Bio::SeqIO::fastq(3pm)

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

SYNOPSIS
  ################## pertains to FASTQ parsing only ##################

  # grabs the FASTQ parser, specifies the Illumina variant
  my $in = Bio::SeqIO->new(-format    => 'fastq-illumina',
                           -file      => 'mydata.fq');

  # simple 'fastq' format defaults to 'sanger' variant
  my $out = Bio::SeqIO->new(-format    => 'fastq',
                            -file      => '>mydata.fq');

  # $seq is a Bio::Seq::Quality object
  while (my $seq = $in->next_seq) {
      $out->write_seq($seq);  # convert Illumina 1.3 to Sanger format
  }

  # for 4x faster parsing, one can do something like this for raw data
  use Bio::Seq::Quality;

  # $data is a hash reference containing all arguments to be passed to
  # the Bio::Seq::Quality constructor
  while (my $data = $in->next_dataset) {
      # process $data, such as trim, etc
      my $seq = Bio::Seq::Quality->new(%$data);

      # for now, write_seq only accepts Bio::Seq::Quality, but may be modified
      # to allow raw hash references for speed
      $out->write_seq($data);
  }

DESCRIPTION
This object can transform Bio::Seq and Bio::Seq::Quality objects to and from FASTQ flat file databases.

FASTQ is a file format used frequently at the Sanger Centre and in next-gen sequencing to bundle a FASTA sequence and its quality data. A typical FASTQ entry takes the form:

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

where:

  @ = descriptor, followed by one or more sequence lines
  + = optional descriptor (if present, must match first one), followed by one or
      more qual lines

When writing FASTQ output the redundant descriptor following the '+' is by default left off to save disk space. If needed, one can set the quality_header() flag in order for this to be printed.

  FASTQ and Bio::Seq::Quality mapping
FASTQ files have sequence and quality data on single line or multiple lines, and the quality values are single-byte encoded. Data are mapped very simply to Bio::Seq::Quality instances:

    Data                                        Bio::Seq::Quality method
    ------------------------------------------------------------------------
    first non-whitespace chars in descriptor    id^
    descriptor line                             desc^
    sequence lines                              seq
    quality                                     qual*
    FASTQ variant                               namespace

    ^ first nonwhitespace chars are id(), everything else after (to end of line)
      is in desc()
    * Converted to PHRED quality scores where applicable ('solexa')

  FASTQ variants
This parser supports all variants of FASTQ, including Illumina v 1.0 and 1.3:

    variant                note
    -----------------------------------------------------------
    sanger                 original
    solexa                 Solexa, Inc. (2004), aka Illumina 1.0
    illumina               Illumina 1.3

The variant can be specified by passing by either passing the additional -variant parameter to the constructor:

  my $in = Bio::SeqIO->new(-format    => 'fastq',
                           -variant   => 'solexa',
                           -file      => 'mysol.fq');

or by passing the format and variant together (Bio::SeqIO will now handle this and convert it accordingly to the proper argument):

  my $in = Bio::SeqIO->new(-format    => 'fastq-solexa',
                           -file      => 'mysol.fq');

Variants can be converted back and forth from one another; however, due to the difference in scaling for solexa quality reads, converting from 'illumina' or 'sanger' FASTQ to solexa is not recommended.

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHORS - Chris Fields (taken over from Tony Cox)
Email: cjfields at bioperl dot org

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

Bio::SeqIO interface methods

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

  write_seq
 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::Quality
 Note     : This now conforms to SeqIO spec (module output is same format as
            next_seq)
 Status   : Stable

  variant
 Title   : variant
 Usage   : $format  = $obj->variant();
 Function: Get and set method for the quality sequence variant.  This is
           important for indicating the encoding/decoding to be used for
           quality data.

           Current values accepted are:
            'sanger'   (original FASTQ)
                ASCII encoding from 33-126, PHRED quality score from 0 to 93
            'solexa'   (aka illumina1.0)
                ASCII encoding from 59-104, SOLEXA quality score from -5 to 40
            'illumina' (aka illumina1.3)
                ASCII encoding from 64-104, PHRED quality score from 0 to 40

            (Derived from the MAQ website):
            For 'solexa', scores are converted to PHRED qual scores using:
                $Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10)

 Returns : string
 Args    : new value, string

Plugin-specific methods

  next_dataset
 Title    : next_dataset
 Usage    : $obj->next_dataset
 Function : returns a hash reference containing the parsed data
 Returns  : hash reference
 Args     : none
 Status   : Stable

  write_fastq
 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::Quality object
 Status  : Deprecated (delegates to write_seq)

  write_fasta
 Title   : write_fasta
 Usage   : $stream->write_fasta(@seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq object
 Note    : This method does not currently delegate to Bio::SeqIO::fasta
           (maybe it should?).  Not sure whether we should keep this as a
           convenience method.
 Status  : Unstable

  write_qual
 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::Quality object
 Note    : This method does not currently delegate to Bio::SeqIO::qual
           (maybe it should?).  Not sure whether we should keep this as a
           convenience method.
 Status  : Unstable

  validate
 Title    : validate
 Usage    : $obj->validate(0)
 Function : flag for format/qual range validation - default is 1, validate
 Returns  : Bool (0/1)
 Args     : Bool (0/1)
 Status   : Stable (may be moved to interface)

  quality_header
 Title    : quality_header
 Usage    : $obj->quality_header
 Function : flag for printing quality header - default is 0, no header
 Returns  : Bool (0/1)
 Args     : Bool (0/1)
 Status   : Unstable (name may change dep. on feedback)