--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getIndelRates_3way.py	Tue Apr 01 10:52:01 2014 -0400
@@ -0,0 +1,244 @@
+#!/usr/bin/env python
+#Guruprasad Ananda
+
+import sys, os, tempfile
+import fileinput
+from warnings import warn
+
+from galaxy.tools.util.galaxyops import *
+from bx.intervals.io import *
+
+from bx.intervals.operations import quicksect
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+
+def counter(node, start, end, sort_col):
+    global full, blk_len, blk_list
+    if node.start < start:
+        if node.right:
+            counter(node.right, start, end, sort_col)
+    elif start <= node.start <= end and start <= node.end <= end:
+        full += 1
+        if node.other[0] not in blk_list:
+            blk_list.append(node.other[0])
+            blk_len += int(node.other[sort_col+2])
+        if node.left and node.left.maxend > start:
+            counter(node.left, start, end, sort_col)
+        if node.right:
+            counter(node.right, start, end, sort_col)
+    elif node.start > end:
+        if node.left:
+            counter(node.left, start, end, sort_col)
+
+
+infile = sys.argv[1]
+fout = open(sys.argv[2],'w')
+int_file = sys.argv[3]
+if int_file != "None": #User has specified an interval file
+    try:
+        fint = open(int_file, 'r')
+        dbkey_i = sys.argv[4]
+        chr_col_i, start_col_i, end_col_i, strand_col_i = parse_cols_arg( sys.argv[5] )
+    except:
+        stop_err("Unable to open input Interval file")
+
+
+def main():
+    for i, line in enumerate( file ( infile )):
+        line = line.rstrip('\r\n')
+        if len( line )>0 and not line.startswith( '#' ):
+            elems = line.split( '\t' )
+            break
+        if i == 30:
+            break # Hopefully we'll never get here...
+        
+    if len( elems ) != 18:
+        stop_err( "This tool only works on tabular data output by 'Fetch Indels from 3-way alignments' tool. The data in your input dataset is either missing or not formatted properly." )
+    
+    for i, line in enumerate( file ( infile )):
+        line = line.rstrip('\r\n')
+        elems = line.split('\t')
+        try:
+            assert int(elems[0])
+            assert len(elems) == 18
+            if int_file != "None":
+                if dbkey_i not in elems[3] and  dbkey_i not in elems[8] and dbkey_i not in elems[13]:
+                    stop_err("The species build corresponding to your interval file is not present in the Indel file.") 
+                if dbkey_i in elems[3]:
+                    sort_col = 4
+                elif dbkey_i in elems[8]:
+                    sort_col = 9
+                elif dbkey_i in elems[13]:
+                    sort_col = 14
+            else:
+                species = []
+                species.append( elems[3].split('.')[0] )
+                species.append( elems[8].split('.')[0] )
+                species.append( elems[13].split('.')[0] )
+                sort_col = 0    #Based on block numbers
+            break
+        except:
+            continue
+    
+    fin = open(infile, 'r')
+    skipped = 0
+    
+    if int_file == "None":
+        sorted_infile = tempfile.NamedTemporaryFile()
+        cmdline = "sort -n -k"+str(1)+" -o "+sorted_infile.name+" "+infile
+        try:
+            os.system(cmdline)
+        except:
+            stop_err("Encountered error while sorting the input file.")
