Randomly selecting sequences and generating specific output files Post: 302786047

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Top Forums Shell Programming and Scripting Randomly selecting sequences and generating specific output files Post 302786047 by Xterra on Tuesday 26th of March 2013 06:04:19 PM

03-26-2013

Registered User

Randomly selecting sequences and generating specific output files

I have two files containing hundreds of different sequences with the same Identifiers (ID-001, ID-002, etc.,), something like this:
Infile1:

Code:

ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGGAGAGAAGCTAGATACA 
ID-002 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-004 ATTTGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATAGT

Infile2:

Code:

ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGG 
ID-002 ATGGGAGCGGGGGCGTCTGTTTTGAGGGG 
ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGG 
ID-004 ATTTGAGCGGGGGCGTCTGTTTTGAGGGG 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGG

I need an awk script that can randomly select a number of sequences, let say 3, with the same IDs from both input files and generate two different outfiles, something like this:
Outfile1-1:

Code:

ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGGAGAGAAGCTAGATACA 
ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATAGT

Oufile2-1:

Code:

ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGG 
ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGG 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGG

I need to repeat this process a number of times, let say 10 times, and generate the corresponding Outfiles (Outfile1-2 and Outfile2-2; Outfile1-3 and Outfile2-3; Outfile1-4 and Outfile2-4; etc.,). Thus, the second pair of files will look like this:
Outfile1-2:

Code:

ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-004 ATTTGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATAGT

Outfile2-2:

Code:

ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGG 
ID-004 ATTTGAGCGGGGGCGTCTGTTTTGAGGGG 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGG

I really do not know how to do the randomization, and therefore, any help will be greatly appreciated.

Last edited by Scrutinizer; 03-27-2013 at 02:37 AM.. Reason: code tags instead of quote tags and format removal

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