BedTotalSize: Difference between revisions

Latest revision as of 09:16, 15 September 2006

you can do this in awk with the single line statement:

awk '{sum += $3-$2}END{printf "total size: %d\n",sum}' file.bed

@@ Line 1: / Line 1: @@
+you can do this in awk with the single line statement:
 <pre>
-#!/usr/bin/env python
+awk '{sum += $3-$2}END{printf "total size: %d\n",sum}' file.bed
+</pre>
-from sys import *
-import sys
-from re import *
-if len(argv)==2:
-        print " Will read bed-style features from stdin"
-        print " Will add all features-lengths together"
-        print ""
-        print " SYNTAX: "
-        print " totalSize "
-        exit()
+[[Category:User Developed Scripts]]
-line = sys.stdin.readline()
-sum = 0
-while line!="":
-    fields = line.split()
-    start = int(fields[1])
-    stop = int(fields[2])
-    sum += (stop-start+1)
-    line = sys.stdin.readline()
-print "Total length of all features: "+str(sum)
-</pre>
-<pre>
-#  you could also do this in awk with the single line statement:
-#
-#  awk '{sum += $3-$2}END{printf "total size: %d\n",sum}' file.bed
-#
-#  Plus, I don't think you want to add 1 to your stop-start calculation.
-#  This relates to the subtle nature of the "0-relative" vs. "1-relative"
-#  coordinate systems.  When in 0-relative you don't need the + or - 1's anywhere.
-</pre>