diff mothur/lib/galaxy/datatypes/metagenomics.py @ 26:5c77423823cb

Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)

--- a/mothur/lib/galaxy/datatypes/metagenomics.py	Wed May 16 12:28:44 2012 -0500
+++ b/mothur/lib/galaxy/datatypes/metagenomics.py	Wed May 16 13:12:05 2012 -0500
@@ -17,6 +17,9 @@
 from galaxy.datatypes.sequence import Fasta
 from galaxy import util
 from galaxy.datatypes.images import Html
+import pkg_resources
+pkg_resources.require("simplejson")
+import simplejson
 
 
 log = logging.getLogger(__name__)
@@ -1260,6 +1263,56 @@
         return False
 
 
+## Biom 
+
+class BiologicalObservationMatrix( Text ):
+    file_ext = 'biom'
+    """
+    http://biom-format.org/documentation/biom_format.html
+    The format of the file is JSON:
+    {
+    "id":null,
+    "format": "Biological Observation Matrix 0.9.1-dev",
+    "format_url": "http://biom-format.org",
+    "type": "OTU table",
+    "generated_by": "QIIME revision 1.4.0-dev",
+    "date": "2011-12-19T19:00:00",
+    "rows":[
+            {"id":"GG_OTU_1", "metadata":null},
+            {"id":"GG_OTU_2", "metadata":null},
+            {"id":"GG_OTU_3", "metadata":null},
+        ],
+    "columns": [
+            {"id":"Sample1", "metadata":null},
+            {"id":"Sample2", "metadata":null}
+        ],
+    "matrix_type": "sparse",
+    "matrix_element_type": "int",
+    "shape": [3, 2],
+    "data":[[0,1,1],
+            [1,0,5],
+            [2,1,4]
+           ]
+    }
+
+    """
+
+    def __init__(self, **kwd):
+        Text.__init__( self, **kwd )
+
+    def sniff( self, filename ):
+        if os.path.getsize(filename) < 50000:
+            try:
+                data = simplejson.load(open(filename))
+                if data['format'].find('Biological Observation Matrix'):
+                    return True
+            except:
+                pass
+        return False
+
+
+
+
 ## Qiime Classes
 
 class QiimeMetadataMapping(Tabular):