Summary

Bio::SeqIO::fastq - fastq sequence input/output stream

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

Do not use this module directly. Use it via the Bio::SeqIO class.

Description

This object can transform Bio::Seq and Bio::Seq::SeqWithQuality
objects to and from fastq flat file databases.
Fastq is a file format used frequently at the Sanger Centre to bundle
a fasta sequence and its quality data. A typical fastaq entry takes
the from:

  @HCDPQ1D0501
  GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT.....
  +HCDPQ1D0501
  !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65.....

Fastq files have sequence and quality data on a single line and the
quality values are single-byte encoded. To retrieve the decimal values
for qualities you need to subtract 33 (or Octal 41) from each byte and
then convert to a '2 digit + 1 space' integer. You can check if 33 is
the right number because the first byte which is always '!'
corresponds to a quality value of 0.

Methods

Methods description

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq::SeqWithQuality object
 Args    : NONE

 Title   : write_seq
 Usage   : $stream->write_seq(@seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq::SeqWithQuality or Bio::seq object

 Title   : write_qual
 Usage   : $stream->write_qual(@seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq::SeqWithQuality object

 Title   : write_fastq
 Usage   : $stream->write_fastq(@seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq::SeqWithQuality object

Methods code

sub _initialize {

  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);  
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(new Bio::Seq::SeqFactory(-verbose => $self->verbose(), -type => 'Bio::Seq::SeqWithQuality'));      
  }

}

sub next_seq {

  my( $self ) = @_;
  my $seq;
  my $alphabet;
  local $/ = "\n\@";

  return unless my $entry = $self->_readline;

  if ($entry eq '@')  {  # very first one
    return unless $entry = $self->_readline;
  }
  my ($top,$sequence,$top2,$qualsequence) = $entry =~ /^
                                                        \@?(.+?)\n
                                                        ([^\@]*?)\n
                                                        \+?(.+?)\n
                                                        (.*)\n
                                                      /xs
    or $self->throw("Can't parse fastq entry");
  my ($id,$fulldesc) = $top =~ /^\s*(\S+)\s*(.*)/
    or $self->throw("Can't parse fastq header");
  if ($id eq '') {$id=$fulldesc;}   # FIX incase no space between \@ and name
  $sequence =~ s/\s//g;             # Remove whitespace
  $qualsequence =~ s/\s//g;
  
  if(length($sequence) != length($qualsequence)){
    $self->warn("Fastq sequence/quality data length mismatch error\n");
    $self->warn("Sequence: $top, seq length: ",length($sequence), " Qual length: ", length($qualsequence), "\n ");
    $self->warn("$sequence\n");
    $self->warn("$qualsequence\n");
    $self->warn("FROM ENTRY:\n\n $entry\n");
  }

  my @qual = split('', $qualsequence);

  my $qual;
  foreach (@qual) {$qual .=  (unpack("C",$_) - 33) ." "};
  

  # for empty sequences we need to know the mol.type
  $alphabet = $self->alphabet();
  if(length($sequence) == 0) {
      if(! defined($alphabet)) {
	  # let's default to dna
	  $alphabet = "dna";
      }
  } else {
      # we don't need it really, so disable
      $alphabet = undef;
  }

  # create the SeqWithQuality object
  $seq = $self->sequence_factory->create(
					 -qual         => $qual,
					 -seq          => $sequence,
					 -id           => $id,
					 -primary_id   => $id,
					 -desc         => $fulldesc,
					 -alphabet     => $alphabet
					 );
  
  # if there wasn't one before, set the guessed type
  $self->alphabet($seq->alphabet());
  
  return $seq;

}

sub write_seq {

   my ($self,@seq) = @_;
   foreach my $seq (@seq) {
     my $str = $seq->seq;
     my $top = $seq->display_id();
     if ($seq->can('desc') and my $desc = $seq->desc()) {
	 $desc =~ s/\n//g;
        $top .= " $desc";
     }
     if(length($str) > 0) {
	    $str =~ s/(.{1,60})/$1\n/g;
     } else {
	    $str = "\n";
     }
     
     $self->_print (">",$top,"\n",$str) or return;
   }

   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return 1;

}

sub write_qual {

   my ($self,@seq) = @_;
   foreach my $seq (@seq) {
     unless ($seq->isa("Bio::Seq::SeqWithQuality")){
        warn("You can write FASTQ without supplying a Bio::Seq::SeqWithQuality object! ", ref($seq), "\n");
        next;
     } 
     my @qual = @{$seq->qual};
     my $top = $seq->display_id();
     if ($seq->can('desc') and my $desc = $seq->desc()) {
	 $desc =~ s/\n//g;
        $top .= " $desc";
     }
     my $qual = "" ;
     if(scalar(@qual) > 0) {
        my $max = 60;
        for (my $q = 0;$q<scalar(@qual);$q++){
            $qual .= $qual[$q] . " ";
            if(length($qual) > $max){
                $qual .= "\n";
                $max += 60;
            }
        }
     } else {
	    $qual = "\n";
     }
     
     $self->_print (">",$top,"\n",$qual,"\n") or return;
   }
   return 1;

}

sub write_fastq {

   my ($self,@seq) = @_;
   foreach my $seq (@seq) {
     unless ($seq->isa("Bio::Seq::SeqWithQuality")){
        warn("You can write FASTQ without supplying a Bio::Seq::SeqWithQuality object! ", ref($seq), "\n");
        next;
     } 
     my $str = $seq->seq;
     my @qual = @{$seq->qual};
     my $top = $seq->display_id();
     if ($seq->can('desc') and my $desc = $seq->desc()) {
	 $desc =~ s/\n//g;
        $top .= " $desc";
     }
     if(length($str) == 0) {
	    $str = "\n";
     }
     my $qual = "" ;
     if(scalar(@qual) > 0) {
        for (my $q = 0;$q<scalar(@qual);$q++){
            $qual .= chr($qual[$q] + 33);
        }
     } else {
	    $qual = "\n";
     }
     
     $self->_print ("\@",$top,"\n",$str,"\n") or return;
     $self->_print ("+",$top,"\n",$qual,"\n") or return;
   }
   return 1;

}

General documentation

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Email: avc@sanger.ac.uk

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _