Mercurial > repos > estrain > seqsero_v1

comparison SeqSero/libs/splitPairedEndReads.pl @ 0:c577b57b7c74 draft

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author estrain
date Wed, 06 Dec 2017 15:59:29 -0500
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-1:000000000000 0:c577b57b7c74
1 use strict;
2 use warnings;
3 my $file = $ARGV[0];
4 open(FILE, "<$file") || die "cannot open $file\n";
5 open(OUT1, ">$file\_1") || die "cannot open $file\_1\n";
6 open(OUT2, ">$file\_2") || die "cannot open $file\_2\n";
7 while(<FILE>){
8 chomp;
9 print OUT1 "$_\/1\n";
10 print OUT2 "$_\/2\n";
11 my $newline = <FILE>; chomp($newline);
12 print OUT1 substr($newline, 0, length($newline)/2)."\n";
13 print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n";
14 $newline = <FILE>; chomp($newline);
15 print OUT1 "$newline\/1\n";
16 print OUT2 "$newline\/2\n";
17 $newline = <FILE>; chomp($newline);
18 print OUT1 substr($newline, 0, length($newline)/2)."\n";
19 print OUT2 substr($newline, length($newline)/2, length($newline)/2)."\n";
20 }
21 close(FILE);