+        print >> fout, "#Block\t%s_InsRate\t%s_InsRate\t%s_InsRate\t%s_DelRate\t%s_DelRate\t%s_DelRate" % ( species[0], species[1], species[2], species[0], species[1], species[2] )
+        prev_bnum = -1
+        sorted_infile.seek(0)
+        for line in sorted_infile.readlines():
+            line = line.rstrip('\r\n')
+            elems = line.split('\t')
+            try:
+                assert int(elems[0])
+                assert len(elems) == 18
+                new_bnum = int(elems[0])
+                if new_bnum != prev_bnum:
+                    if prev_bnum != -1:
+                        irate = []
+                        drate = []
+                        for i, elem in enumerate(inserts):
+                            try:
+                                irate.append(str("%.2e" % (inserts[i]/blen[i])))
+                            except:
+                                irate.append('0')
+                            try:
+                                drate.append(str("%.2e" % (deletes[i]/blen[i])))
+                            except:
+                                drate.append('0')
+                        print >> fout, "%s\t%s\t%s" % ( prev_bnum, '\t'.join(irate) , '\t'.join(drate) )
+                    inserts = [0.0, 0.0, 0.0]
+                    deletes = [0.0, 0.0, 0.0]
+                    blen = []
+                    blen.append( int(elems[6]) )
+                    blen.append( int(elems[11]) )
+                    blen.append( int(elems[16]) )
+                line_sp = elems[1].split('.')[0]
+                sp_ind = species.index(line_sp)
+                if elems[1].endswith('insert'):
+                    inserts[sp_ind] += 1
+                elif elems[1].endswith('delete'):
+                    deletes[sp_ind] += 1
+                prev_bnum = new_bnum
+            except Exception, ei:
+                #print >>sys.stderr, ei
+                continue
+        irate = []
+        drate = []
+        for i, elem in enumerate(inserts):
+            try:
+                irate.append(str("%.2e" % (inserts[i]/blen[i])))
+            except:
+                irate.append('0')
+            try:
+                drate.append(str("%.2e" % (deletes[i]/blen[i])))
+            except:
+                drate.append('0')
+        print >> fout, "%s\t%s\t%s" % ( prev_bnum, '\t'.join(irate) , '\t'.join(drate) )
+        sys.exit()
+    
+    inf = open(infile, 'r')
+    start_met = False
+    end_met = False
+    sp_file = tempfile.NamedTemporaryFile()
+    for n, line in enumerate(inf):
+        line = line.rstrip('\r\n')
+        elems = line.split('\t')
+        try:
+            assert int(elems[0])
+            assert len(elems) == 18
+            if dbkey_i not in elems[1]:
+                if not(start_met):
+                    continue
+                else:
+                    sp_end = n
+                    break
+            else:
+                print >> sp_file, line
+                if not(start_met):
+                    start_met = True
+                    sp_start = n
+        except:
+            continue
+    
+    try:
+        assert sp_end
+    except:
+        sp_end = n+1
+    
+    sp_file.seek(0)
+    win = NiceReaderWrapper( fileinput.FileInput( int_file ),
+                                chrom_col=chr_col_i,
+                                start_col=start_col_i,
+                                end_col=end_col_i,
+                                strand_col=strand_col_i,
+                                fix_strand=True)
+    
+    indel = NiceReaderWrapper( fileinput.FileInput( sp_file.name ),
+                                chrom_col=1,
+                                start_col=sort_col,
+                                end_col=sort_col+1,
+                                strand_col=-1,
+                                fix_strand=True)
+    
+    indelTree = quicksect.IntervalTree()
+    for item in indel:
+        if type( item ) is GenomicInterval:
+            indelTree.insert( item, indel.linenum, item.fields )
+    result = []
+    
+    global full, blk_len, blk_list
+    for interval in win:
+        if type( interval ) is Header:
+            pass
+        if type( interval ) is Comment:
+            pass
+        elif type( interval ) == GenomicInterval:
+            chrom = interval.chrom
+            start = int(interval.start)
+            end = int(interval.end)
+            if start > end:
+                warn( "Interval start after end!" )
+            ins_chr = "%s.%s_insert" % ( dbkey_i, chrom )
+            del_chr = "%s.%s_delete" % ( dbkey_i, chrom )
+            irate = 0
+            drate = 0
+            if ins_chr not in indelTree.chroms and del_chr not in indelTree.chroms:
+                pass
+            else:
+                if ins_chr in indelTree.chroms:
+                    full = 0.0
+                    blk_len = 0
+                    blk_list = []
+                    root = indelTree.chroms[ins_chr]    #root node for the chrom insertion tree
+                    counter(root, start, end, sort_col)
+                    if blk_len:
+                        irate = full/blk_len
+                
+                if del_chr in indelTree.chroms:
+                    full = 0.0
+                    blk_len = 0
+                    blk_list = []
+                    root = indelTree.chroms[del_chr]    #root node for the chrom insertion tree
+                    counter(root, start, end, sort_col)
+                    if blk_len:
+                        drate = full/blk_len
+                
+            interval.fields.append(str("%.2e" %irate))
+            interval.fields.append(str("%.2e" %drate))
+            print >> fout, "\t".join(interval.fields)
+            fout.flush()
+
+
+if __name__ == "__main__":
+    main()