generating midpoints on a bedfile

Question

[a.rex]

I have the following befile:

name           start    end                              id                                                            length
scaffold1       1       160     NB501801:1:HN3WLBGXY:4:11601:9830:10032          159
scaffold1       1       164     NB501801:1:HN3WLBGXY:3:13412:18598:13811        163
scaffold1       1       167     NB501801:1:HN3WLBGXY:3:22404:14294:20264        166
scaffold1      15      189     NB501801:1:HN3WLBGXY:2:23204:7996:11409           174
scaffold1       1       201     NB501801:1:HN3WLBGXY:3:21609:2881:5564             200
scaffold1       46      230     NB501801:1:HN3WLBGXY:4:23510:23247:4818          184

I want to generate an extra column in this file with the midpoint. Is there a quick method for doing this using bedtools? How can I do this with python?

Answer 1

[WouterDeCoster]

There probably is a quick awk way to do this, but since you ask specifically for python, try something like the following untested code bit:

import sys

with open(sys.argv[1]) as inbed:
    for line in inbed:
        if line.startswith('name'):
           print(line.strip() + "\tmidpoint")
        else:
           print(line.strip() + "\t" + str((int(line.split('\t')[1]) + int(line.split('\t')[2]))/2))

Save as addMidpoint.py, execute as python addMidpoint.py yourinput.bed > youroutput.be

[a.rex]

Thanks for your help. However, when I run this code an error appears. It seems that there is a concatenation of string and integer in the last line. I can't seem to rectify this. Sorry - any further help would be appreciated.

[WouterDeCoster]

Wow, had some ridiculous blunders in my code. Can you check again?

[a.rex]

Works perfectly now! Thank you.