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package FASTX::Seq;
#ABSTRACT: A class for representing a sequence for FASTX::Reader
use 5.012;
use warnings;
use Carp qw(confess);
use Data::Dumper;
$Data::Dumper::Sortkeys = 1;
use File::Basename;
$FASTX::Seq::VERSION = $FASTX::Reader::VERSION;
require Exporter;
our @ISA = qw(Exporter);
sub new {
  
    my ($class, $seq, $name, $comment, $qual) = @_;
  
    if ( defined $seq && defined $qual
      && (length($seq) != length($qual))) {
        confess "Sequence/quality length mismatch";
    }
  
    my $self = bless {}, $class;
    # Required
    $self->{seq}  = $seq  // '';
    $self->{name} = $name   // undef;
    $self->{comment} = $comment // undef;
    $self->{qual} = $qual // undef;
  
    return $self;
  
}
sub seq : lvalue {
    # Update sequence
    my ($self, $new_val) = @_;
    $self->{seq} = $new_val if (defined $new_val);
    return $self->{seq};
}
sub name : lvalue {
    # Update name
    my ($self, $new_val) = @_;
    $self->{seq} = $new_val if (defined $new_val);
    return $self->{name};
}
sub qual : lvalue {
    # Update quality
    my ($self, $new_val) = @_;
    $self->{qual} = $new_val if (defined $new_val);
    return $self->{qual};
}
sub comment : lvalue {
    # Update comment
    my ($self, $new_val) = @_;
    $self->{comment} = $new_val if (defined $new_val);
    return $self->{comment};
}
sub rev {
    # Update comment
    my ($self) = @_;
    $self->{seq} = reverse($self->{seq});
    $self->{qual} = reverse($self->{qual}) if (defined reverse($self->{qual}));
    return $self;
}
sub len {
    # Update comment
    my ($self) = @_;
    return length($self->{seq});
}
sub rc {
    # Update comment
    my ($self) = @_;
    $self->{seq} = reverse($self->{seq});    
    if ($self->{seq} =~ /U/i) {
        $self->{seq} =~ tr/ACGURYSWKMBDHVacguryswkmbdhv/UGCAYRSWMKVHDBugcayrswmkvhdb/;
    } else {                      
        $self->{seq} =~ tr/ACGTRYSWKMBDHVacgtryswkmbdhv/TGCAYRSWMKVHDBtgcayrswmkvhdb/;
    }
    $self->{qual} = reverse($self->{qual}) if (defined reverse($self->{qual}));
    return $self;
}
sub asfasta {
    # Update comment
    my ($self) = @_;
    my $space = length($self->{comment}) > 0 ? " " : "";
    my $name  = $self->{name} // "sequence";
    my $comment = length($self->{comment}) > 0 ? " " . $self->{comment} : "";
    return ">" . $name . $comment . "\n" . $self->{seq} . "\n";
}
sub asfastq {
    # Update comment
    my ($self) = @_;
    my $name  = $self->{name} // "sequence";
    my $comment = length($self->{comment}) > 0 ? " " . $self->{comment} : "";
    my $quality = defined $self->{qual} ? " " . $self->{qual} : "I" x length($self->{seq});
    return "@" . $name . $comment . "\n" . $self->{seq} . "\n+\n" . $quality;
}
1;
__END__
HideShow 104 lines of Pod
=pod
=encoding UTF-8
=head1 NAME
FASTX::Seq - A class for representing a sequence for FASTX::Reader
=head1 VERSION
version 1.5.1
=head1 SYNOPSIS
A sequence object supported from C<FASTX::Reader> structured as
a C<BioX::Seq> record, but keeping the attribute names as the
scalar natively provided by C<FASTX::Reader>.
  use FASTX::Seq;
  my $fastq = new($seq, $name, $comment, $qual);
  my $fasta = new($seq, $name, $comment);
  my $barseq = new("ATGC"); 
  # Change attribute
  $fastq->seq("ATGCTT");
=head2 new($seq, $name, $comment, $qual)
Create a new instance of C<FASTX::Seq>.
The sequence is the only required field.
=head2 seq()
Get or update the sequence field.
    my $seq = $fastq->seq();
    $fastq->seq("ATGCTT");
=head2 name()
Get or update the sequence field.
    my $seq = $fastq->name();
    $fastq->name("seq1");
=head2 qual()
Get or update the sequence field.
    my $seq = $fastq->qual();
    $fastq->qual("IIIII");
=head2 comment()
Get or update the sequence field.
    my $seq = $fastq->comment();
    $fastq->comment("len=" . length($fastq->seq()));
=head2 rev()
Reverse (no complement) the sequence.
    my $rev = $fastq->rev();
=head2 len()
Length of the sequence
    my $len = $fastq->len();
=head2 rc()
Reverse and complement the sequence.
    my $rc = $fastq->rc();
=head2 asfasta()
Return the sequence as a FASTA string.
    my $fasta = $seq->asfasta();
=head2 asfastq()
Return the sequence as a FASTQ string. Will use a dummy fixed value quality
if the sequence didnt have a quality string.
    my $fasta = $seq->asfastq();
=head1 AUTHOR
Andrea Telatin <andrea@telatin.com>
=head1 COPYRIGHT AND LICENSE
This software is Copyright (c) 2019 by Andrea Telatin.
This is free software, licensed under:
  The MIT (X11) License
=cut