Given range random intervals from the given set (Bioinformatic problem)

poegi has asked for the wisdom of the Perl Monks concerning the following question:

I do have:

Ranges:
500
450
899
461

Genome Data (SequenceName and it's length (from 1 to milions)): 
nameA 985544
nameB 454552
nameC 47884
....
....
[download]

I want to: Generate given range random intervals from Genome Data.

Workflow goes like that:

1. Script takes range from (Ranges);

2. Randomly chooses name from Genome Date;

3. Randomly 'picks up' given range interval from the name's length.

Any help?

PS.: Problem from the biological perspective is:

I have sequences of interest from the Genome Data with Name and Sequences. I want to randomly generate save length sequences from the same dataset. Right now my script only generates positions, but not the intervals

Comment on Given range random intervals from the given set (Bioinformatic problem) Download Code

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Re: Given length random intervals from the given set (Bioinformatic problem) by moritz (Cardinal) on Apr 04, 2012 at 07:59 UTC
Update: OP changed the question completely, so now my reply only makes limited sense. Most of the perl monks who read your question are pretty good at Perl, but know next to nothing at about biology. So if you want helpful replies, you should explain what you mean with Generate given Length random intervals from Genome data in a way that doesn't require prior biology knowledge. And you also need to explain how that should lead to the expected output. Also we don't know what `length.pl` does, so we can't even try to run your program. Perl 6 - second systems done right	[reply] [d/l]
Re: Given range random intervals from the given set (Bioinformatic problem) by Sinistral (Monsignor) on Apr 04, 2012 at 13:32 UTC
Have you seen the ever popular BioPerl site? They might be able to help better than the Monks, since Bioinformatics is the specialization of the site.	[reply]
Re: Given range random intervals from the given set (Bioinformatic problem) by snape (Pilgrim) on Apr 04, 2012 at 21:09 UTC
This may help you `use strict; use warnings; my %rangeFile; ## hash my %geneomeFile; ## From the Range Data File open my $IN2, "RangeFile.txt" or die $! while(<$IN1>){ chomp($_); $rangeFile{$_} = 1; } close($IN1); ## From Genome Data open my $IN2, "GenomeFile.txt" or die $! while(<$IN2>){ chomp($_); my @line = split('\t', $_); ## considering if genome data is t +ab-del file $genomeFile{$_} = 1; } close($IN2); ## Randomly Choosing Name from Genome Data foreach (rand keys %hash){ #### Code for step 3 ### }` [download] Btw, I didnt understan your step 3.	[reply] [d/l]