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|
#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling);
my $usage = <<_EOUSAGE_;
##########################################################
#
# -I <string> input.fq
#
# --ignore_dirty ignores poorly formed entries
#
# -a <int> append "/num" to the accession name.
#
# -v verbose
#
###########################################################
_EOUSAGE_
;
my $inputFile;
my $ignore_dirty = 0;
my $append_num;
my $VERBOSE = 0;
&GetOptions( 'I=s' => \$inputFile,
'ignore_dirty' => \$ignore_dirty,
'a=i' => \$append_num,
'v' => \$VERBOSE,
);
unless ($inputFile) {
die $usage;
}
my $fh;
if ($inputFile =~ /\.gz$/) {
open ($fh, "gunzip -c $inputFile | ") or die $!;
}
else {
open ($fh, $inputFile) or die "Error, cannot open $inputFile";
}
my $counter = 0;
my $num_clean = 0;
my $num_dirty = 0;
my @rec;
my $line = <$fh>;
while ($line) {
if ($line =~ /^\@/) {
$counter++;
print STDERR "\r[$counter] [$num_clean clean] [$num_dirty dirty] " if ($counter % 10000 == 0 && $VERBOSE);
push (@rec, $line);
$line = <$fh>;
for (1..3) {
push (@rec, $line);
$line = <$fh>;
}
my $record_text = join("", @rec);
my $header = shift @rec;
my $seq = shift @rec;
my $qual_header = shift @rec;
my $qual_line = shift @rec;
chomp $header;
chomp $seq if $seq;
chomp $qual_header if $qual_header;
chomp $qual_line if $qual_line;
my @header_pts = split(/\s+/, $header);
if (scalar @header_pts > 1) {
$header = shift @header_pts;
}
if ($header && $seq && $qual_header && $qual_line &&
$qual_header =~ /^\+/ && length($seq) == length($qual_line)) {
# can do some more checks here if needed to be sure that the lines are formatted as expected.
$header =~ s/^\@//;
## convert casava format over
my @pts = split(/\s+/, $header);
if (scalar @pts > 1 && $pts[1] =~ /^([12]):/) {
my $val = $1;
$header = $pts[0] . "/$val";
}
elsif ($append_num) {
$header .= "/$append_num";
}
print "$header\t$seq\t$qual_line\n";
$num_clean++;
}
else {
$num_dirty++;
unless ($ignore_dirty) {
die "Error, improperly formatted entry:\n\n$record_text ";
}
}
@rec = ();
} else {
$line = <$fh>;
}
}
exit(0);
|
