-
Notifications
You must be signed in to change notification settings - Fork 7
/
fastq-se2ipe.pl
executable file
·52 lines (43 loc) · 1.1 KB
/
fastq-se2ipe.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
#!/usr/bin/env perl
use strict;
use warnings;
my $fastqfile = $ARGV[0];
die "Missing single-end .fastq file" unless ($fastqfile);
die "Wrong single-end .fastq file ($fastqfile)" unless (-e $fastqfile);
my $id;
my $desc;
my $seq;
my $qual;
open(IN, "<", $fastqfile) or die $!;
while(<IN>) {
chomp;
if ($. % 4 == 1) {
($id, $desc)=$_=~/^(\S+)(?:\s*(.*))?/;
} elsif ($. % 4 == 2) {
$seq=$_;
} elsif ($. % 4 == 0) {
$qual=$_;
my $newqual=$qual;
my $newseq=$seq;
print $id,(($desc) ? " $desc" : ''),"\n",
$newseq,"\n",
'+',"\n",
$newqual,"\n";
my $newqualrev = reverse($newqual);
my $newseqrev = reverse($newseq);
my $newseqrevcom = $newseqrev;
$newseqrevcom =~tr/acgtnACGTN/tgcanTGCAN/;
if ($desc) {
if ($desc=~/^\s*1\b/) {
$desc=~s/1\b/2/;
} elsif ($desc=~/^\s*2\b/) {
$desc=~s/2\b/1/;
}
}
print $id,(($desc) ? " $desc" : ''),"\n",
$newseqrevcom,"\n",
'+',"\n",
$newqualrev,"\n";
}
}
close(IN);