This is my “first” ruby script after hello world, so i’m sure there’s probably a better way to code it.

The process of extracting the pair files and gff file generation using the NimbleScan GUI can be tedious and time consuming if you have more than one design file. For NimbleGen’s new HD2 arrays, there are 12 blocks x 2 colors = 24 images per genome wide set to process. For repetative and limited tasks, it is much easier to run NimbleScan2.3 via command line and automatically match up the corresponding ndf and pos files to generate the corresponding pair and gff files.

The script is run within the folder which contains the “gridded” image files. Unfortunately, the automatic alignment of the grid to the spots is not optimized such that manual adjustment is still required after the “auto-align” to ensure proper placement of the grid. However, once the image is gridded and saved, NimbleScan can do the processing without the GUI.

The argument to the script is pair, gff, or both depending upon which files you want to generate. Note that gff requires the pair files, so most of the time you just run both.

bin is the NimbleScan binary executable

designpath is where you have the design files stored

designfile is the common prefix to the ndf and pos files… you may have to edit this if yours is different

maxthread is the max number of concurrent threads to run.. if you only have 1 or 2 cpus, then decrease this number to avoid thrashing

Note: the image files are named something_Anumber_something.tif the script keys off of the _Anumber_ and uses the number to obtain the correct ndf or pos file. A01 refers to design file 01, A02 -> designfile 02 and so on.

The image files must also have something_635_ and something_532_ in order to match the red and green channels from the same array block.

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#!/usr/bin/ruby

# $Id: nimblescan.rb,v 1.2 2007/09/11 17:16:53 kching Exp $
#
#
#

# puts “hello ruby\n”

# get list of tif files

bin = ‘NimbleScan’

designpath = “/var/NimbleScan2/Design/”
designfile = “2007-06-19_HG18_Economy_”
#NimbleScan -xprobes -a -S -o ./PairData/ -n /var/NimbleScan2/Design/2007-06-19_HG18_Economy_01.ndf -i rdh_161_ng120987_A01_H3K4me3_hESC_090607_5
32_grid.tif

paircmd = ” -xprobes -a -S -n ”
gffcmd = ” gff -n -R -x ”
#NimbleScan gff -n -R -x -o ./GFF/ -c rdh_161_ng120987_A01_H3K4me3_hESC_090607 -p /var/NimbleScan2/Design/2007-06-19_HG18_Economy_01.pos ./PairDa
ta/rdh_161_ng120987_A01_H3K4me3_hESC_090607_635_grid.pair ./PairData/rdh_161_ng120987_A01_H3K4me3_hESC_090607_532_grid.pair

ARGV.each{ |option|
#puts option + “\n”
if(option=~/gff/i)
$command=’gff’
elsif(option=~/pair/i)
$command=’pair’
elsif(option=~/both/i)
$command=’both’
end
}

if(! (defined? $command) )
puts “usage script < gff | pair | both >\n”
exit
end

ls = `ls -1 *_635_*.tif`
ls = ls.chomp
files = ls.split(/\n/)

#puts ls

$maxthread = 5;

$threads = []

files.each{ |file|
# generate the 532 file
file532 = file.sub(/_635_/, ‘_532_’)
file=~/_A(\d\d)_/
blocknum = $1
#puts “block “+blocknum+”\n”
#puts “name ” + file + “\n”
#puts “new name ” + file532 + “\n”

if($command == ‘pair’ || $command == ‘both’ )
cmd = bin + paircmd + designpath + designfile + blocknum + “.ndf” + ” -i ” + file
$threads << Thread.new(cmd) { |mycmd|
puts cmd + “\n”
system(cmd);
}
cmd = bin + paircmd + designpath + designfile + blocknum + “.ndf” + ” -i ” + file532
$threads << Thread.new(cmd) { |mycmd|
puts cmd + “\n”
system(cmd);
}
end

threadlist = Thread.list;
while(threadlist.length >= $maxthread)
threadlist = Thread.list;
puts “Threadcount ” + threadlist.length.to_s + ” join thread\n”
sleep(10);
$threads[0].join;
end
}

$threads.each { |mythread| mythread.join }

ls = `ls -1 *_635_*.pair`
ls = ls.chomp
files = ls.split(/\n/)

files.each{ |file|
file532 = file.sub(/_635_/, ‘_532_’)
file=~/_A(\d\d)_/
blocknum = $1

file=~/(.+)_635_grid\.pair/
rootname = $1

if($command == ‘gff’ || $command == ‘both’ )

cmd = bin + gffcmd + ” -c “+ rootname + ” -p ” + designpath + designfile + blocknum + “.pos ” + file + ” ” + file532
$threads << Thread.new(cmd) { |mycmd|
puts cmd + “\n”
system(cmd);
}

end

threadlist = Thread.list;
while(threadlist.length >= $maxthread)
threadlist = Thread.list;
puts “Threadcount “+ threadlist.length.to_s + ” join thread\n”
sleep(10);
$threads[0].join;
end
}

$threads.each { |mythread| mythread.join }

ruby script to autogenerate pair and gff files