--- a/reprof.py	Mon Nov 30 20:10:58 2015 -0500
+++ b/reprof.py	Wed Dec 02 15:01:36 2015 -0500
@@ -13,7 +13,7 @@
 def run_reprof(query_path, modeldir):
     outtmp = tempfile.NamedTemporaryFile(delete=False)
     cmd = [
-        './reprof/scripts/reprof',
+        'reprof',
         '-i', query_path,
         '--modeldir=%s' % modeldir,
         '-o', outtmp.name
@@ -75,6 +75,22 @@
     with open(path, 'a') as handle:
         GFF.write([rec], handle)
 
+def storeClassData(path, id, phel):
+    h = float(phel.count('H')) / float(len(phel))
+    e = float(phel.count('E')) / float(len(phel))
+
+    if h > .45 and e < .05:
+        classification = 'all-alpha'
+    elif h < .05 and e > .45:
+        classification = 'all-beta'
+    elif h > .3 and e > .2:
+        classification = 'alpha-beta'
+    else:
+        classification = 'mixed'
+
+    with open(path, 'a') as handle:
+        handle.write("{0}\t{1}\n".format(id, classification))
+
 def main(fasta, modeldir):
     for record in SeqIO.parse(fasta, 'fasta'):
         tmp = tempfile.NamedTemporaryFile(delete=False)
@@ -86,23 +102,24 @@
         for col in ('RI_S', 'P10', 'RI_A', 'PACC', 'PREL', 'pH', 'pE', 'pL'):
             storeWigData(data['idx'], data[col], record.id, col + '.wig')
 
+        eco = ['{ECO:0000255|reprof_1.0.1}']
         storeGff3Data(
             'secondary_structure.gff3', record.id, data['idx'], data['PHEL'],
             {
                 'H': {
                     'type': 'peptide_helix',
-                    'label': ['Helix'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Helix'],
+                    'evidence': eco,
                 },
                 'E': {
                     'type': 'beta_strand',
-                    'label': ['Extended/Sheet'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Extended/Sheet'],
+                    'evidence': eco,
                 },
                 'L': {
                     'type': 'loop',
-                    'label': ['Loop'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Loop'],
+                    'evidence': eco,
                 }
             }
         )
@@ -112,17 +129,19 @@
             {
                 'B': {
                     'type': 'experimental_result_region',
-                    'label': ['Buried'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Buried'],
+                    'evidence': eco,
                 },
                 'E': {
                     'type': 'experimental_result_region',
-                    'label': ['Exposed'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Exposed'],
+                    'evidence': eco,
                 },
             }
         )
 
+        storeClassData('report.tsv', record.id, data['PHEL'])
+
 
 if __name__ == '__main__':
     # Grab all of the filters from our plugin loader