeMap = getattr(self, self.firstKey + "_map")
+        comment = None
+        if 'comment' in self['cgformat']:
+            comment = self['cgformat']['comment']
+        linenum = 0
+        for row in read:
+            linenum += 1
+            r = self.__row_class__()
+            if comment is None or not row[0].startswith(comment):
+                for i, col in enumerate(cols):
+                    isOptional = False
+                    if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'optional' in self['cgformat']['columnDef'][col]:
+                        isOptional = self['cgformat']['columnDef'][col]['optional']
+                    if len(row) > i:
+                        try:
+                            setattr(r, col, colType[col](row[i]))
+                        except ValueError:
+                            raise ValueError( "col invalid type %s on line %d" % (row[i], linenum))
+                    else:
+                        if isOptional:
+                            setattr(r, col, None)
+                        else:
+                            print row
+                            raise InvalidFormat("missing colum " + col)
+                            
+                if not self.groupKey:
+                    if self.secondKey is not None:
+                        key1 = getattr(r, self.firstKey )                    
+                        key2 = getattr(r, self.secondKey )
+                        if key1 not in storeMap:
+                            storeMap[key1] = {}
+                        storeMap[key1][key2] = r
+                    else:
+                        storeMap[ getattr(r, self.firstKey ) ] = r
+                else:
+                    key1 = getattr(r, self.firstKey )
+                    if self.secondKey is not None:
+                        key2 = getattr(r, self.secondKey )
+                        if key1 not in storeMap:
+                            storeMap[key1] = {}
+                        if key2 not in storeMap[key1]:
+                            storeMap[key1][key2] = []
+                        storeMap[key1][key2].append(r)
+                    else:
+                        if key1 not in storeMap:
+                            storeMap[key1] = []
+                        storeMap[key1].append(r)
+        self.loaded = True
+    
+    """
+    def __getattr__(self, item):
+        if not self.loaded:
+            self.load()
+
+        if item == "get_" + self.firstKey + "_list":
+            return self.__get_firstmap__().keys
+        if item == "get_by_" + self.firstKey:
+            return self.__get_firstmap__().__getitem__                
+        if item == "get_" + self.firstKey + "_values":
+            return self.__get_firstmap__().values      
+        if item == "get_" + self.firstKey + "_map":
+            return self.__get_firstmap__
+        if item == "has_" + self.firstKey:
+            return self.__get_firstmap__().__contains__
+        raise AttributeError(item)
+    """
+        
+    def get_key_list(self):
+        """
+        List keys
+        """
+        if not self.loaded:
+            self.load()    
+        return self.__get_firstmap__().keys()
+    
+    def get_by(self, key):
+        """
+        get by key
+        """
+        if not self.loaded:
+            self.load()    
+        return self.__get_firstmap__().__getitem__(key)
+    
+    def get_values(self):
+        """
+        get values
+        """
+        if not self.loaded:
+            self.load()    
+        return self.__get_firstmap__().values()
+    
+    def get_map(self):
+        """
+        get key map
+        """
+        if not self.loaded:
+            self.load()
+        return self.__get_firstmap__()
+    
+    def has_key(self, key):
+        """
+        Does the table have a key
+        """
+        if not self.loaded:
+            self.load()
+        return self.__get_firstmap__().__contains__(key)
+        def __get_firstmap__(self):
+            return getattr(self, self.firstKey + "_map")
+    
+    def init_blank(self):
+        self.free()
+        self['cgdata'] = { 'type' : self['cgformat']['name'] }
+        self.loaded = True
+    
+    def insert(self, name, vals):
+        storeMap = getattr(self, self.firstKey + "_map")
+        cols = self['cgformat']['columnOrder']
+        r = self.__row_class__()
+        for col in cols:
+            isOptional = False
+            if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'optional' in self['cgformat']['columnDef'][col]:
+                isOptional = self['cgformat']['columnDef'][col]['optional']
+            if col in vals:
+                setattr(r, col, vals[col])
+            else:
+                if isOptional:
+                    setattr(r, col, None)
+                else:
+                    raise InvalidFormat("missing colum " + col)                            
+                            
+        if not self.groupKey:
+            if self.secondKey is not None:
+                key1 = getattr(r, self.firstKey )                    
+                key2 = getattr(r, self.secondKey )
+                if key1 not in storeMap:
+                    storeMap[key1] = {}
+                storeMap[key1][key2] = r
+            else:
+                storeMap[ getattr(r, self.firstKey ) ] = r
+        else:
+            key1 = getattr(r, self.firstKey )
+            if self.secondKey is not None:
+                key2 = getattr(r, self.secondKey )
+                if key1 not in storeMap:
+                    storeMap[key1] = {}
+                if key2 not in storeMap[key1]:
+                    storeMap[key1][key2] = []
+                storeMap[key1][key2].append(r)
+            else:
+                if key1 not in storeMap:
+                    storeMap[key1] = []
+                storeMap[key1].append(r)
+    
+    def write(self, handle):
+        writer = csv.writer(handle, delimiter="\t", lineterminator="\n")
+        for row in self.row_iter():
+            orow = []
+            for col in self['cgformat']['columnOrder']:
+                orow.append( getattr(row, col) )
+            writer.writerow(orow)
+        
+    
+    def row_iter(self):
+        if not self.groupKey:
+            keyMap = getattr(self, self.firstKey + "_map")
+            for rowKey in keyMap:
+                yield keyMap[rowKey]
+        else:
+            keyMap = getattr(self, self.firstKey + "_map")
+            for rowKey in keyMap:
+                for elem in keyMap[rowKey]:
+                    yield elem
+        
+    def __get_firstmap__(self):
+        return getattr(self, self.firstKey + "_map")