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Re: Random shuffling

by hexcoder (Deacon)
on Jun 20, 2015 at 15:47 UTC ( #1131265=note: print w/replies, xml ) Need Help??

in reply to Random shuffling

If your DNA sequences don't contain any separators, the code looks okay to me.

I would optimize the processing in order to avoid wasting time and memory.

  • You only need to hold two input lines in memory, since there are no dependencies to other lines.
  • One random shuffle should be enough to make it random.
  • I would check whether the input file contains an even number of lines, that is when retrieving a pair of lines, check first, if the DNA sequence line is present.
  • $final_seq should be initialized to the empty string in order to avoid a warning on an 'undefined' value.
So in summary I would write it like this (untested!):
use strict; use warnings; use List::Util 'shuffle'; # Idea from +d=199901 my $input = shift @ARGV; open(IN, '<', $input) or die "Can't read multifasta input genomic DNA +file $input : $!\n"; my $destination = $input."_1MBWindow_ListUtilshuffle.fasta"; open(OUT, '>', $destination) or die "Can't write to file $destination: + $!\n"; my $window = 1000000; # hard coded for shuffle window to be 1MB i.e 10 +^6 my ($seq_id, $seq); # process every alternate line with ID (and its corresponding sequence + in next line) while (defined($seq_id = <IN>) { if (!defined($seq = <IN>) { last; } chomp $seg_id; chomp $seg; my $final_seq = ''; for (my $i = 1; $i <= length $seq; $i += $window ) { my $s = substr ($seq, $i - 1, $window); my @temp_seq_array = split //, $s; @temp_seq_array = shuffle @temp_seq_array; # using the List::U +til module AND Shuffles EACH window!!! my $rand_shuffled_seq = join ('', @temp_seq_array,); $final_seq .= $rand_shuffled_seq; # concatenates the shuffled DNA +seq to the 3' end of the previous 1MB fragment } print OUT $seq_id, "\n",$final_seq,"\n"; } close IN; close OUT;

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Re^2: Random shuffling
by onlyIDleft (Scribe) on Jun 21, 2015 at 00:13 UTC

    Please see my UPDATE 1 to the original post, perhaps your answer may change or need modification in light of the additional info I have provided?

Re^2: Random shuffling
by onlyIDleft (Scribe) on Jun 20, 2015 at 18:27 UTC

    Thank you hexcoder. I appreciate your inputs to write out a modified version of my script to make the runs quicker and more memory efficient. Cheers! PS. There are no separators in the DNA sequences....

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