My intention is to simulate random positions.

I do have: Range (length of my gene) - this should be Start & End positions; Genome - dataset where those ranges should be randomly "attached" hence getting random position.

I already have this: Input - ranges & genome dataset (lots of letters - sorry guys can't post it here).

There is some kind of a mistake in that script and I can't spot it - hope someone could easily solve this misspelling. Whole idea of the script is to: split genome into chromosomes (names) -> get their length -> "attach" my range -> get start & end.

 #!/usr/bin/perl

 use strict;
 use warnings;
 use File::Spec;

my @name;
my @length;
open(GENDATA, "<$ARGV[1]");
while (<GENDATA>) {
    chomp($_);
    my @field=split(/\t/, $_);
    push(@length, $field[1]);
    push(@name, $field[0]);
}
close(GENDATA);

open(RANGE, "<$ARGV[0]");
while (<RANGE>) {
  chomp($_);
 my $simlen = $_;
 my $randname = 0;
 my $randpos = 0;
   do {
    $randname = int(rand(scalar(@name)));
    $randpos = int(rand($length[$randname] - $simlen - 1));
   print $name[$randname] ."\t". $randpos ."\t". ($randpos + $simlen) 
+."\n";
}}
close(RANGE);
[download]

Examples:

Range

48
479
324
69
12
[download]

Gendata

>chr4.fa_58086846_58087846
GGGATAAGGTGGAAGCAATGATTTAATCACCACAGAAGAAATGTGCTCTGATTAATTGGG
AAGAAAGATTTTAAAATTAGAGTTATTCAGAAAGCCTGTCAGGAGACCAGGAAGAGAGGA
AAGGATGTGTGTCAACACCTACAGAAAGCTGTCTGTGAAGCTGGGTTATAACCTGATACT
TCTGGTCTTCCCTGTAACTAAATGTCCTTTGCTGAGGCCTGAGGCAGACCCTTACTCTGG
GTTTCCTGTTCCTGTATGACTAGTTTCAGTCAGGCTTTACGTAGTCATTCTGCCCTGCAG
AGCAATCACAGGAGGTAAGAAGGCATGGTCGTTAATAGCATGGGCTATGCTGTTGGACTT
GAATTTGGTCTTGTTTCTATCACATTCTGTAATTTAGTTGAAAAATGGAAATAACACCTA
TCTCAAGGGTTTGTTGCAAAGACTACATGAGATTATACATGCACAGCGCTTAGTACAGTG
TCTGATACATAGTAAATGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTATTATACTCTAAG
TTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTG
GTGCGCTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTC
CCCCCTCCCCCGACCCCACCTCAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATG
TGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTC
TTGCGATAGTTTACTGAGAATGATGGTTTCCAATTTCATCCATGTCCCTACAAAGGATAT
GAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGAGTAAATGTTCT
TTAGCAGCTGTCATTATCATTTTAGAGACAGAGTCTTGCTGGCATTATCTTCCCCATTTT
GCTCATGGAGAAACTGAAATAAGAAAATTATAGTCTGACT
[download]