diff termenrichment.py @ 1:646b05282962

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/termenrichment.py	Tue Feb 12 13:46:10 2013 -0500
@@ -0,0 +1,51 @@
+"""
+Term enrichment datatypes
+
+"""
+import pkg_resources
+pkg_resources.require( "bx-python" )
+
+import logging, os, sys, time, tempfile, shutil
+import data
+from galaxy import util
+from galaxy.datatypes.sniff import *
+from galaxy.web import url_for
+from cgi import escape
+import urllib
+from bx.intervals.io import *
+from galaxy.datatypes import metadata
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.tabular import Tabular
+import math
+
+log = logging.getLogger(__name__)
+
+class TermEnrichmentResult( data.Text ):
+    """Any term enrichment format"""
+    file_ext = "enrichment"
+
+    def init_meta( self, dataset, copy_from=None ):
+        data.Text.init_meta( self, dataset, copy_from=copy_from )
+
+
+class TerfTab( TermEnrichmentResult ):
+    """TERF TSV Format"""
+    file_ext = "terf"
+
+    def init_meta( self, dataset, copy_from=None ):
+        data.Text.init_meta( self, dataset, copy_from=copy_from )
+    def sniff( self, filename ):
+        """
+        Determines whether the file is in TERF format
+        """
+        headers = get_headers( filename, '\n' )
+        try:
+            for hdr in headers:
+                if hdr and hdr[0].startswith( '##terf-version' ) :
+                    return True
+            return False
+        except:
+            return False
+
+
+