--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gops_cluster.py	Tue Apr 01 10:51:55 2014 -0400
@@ -0,0 +1,129 @@
+#!/usr/bin/env python
+"""
+Cluster regions of intervals.
+
+usage: %prog in_file out_file
+    -1, --cols1=N,N,N,N: Columns for start, end, strand in file
+    -d, --distance=N: Maximum distance between clustered intervals
+    -v, --overlap=N: Minimum overlap require (negative distance)
+    -m, --minregions=N: Minimum regions per cluster
+    -o, --output=N: 1)merged 2)filtered 3)clustered 4) minimum 5) maximum
+"""
+import sys, traceback, fileinput
+from warnings import warn
+from bx.intervals import *
+from bx.intervals.io import *
+from bx.intervals.operations.find_clusters import *
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def main():
+    distance = 0
+    minregions = 2
+    output = 1
+    upstream_pad = 0
+    downstream_pad = 0
+
+    options, args = doc_optparse.parse( __doc__ )
+    try:
+        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
+        if options.distance: distance = int( options.distance )
+        if options.overlap: distance = -1 * int( options.overlap )
+        if options.output: output = int( options.output )
+        if options.minregions: minregions = int( options.minregions )
+        in_fname, out_fname = args
+    except:
+        doc_optparse.exception()
+
+    g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
+                            chrom_col=chr_col_1,
+                            start_col=start_col_1,
+                            end_col=end_col_1,
+                            strand_col=strand_col_1,
+                            fix_strand=True )
+
+    # Get the cluster tree
+    try:
+        clusters, extra = find_clusters( g1, mincols=distance, minregions=minregions)
+    except ParseError, exc:
+        fail( "Invalid file format: %s" % str( exc ) )
+
+    f1 = open( in_fname, "r" )
+    out_file = open( out_fname, "w" )
+    
+    # If "merge"
+    if output == 1:
+        fields = ["."  for x in range(max(g1.chrom_col, g1.start_col, g1.end_col)+1)]
+        for chrom, tree in clusters.items():
+            for start, end, lines in tree.getregions():
+                fields[g1.chrom_col] = chrom
+                fields[g1.start_col] = str(start)
+                fields[g1.end_col] = str(end)
+                out_file.write( "%s\n" % "\t".join( fields ) )
+
+    # If "filtered" we preserve order of file and comments, etc.
+    if output == 2:
+        linenums = dict()
+        for chrom, tree in clusters.items():
+            for linenum in tree.getlines():
+                linenums[linenum] = 0
+        linenum = -1
+        f1.seek(0)
+        for line in f1.readlines():
+            linenum += 1
+            if linenum in linenums or linenum in extra:
+                out_file.write( "%s\n" % line.rstrip( "\n\r" ) )
+
+    # If "clustered" we output original intervals, but near each other (i.e. clustered)
+    if output == 3:
+        linenums = list()
+        f1.seek(0)
+        fileLines = f1.readlines()
+        for chrom, tree in clusters.items():
+            for linenum in tree.getlines():
+                out_file.write( "%s\n" % fileLines[linenum].rstrip( "\n\r" ) )
+
+    # If "minimum" we output the smallest interval in each cluster
+    if output == 4 or output == 5:
+        linenums = list()
+        f1.seek(0)
+        fileLines = f1.readlines()
+        for chrom, tree in clusters.items():
+            regions = tree.getregions()
+            for start, end, lines in tree.getregions():
+                outsize = -1
+                outinterval = None
+                for line in lines:
+                    # three nested for loops?
+                    # should only execute this code once per line
+                    fileline = fileLines[line].rstrip("\n\r")
+                    try:
+                        cluster_interval = GenomicInterval( g1, fileline.split("\t"), 
+                                                            g1.chrom_col, 
+                                                            g1.start_col,
+                                                            g1.end_col, 
+                                                            g1.strand_col, 
+                                                            g1.default_strand,
+                                                            g1.fix_strand )
+                    except Exception, exc:
+                        print >> sys.stderr, str( exc )
+                        f1.close()
+                        sys.exit()
+                    interval_size = cluster_interval.end - cluster_interval.start
+                    if outsize == -1 or \
+                       ( outsize > interval_size and output == 4 ) or \
+                       ( outsize < interval_size and output == 5 ) :
+                        outinterval = cluster_interval
+                        outsize = interval_size
+                out_file.write( "%s\n" % outinterval )
+
+    f1.close()
+    out_file.close()
+    
+    if g1.skipped > 0:
+        print skipped( g1, filedesc="" )
+
+if __name__ == "__main__":
+    main()