15) Perl script to randomly shuffle sequences in a fasta file

This perl script randomly shuffles the order of sequences in a fasta file. Upon execution, specify your input file (without .fasta extension) and total no. of sequences.

Output:  Output file xxx_shuffled.fasta will be produced

Note: Again, this script is cut out from a sub-routine and there may be bugs in terms of variable names and definitions.

#! /usr/bin/perl

print "Please enter filename (without extension): ";

$input = <>;

chomp ($input);

print "Please enter total no. of sequence in fasta file: ";

$orig_size= <>*2-1;

chomp ($orig_size);

open (INFILE, "$input.fasta") or die "Error opening input file for shuffling!";

open (SHUFFLED, ">"."$input"."_shuffled.fasta") or die "Error creating shuffled output file!";

@array = (0); # Need to initialise 1st element in array1&2 for the shift function

@array2 = (0);

$i = 1;

$index = 0;

$index2 = 0;

while (my @line=<INFILE>){

while ($i<=$orig_size) { 

$array[$i] = $line[$index];

$array[$i]=~ s/(.)\s/$1/seg;

$index++;

$array2[$i] = $line[$index];

$array2[$i]=~ s/(.)\s/$1/seg;

$i++;

$index++;

}

}

    my $array = shift (@array); 

    my $array2 = shift (@array2);

    for ($i = $header_size; --$i; ) { 

        my $j = int rand ($i+1);

        next if $i == $j;

        @array[$i,$j] = @array[$j,$i];

@array2[$i,$j] = @array2[$j,$i];

    }

while ($index2<=$header_size) { 

print SHUFFLED "$array[$index2]\n";

print SHUFFLED "$array2[$index2]\n";

$index2++;

}

close(INFILE);

close(SHUFFLED);

}