Creating Mappability Map file

[AL_B]

Hi,
I have downloaded the mappability map code, from:

http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/

I followed the instructions from the README file.
I downloaded the .fa files, I created the executable files by using the makefile
and I used the command python compile.py.
I don't really understand the part:
"use CountMap.py in the usual way to access the data"
So... what is the "usual way"? what do I do from this point to get my mappability_map.txt file?

Thanks in advance to anyone that will try to help.

[maciosz]

Hi,
It took me a while to find answer for that one myself, before I decided to simply look at the code. I figured out you should run map.py script, but first - you need to edit it, because the original version is suitable for human chromosomes. For example, my data consist from seven chromosomes named 1, 2, 3, 4, 5 and Mt, Pt. So I changed the beginning of the code to look like that:

for i in xrange(1,8):
  if i<= 5:
    chr = str(i)
  elif i ==6:
    chr = "Mt"
  else
    chr = "Pt"

Also, I removed "chr" from next lines:

nicechr = chr
filename = chr + "b.out"

beacuse my files' names don't start with "chr".

Then I simply run

python map.py > map.txt

in the same directory where the script were and all files generated by compile.py.

I'm not positive if this is correct way to do that, because in the next step I get some weird errors, but I think it's not because of the mappability file.