BedTotalSize: Difference between revisions

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(deleted the useless python thing, hiram's version if of course better and faster as well)
 
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you can do this in awk with the single line statement:
<pre>
<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()
 
 


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)
[[Category:User Developed Scripts]]
</pre>

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
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