/usr/share/seqsero/libs/splitPairedEndReads.pl is in seqsero 1.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | use strict;
use warnings;
my $file = $ARGV[0];
open(FILE, "<$file") || die "cannot open $file\n";
open(OUT1, ">$file\_1") || die "cannot open $file\_1\n";
open(OUT2, ">$file\_2") || die "cannot open $file\_2\n";
while(<FILE>){
chomp;
print OUT1 "$_\/1\n";
print OUT2 "$_\/2\n";
my $newline = <FILE>; chomp($newline);
print OUT1 substr($newline, 0, length($newline)/2)."\n";
print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n";
$newline = <FILE>; chomp($newline);
print OUT1 "$newline\/1\n";
print OUT2 "$newline\/2\n";
$newline = <FILE>; chomp($newline);
print OUT1 substr($newline, 0, length($newline)/2)."\n";
print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n";
}
close(FILE);
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