Group samples on group in igv

bin/igv_files_to_session.py

@@ -99,6 +99,16 @@ def igv_files_to_session(XMLOut, ListFile, Genome, GtfBed, PathPrefix=""):
             break
             fout.close()
 
+
+    ## Construct groups
+    groups = {}
+    group_num = 1
+    for ifile, colour in fileList:
+        group = os.path.basename(ifile).split('_R')[0]
+        if group not in groups:
+            groups[group] = group_num
+            group_num = group_num + 1
+
     ## ADD RESOURCES SECTION
     XMLStr = '<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n'
     XMLStr += '<Session genome="%s" hasGeneTrack="true" hasSequenceTrack="true" locus="All" version="8">\n' % (Genome)
@@ -159,8 +169,8 @@ def igv_files_to_session(XMLOut, ListFile, Genome, GtfBed, PathPrefix=""):
             )
         elif extension in [".bw", ".bigwig", ".tdf", ".bedGraph", ".bedgraph"]:
             XMLStr += (
-                '\t\t<Track altColor="0,0,178" autoScale="true" autoscaleGroup="1" clazz="org.broad.igv.track.DataSourceTrack" color="%s" '
-                % (colour)
+                '\t\t<Track altColor="0,0,178" autoScale="true" autoscaleGroup="%s" clazz="org.broad.igv.track.DataSourceTrack" color="%s" '
+                % (groups[os.path.basename(ifile).split('_R')[0]], colour)
             )
             XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="12" height="100" '
             XMLStr += (