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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Nuc_translator;
use IO::Uncompress::Gunzip;
use Getopt::Long qw(:config no_ignore_case bundling);
my $usage = <<_EOUSAGE_;
##########################################################
#
# -I <string> input.fq or "input1.fq,input2.fq,input3.fq"
#
# --ignoreDirty ignores poorly formed entries
#
# -a <int> append "/num" to the accession name.
#
# --rev reverse complement nucleotide sequence.
#
###########################################################
_EOUSAGE_
;
my $inputFile;
my $ignore_dirty = 0;
my $append_num;
my $revcomp_flag = 0;
&GetOptions( 'I=s' => \$inputFile,
'ignore_dirty' => \$ignore_dirty,
'a=i' => \$append_num,
'rev' => \$revcomp_flag,
);
unless ($inputFile) {
die $usage;
}
main: {
my @files = split(/,/, $inputFile);
foreach my $file (@files) {
$file =~ s/\s//g;
if ($file =~ /\w/) {
&fastQ_to_fastA($file);
}
}
exit(0);
}
sub fastQ_to_fastA {
my ($file) = @_;
my $fh = new IO::Uncompress::Gunzip($file) or die "Error, cannot open file $file";
my $counter = 0;
my $num_clean = 0;
my $num_dirty = 0;
while (my $line = <$fh>) {
$line =~ s/\cM//g; # remove any cntrl-M characters (sometimes derived from MS-windows text files)
if ($line =~ /^\@/) {
$counter++;
# print STDERR "\r[$counter] [$num_clean clean] [$num_dirty dirty] " if ($counter % 10000 == 0);
my $header = $line;
my $seq = <$fh>;
my $qual_header = <$fh>;
my $qual_line = <$fh>;
chomp $header;
chomp $seq if $seq;
chomp $qual_header if $qual_header;
chomp $qual_line if $qual_line;
if ($header && $seq && $qual_header && $qual_line =~ /\S/ &&
$qual_header =~ /^\+/ && length($seq) == length($qual_line)) {
# can do some more checks here if needed to be sure that the lines are formatted as expected.
substr($header,0,1,''); # strip beginning "@"
my @header_parts = split(/\s+/, $header);
$header = shift @header_parts;
if (@header_parts && $header !~ m|/[12]$| && $header_parts[0] =~ /^([12])\:/) {
$header .= "/$1";
}
if (defined $append_num) {
$header .= "/$append_num";
}
if ($revcomp_flag) {
$seq = &reverse_complement($seq);
}
print ">$header\n$seq\n";
$num_clean++;
}
else {
$num_dirty++;
unless ($ignore_dirty) {
die "Error, improperly formatted entry:\n\n$header\n$seq\n$qual_header\n$qual_line\n";
}
}
}
}
return;
}
|
