我正在尝试使用以下脚本来打乱文件中序列(行)的顺序。我不确定如何“初始化”值——请帮忙!
print "Please enter filename (without extension): ";
my $input = <>;
chomp $input;
use strict;
use warnings;
print "Please enter total no. of sequence in fasta file: ";
my $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!";
my @array = (0); # Need to initialise 1st element in array1&2 for the shift function
my @array2 = (0);
my $i = 1;
my $index = 0;
my $index2 = 0;
while (my @line = <INFILE>){
while ($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 = my $header_size; $i >= 0; $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 <= my $header_size) {
print SHUFFLED "$array[$index2]\n";
print SHUFFLED "$array2[$index2]\n";
$index2++;
}
close INFILE;
close SHUFFLED;
我收到以下警告:
Use of uninitialized value in substitution (s///) at fasta_corrector6.pl line 27, <INFILE> line 578914.
Use of uninitialized value in substitution (s///) at fasta_corrector6.pl line 31, <INFILE> line 578914.
Use of uninitialized value in numeric ge (>=) at fasta_corrector6.pl line 40, <INFILE> line 578914.
Use of uninitialized value in addition (+) at fasta_corrector6.pl line 41, <INFILE> line 578914.
Use of uninitialized value in numeric eq (==) at fasta_corrector6.pl line 42, <INFILE> line 578914.
Use of uninitialized value in numeric le (<=) at fasta_corrector6.pl line 47, <INFILE> line 578914.
Use of uninitialized value in numeric le (<=) at fasta_corrector6.pl line 50, <INFILE> line 578914.