--- a/resize.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-'''
-change start and end of interval files
-'''
-
-import sys
-
-def resize(infile,outfile,expr_start,expr_end,strand):
-    fin = open(infile)
-    fout = open(outfile,'w')
-    if expr_start[0:3] == 'end':
-        c1 = 2
-        n1 = int(expr_start[3:])
-    else:
-        c1 = 1
-        n1 = int(expr_start[5:])
-    if expr_end[0:3] == 'end':
-        c2 = 2
-        n2 = int(expr_end[3:])
-    else:
-        c2 = 1
-        n2 = int(expr_end[5:])
-    if strand == 'ignore':
-        for line in fin:
-            flds = line.strip().split('\t')
-            start = int(flds[c1]) + n1
-            if start >= 0:
-                end = int(flds[c2]) + n2
-                if end >= start:
-                    flds[1] = str(start)
-                    flds[2] = str(end)
-                    fout.write('\t'.join(flds)+'\n')
-    else:# upstream downstream
-       for line in fin:
-            flds = line.strip().split('\t')
-            if flds[5] == '+':
-                start = int(flds[c1]) + n1
-                if start >= 0:
-                    end = int(flds[c2]) + n2
-                    if end >= start: 
-                        flds[1] = str(start)
-                        flds[2] = str(end)
-                        fout.write('\t'.join(flds)+'\n')
-            else: # on the - strand
-                start = int(flds[3-c2]) - n2 # end=end+n2
-                if start >= 0:
-                    end = int(flds[3-c1]) - n1
-                    if end >= start:
-                        flds[1] = str(start)
-                        flds[2] = str(end)
-                        fout.write('\t'.join(flds)+'\n')
-    fin.close()
-    fout.close()
-
-if __name__ == "__main__":
-    resize(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5])
-    # python resize.py in.bed out.bed start-3 end+5 both
-    # python resize.py <input.bed> <output.bed> expr_start expr_end strand(both/+/-)